Contacts of the helix formed by residues 7 - 42 (chain M) in PDB entry 6T9L
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 7 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M ILE* 1.3 81.7 - - - +
8M ILE* 1.3 66.1 + - - +
9M ASP* 2.4 26.8 + - - +
10M SER* 3.1 33.8 + - - +
11M ILE* 3.8 14.7 - - - +
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Residues in contact with ILE 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ARG* 4.9 16.4 - - + +
89L LEU* 4.5 16.8 - - + +
90L GLU* 3.4 36.6 - - - +
93L VAL* 4.6 11.4 - - + -
6M ILE* 6.6 0.4 - - + -
7M THR* 1.3 77.5 - - - +
9M ASP* 1.3 65.6 + - - +
10M SER 3.2 1.1 + - - -
11M ILE* 3.4 10.4 + - + +
12M SER* 3.4 17.9 + - - +
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Residues in contact with ASP 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ARG* 4.2 22.0 - - - +
7M THR* 2.4 35.4 + - - +
8M ILE* 1.3 76.8 - - - +
10M SER* 1.3 59.9 + - - -
12M SER* 2.7 19.3 + - - -
13M ASN* 2.9 23.6 + - - +
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Residues in contact with SER 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M ILE* 5.4 1.4 - - - +
7M THR* 3.1 31.0 + - - -
8M ILE 3.2 0.2 - - - -
9M ASP* 1.3 83.3 + - - +
11M ILE* 1.3 70.7 + - - +
13M ASN* 3.5 15.8 + - - +
14M GLY* 3.5 8.1 + - - -
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Residues in contact with ILE 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L LEU* 4.0 25.4 - - + -
9L LYS* 4.4 27.1 - - + +
12L ILE* 3.7 27.4 - - + -
89L LEU* 5.9 4.3 - - + -
6M ILE* 5.1 13.9 - - + -
7M THR 3.8 11.9 - - - +
8M ILE* 3.4 9.5 + - + +
9M ASP 3.4 0.2 - - - -
10M SER* 1.3 83.8 - - - +
12M SER* 1.3 65.1 + - - +
14M GLY* 3.2 3.8 + - - -
15M ILE* 3.0 30.3 + - + +
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Residues in contact with SER 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82L LEU* 4.7 6.6 - - - +
85L ILE* 3.7 29.6 - - - +
86L ARG* 4.6 12.9 + - - -
89L LEU* 4.4 11.3 - - - +
8M ILE* 3.4 6.6 + - - -
9M ASP* 2.7 34.1 + - - +
11M ILE* 1.3 77.2 - - - +
13M ASN* 1.3 56.3 + - - +
15M ILE* 3.7 10.2 - - - +
16M LEU* 3.0 28.9 + - - +
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Residues in contact with ASN 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L ARG* 6.1 0.6 - - - +
82L LEU* 4.9 18.6 - - - +
9M ASP* 2.9 20.8 + - - +
10M SER* 3.7 9.4 - - - +
11M ILE 3.2 0.4 - - - -
12M SER* 1.3 79.7 + - - +
14M GLY* 1.3 57.4 + - - +
16M LEU* 3.4 8.9 + - - +
17M ASN* 2.8 43.3 + - - +
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Residues in contact with GLY 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L LYS* 6.3 2.9 - - - -
10M SER 3.5 6.5 + - - -
11M ILE* 3.2 7.8 + - - -
13M ASN* 1.3 80.3 - - - +
15M ILE* 1.3 55.8 + - - +
17M ASN* 3.8 7.7 - - - +
18M ASN* 2.9 38.2 + - - -
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Residues in contact with ILE 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ILE* 4.6 11.7 - - + -
13L GLN* 5.3 12.1 - - + +
16L LEU* 5.3 12.1 - - + -
22L TYR* 6.0 1.8 - - + -
25L ILE* 5.1 10.3 - - + -
85L ILE* 5.2 12.1 - - + -
89L LEU* 4.1 26.0 - - + -
11M ILE* 3.0 30.0 + - + +
12M SER* 3.7 11.0 - - - +
13M ASN 3.3 0.2 - - - -
14M GLY* 1.3 73.9 - - - +
16M LEU* 1.3 65.2 + - - +
18M ASN* 3.2 19.6 + - + +
19M LEU* 3.3 28.4 + - + +
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Residues in contact with LEU 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L LEU* 4.7 17.9 - - + -
78L ARG* 4.3 26.5 - - + +
81L VAL* 4.5 24.7 - - + -
82L LEU* 3.7 29.4 - - + -
85L ILE* 5.6 2.6 - - + +
12M SER 3.0 17.2 + - - +
13M ASN* 3.8 9.6 - - - +
15M ILE* 1.3 76.7 - - - +
17M ASN* 1.3 62.0 + - - +
19M LEU* 3.2 8.4 + - + -
20M LEU* 2.9 55.8 + - + +
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Residues in contact with ASN 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ASN* 5.4 0.6 + - - -
70L LEU* 5.9 4.0 - - - +
78L ARG* 5.8 1.2 + - - -
13M ASN* 2.8 29.3 + - - +
14M GLY* 3.8 8.2 - - - +
16M LEU* 1.3 81.8 - - - +
18M ASN* 1.3 63.4 + - - +
20M LEU* 4.0 15.7 - - - +
21M THR* 3.2 25.8 + - - +
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Residues in contact with ASN 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K GLU* 4.7 9.2 + - - +
52K ILE 4.0 11.0 + - - +
53K ASN 2.8 15.7 - - - +
54K SER* 3.6 20.2 + - - -
70K ASN* 4.4 6.4 + - - -
13L GLN* 4.0 21.2 - - - +
14M GLY 2.9 28.7 + - - +
15M ILE* 3.5 10.5 - - - +
16M LEU 3.2 0.2 - - - -
17M ASN* 1.3 78.4 - - - +
19M LEU* 1.3 57.7 + - + +
21M THR* 3.4 8.1 - - - +
22M THR* 2.4 30.3 + - - -
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Residues in contact with LEU 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K ILE 5.4 0.7 - - - +
53K ASN* 4.6 4.7 - - + +
22L TYR* 3.6 33.0 - - + +
25L ILE* 4.4 31.6 - - + +
26L SER* 5.2 7.4 - - - -
29L LEU* 3.8 24.5 - - + -
15M ILE* 3.3 23.6 - - + +
16M LEU* 3.2 9.3 + - + +
18M ASN* 1.3 80.4 - - + +
20M LEU* 1.3 65.5 + - - +
22M THR* 3.5 6.0 + - - -
23M LEU* 3.2 28.6 + - - +
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Residues in contact with LEU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 4.7 10.1 - - + -
33L LEU* 5.4 3.4 - - + -
38L TRP* 5.7 2.0 - - + -
66L GLU* 5.5 0.7 - - - +
70L LEU* 4.5 20.4 - - + -
73L VAL* 4.9 20.2 - - + -
78L ARG* 4.8 15.5 - - - +
16M LEU* 2.9 47.6 + - + +
17M ASN* 4.0 15.3 - - - +
18M ASN 3.4 0.2 - - - -
19M LEU* 1.3 77.3 - - - +
21M THR* 1.3 56.8 + - - +
23M LEU* 3.4 20.8 - - + +
24M ILE* 2.9 44.0 + - + +
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Residues in contact with THR 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K GLY 3.7 20.9 - - - +
70K ASN* 3.8 17.7 + - - +
66L GLU* 3.8 24.6 + - - +
17M ASN 3.2 17.6 + - - +
18M ASN* 3.4 9.4 - - - +
20M LEU* 1.3 80.4 - - - +
22M THR* 1.3 60.0 + - - +
24M ILE* 4.3 2.9 - - - -
25M GLN* 2.9 55.0 + - - +
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Residues in contact with THR 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K ASN* 3.2 40.5 + - - +
55K GLY 4.1 7.6 + - - +
90K ASN* 3.7 25.9 + - - +
18M ASN 2.4 26.9 + - - -
19M LEU* 3.7 7.6 - - - -
20M LEU 3.2 0.6 - - - -
21M THR* 1.3 79.8 - - - +
23M LEU* 1.3 58.3 + - - +
25M GLN* 4.0 6.3 - - - +
26M ASP* 3.2 25.8 + - - +
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Residues in contact with LEU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 3.9 27.8 - - + -
30L LYS* 5.5 16.6 - - + -
33L LEU* 4.5 8.1 - - + -
38L TRP* 3.6 36.1 - - + -
39L VAL* 6.4 0.2 - - + -
19M LEU 3.2 18.6 + - - +
20M LEU* 3.4 20.0 - - + +
22M THR* 1.3 77.0 - - - +
24M ILE* 1.3 70.5 + - + +
26M ASP* 3.3 8.3 + - - +
27M ILE* 3.2 35.0 + - + +
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Residues in contact with ILE 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L TRP* 4.4 11.9 - - + -
62L LEU* 4.5 6.1 - - + -
65L VAL* 4.9 6.1 - - + +
66L GLU* 3.8 48.7 - - + +
69L ALA* 3.8 25.6 - - + -
70L LEU* 4.7 9.0 - - + -
20M LEU* 2.9 29.1 + - + +
21M THR* 4.0 3.8 - - - +
23M LEU* 1.3 88.7 - - + +
25M GLN* 1.3 63.9 + - - +
26M ASP 3.2 0.7 + - - -
27M ILE* 3.3 15.9 + - + +
28M VAL* 3.3 15.3 + - + +
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Residues in contact with GLN 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K GLY* 3.3 4.8 - - - -
56K ALA* 2.6 42.1 + - + +
69K TRP* 3.2 31.9 - - - +
70K ASN* 4.5 1.8 + - - -
88K ASN* 5.2 4.5 + - - +
90K ASN* 6.0 1.6 - - - +
102K TYR* 5.3 0.3 + - - -
58L PHE* 4.5 6.1 - - + -
62L LEU* 3.7 28.3 - - + +
66L GLU* 5.2 2.6 - - + +
21M THR* 2.9 36.1 + - - +
22M THR* 4.2 3.4 - - - +
24M ILE* 1.3 77.0 - - + +
26M ASP* 1.3 61.1 + - - +
28M VAL* 3.6 8.7 - - + +
29M ALA* 3.2 25.1 + - - +
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Residues in contact with ASP 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K ASN* 5.5 0.7 - - - +
90K ASN* 3.2 39.8 - - + +
91K ASN* 4.6 4.2 + - - +
22M THR 3.2 17.8 + - - +
23M LEU* 3.5 10.3 - - - +
24M ILE 3.1 0.8 - - - -
25M GLN* 1.3 76.7 - - - +
27M ILE* 1.3 67.2 + - + +
29M ALA* 4.1 2.8 - - - +
30M ARG* 2.9 52.0 + - - +
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Residues in contact with ILE 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L TRP* 4.9 0.9 - - + -
39L VAL* 4.3 22.2 - - + -
42L VAL* 3.8 28.0 - - + +
43L LYS* 3.8 36.3 - - + -
46L THR* 5.5 1.8 - - + -
23M LEU* 3.2 29.2 + - + +
24M ILE* 3.3 6.9 + - + +
26M ASP* 1.3 80.2 - - + +
28M VAL* 1.3 65.5 + - - +
30M ARG* 3.3 7.8 + - - +
31M GLU* 3.2 31.7 + - + +
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Residues in contact with VAL 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L THR* 4.3 12.1 - - - +
58L PHE* 3.8 16.2 - - + -
61L ILE* 3.8 30.7 - - + -
62L LEU* 3.8 19.7 - - + +
65L VAL* 4.3 12.6 - - + -
24M ILE* 3.3 18.0 + - + +
25M GLN* 3.6 14.1 - - - +
27M ILE* 1.3 81.0 - - - +
29M ALA* 1.3 64.5 + - - +
31M GLU* 3.2 6.1 + - - +
32M THR* 3.1 27.2 + - + +
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Residues in contact with ALA 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K ASN* 5.2 0.4 - - - +
91K ASN* 3.5 22.7 - - - +
93K LEU* 3.7 3.5 - - + +
102K TYR* 3.9 25.7 - - + +
58L PHE* 3.8 5.6 - - + -
25M GLN 3.2 18.1 + - - +
26M ASP 4.1 0.7 - - - +
27M ILE 3.3 0.6 - - - -
28M VAL* 1.3 82.8 - - - +
30M ARG* 1.3 60.0 + - - +
32M THR* 3.2 20.7 - - - +
33M THR* 3.4 16.3 + - - +
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Residues in contact with ARG 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K ASN 3.2 25.7 + - - -
91K ASN* 3.5 29.0 + - + +
93K LEU* 4.8 3.6 - - + -
26M ASP* 2.9 35.2 + - - +
27M ILE* 3.3 8.4 + - - +
28M VAL 3.2 0.4 - - - -
29M ALA* 1.3 77.6 - - - +
31M GLU* 1.3 64.0 + - + +
32M THR 3.4 0.2 - - - -
33M THR* 3.2 16.5 + - - -
34M GLN* 3.2 30.4 + - - +
70N ASP* 4.8 21.9 + - + -
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Residues in contact with GLU 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L LYS* 3.9 29.2 + - + +
46L THR* 3.8 36.3 - - + +
47L LYS* 5.6 5.7 + - - +
50L MET* 5.3 1.4 - - - +
27M ILE* 3.2 22.4 + - + +
28M VAL 3.2 4.2 + - - +
30M ARG* 1.3 79.8 - - - +
32M THR* 1.3 61.8 + - - +
34M GLN* 3.6 19.0 + - - +
35M GLN* 3.2 23.7 + - - +
70N ASP 5.0 3.5 - - - +
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Residues in contact with THR 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K ASP* 4.3 5.1 + - - +
102K TYR* 4.6 5.8 - - + -
46L THR* 5.5 0.4 + - - -
50L MET* 4.4 14.8 - - - +
56L THR* 3.3 32.7 + - - +
57L ASN 5.3 0.2 - - - -
58L PHE* 4.1 19.5 + - + -
61L ILE* 6.1 3.1 - - - -
28M VAL* 3.1 22.5 + - - +
29M ALA* 3.2 16.2 - - - +
31M GLU* 1.3 78.8 - - - +
33M THR* 1.3 66.1 + - + +
35M GLN 3.7 0.3 + - - -
36M GLN* 3.0 28.9 + - - +
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Residues in contact with THR 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K LEU* 3.7 27.2 - - + +
102K TYR* 4.0 23.3 - - + -
103K ILE 5.1 1.3 - - - +
104K GLY* 3.5 20.9 - - - +
29M ALA 3.4 16.0 + - - +
30M ARG* 3.2 14.2 + - - -
32M THR* 1.3 78.9 - - + +
34M GLN* 1.3 67.7 + - - +
36M GLN* 3.3 10.7 + - - +
37M LEU* 3.1 21.0 + - - +
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Residues in contact with GLN 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M ARG* 3.2 27.0 + - - +
31M GLU* 3.8 21.1 + - - +
32M THR 3.4 0.2 - - - -
33M THR* 1.3 84.8 + - - +
35M GLN* 1.3 60.6 + - - +
37M LEU* 3.3 7.9 + - - +
38M LEU* 3.2 29.9 + - + +
70N ASP* 2.7 33.2 + - - +
71N LYS* 3.4 23.9 - - + +
72N PRO* 4.6 10.7 - - + +
74N GLN* 6.4 0.2 - - - +
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Residues in contact with GLN 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L MET* 4.2 30.9 - - + +
56L THR* 5.5 2.7 - - + +
31M GLU 3.2 16.3 + - - +
32M THR 4.1 3.4 - - - +
34M GLN* 1.3 76.7 - - - +
36M GLN* 1.3 65.4 + - - +
38M LEU* 3.2 29.8 + - - +
39M LYS* 3.4 46.1 + - + +
45M LEU* 6.0 1.0 - - - +
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Residues in contact with GLN 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K SER 5.4 0.2 + - - -
101K ASP* 4.6 9.3 + - - +
102K TYR* 3.6 17.6 + - - +
103K ILE* 4.4 0.4 - - - +
104K GLY* 2.9 35.0 + - - +
105K ASN* 3.1 33.9 + - + +
56L THR* 3.9 20.9 - - + +
32M THR* 3.0 20.7 + - - +
33M THR* 3.5 8.9 - - - +
34M GLN 3.3 0.2 - - - -
35M GLN* 1.3 75.8 - - - +
37M LEU* 1.3 56.0 + - - +
39M LYS* 4.7 1.9 - - - +
40M THR* 2.3 36.1 + - - +
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Residues in contact with LEU 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K GLY 3.4 14.1 + - - +
105K ASN* 5.1 9.6 - - - -
107K ASP* 6.0 3.4 - - + +
110K ASN* 4.9 14.6 - - - +
33M THR 3.1 12.7 + - - +
34M GLN* 3.8 7.0 - - - +
35M GLN 3.2 0.2 - - - -
36M GLN* 1.3 75.3 - - - +
38M LEU* 1.3 66.8 + - + +
40M THR* 4.3 3.1 - - - -
41M ARG* 3.1 67.3 + - + +
74N GLN* 4.7 20.4 - - - +
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Residues in contact with LEU 38 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K ARG* 5.1 12.8 - - - +
34M GLN* 3.2 16.7 + - + +
35M GLN* 3.2 31.1 + - - +
37M LEU* 1.3 79.2 - - + +
39M LYS* 1.3 59.9 + - - +
42M TYR* 2.9 46.4 + - + +
45M LEU* 3.9 25.5 - - + +
72N PRO* 5.6 10.1 - - + -
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Residues in contact with LYS 39 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L THR* 6.0 2.2 - - - +
35M GLN* 3.4 38.1 + - + +
36M GLN* 4.9 1.6 - - - +
38M LEU* 1.3 75.5 - - + +
40M THR* 1.3 63.6 + - - +
42M TYR 3.3 16.6 - - - +
43M PRO* 3.4 19.0 - - + +
45M LEU* 5.4 4.5 - - + -
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Residues in contact with THR 40 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ILE* 5.9 6.7 - - + -
105K ASN* 3.6 35.7 + - + +
36M GLN* 2.3 30.0 + - - +
37M LEU* 4.0 5.6 - - - -
38M LEU 3.3 0.4 - - - -
39M LYS* 1.3 79.9 - - - +
41M ARG* 1.3 62.6 + - - +
43M PRO* 4.1 10.0 - - - +
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Residues in contact with ARG 41 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K ASP* 4.7 16.2 + - - +
127K VAL* 3.7 45.0 - - + +
128K PRO* 4.0 15.8 - - - +
37M LEU* 3.1 55.5 + - + +
40M THR* 1.3 77.5 - - - +
42M TYR* 1.3 92.1 + - + +
43M PRO* 3.4 7.8 - - - +
74N GLN* 5.1 8.1 + - - -
75N TYR 5.2 2.2 + - - -
76N ARG* 5.7 1.6 - - - +
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Residues in contact with TYR 42 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127K VAL* 5.7 0.7 - - + -
128K PRO* 2.3 43.6 + - - +
129K SER* 3.2 8.2 + - - -
130K MET* 3.5 32.1 - - + -
133K ARG* 4.5 17.7 - - + +
38M LEU* 2.9 31.9 + - + +
39M LYS* 3.3 10.9 - - - +
41M ARG* 1.3 109.6 + - + +
43M PRO* 1.3 67.1 - - - +
44M ASP* 3.2 7.6 - - - +
45M LEU* 3.3 33.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il