Contacts of the helix formed by residues 13 - 42 (chain B) in PDB entry 6WYG
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 HIS 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.8 1.5 + - - -
11B ASN 4.0 3.2 + - - -
12B TYR* 1.3 74.3 - - - +
14B GLN* 1.3 66.1 + - + +
15B ASP* 2.8 53.3 + - + +
16B SER* 2.8 38.8 + - - +
17B GLU 3.0 10.0 + - - -
124B LYS* 4.2 34.4 - - + +
126B ASP* 4.6 0.8 + - - -
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.4 22.8 + - - +
12B TYR 3.7 2.0 + - - -
13B HIS* 1.3 82.9 + - + +
15B ASP* 1.3 65.7 + - - +
17B GLU* 2.6 26.7 + - - +
18B ALA* 3.0 22.9 + - - +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS* 2.8 29.8 + - + +
14B GLN* 1.3 77.2 - - - +
16B SER* 1.3 59.2 + - - +
18B ALA* 3.3 5.6 + - - +
19B ALA* 2.9 31.2 + - - +
22B ARG* 4.5 2.4 + - - +
120B LEU* 3.7 24.2 - - + +
124B LYS* 4.4 9.5 - - - -
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.8 15.3 - - - -
13B HIS* 2.8 29.7 + - - +
15B ASP* 1.3 72.9 - - - +
17B GLU* 1.3 63.3 + - - -
19B ALA* 3.2 2.5 + - - +
20B ILE* 2.9 28.2 + - - +
120B LEU* 4.1 12.7 - - - +
121B ALA* 4.8 2.3 - - - -
124B LYS* 4.4 12.0 - - - +
126B ASP* 4.4 3.9 + - - -
129B LEU* 3.6 28.4 - - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 2.8 31.3 + - - +
12B TYR* 3.6 13.7 + - + -
13B HIS 3.0 5.7 + - - -
14B GLN* 2.6 36.5 - - - +
15B ASP 3.3 0.2 - - - -
16B SER* 1.3 74.4 - - - +
18B ALA* 1.3 61.9 + - - +
20B ILE 3.2 1.6 + - - -
21B ASN* 3.0 14.9 + - - +
73B GLN* 3.0 37.0 + - - +
78B GLY* 3.5 5.0 - - - -
79B ARG* 2.9 35.1 + - - +
81B PHE* 5.1 3.6 - - - -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN 3.0 15.7 + - - +
15B ASP* 3.8 6.5 - - - +
17B GLU* 1.3 76.0 - - - +
19B ALA* 1.3 57.5 + - - +
21B ASN* 3.1 12.7 + - - +
22B ARG* 2.9 48.6 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP 2.9 17.8 + - - +
16B SER* 3.8 3.6 - - - +
18B ALA* 1.3 76.5 - - - +
20B ILE* 1.3 58.2 + - - +
22B ARG* 3.3 25.6 + - - +
23B GLN* 2.9 28.4 + - - +
117B LEU* 3.6 20.9 - - + +
120B LEU* 3.7 19.1 - - + -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.4 13.0 - - - +
16B SER 2.9 21.4 + - - +
19B ALA* 1.3 74.3 - - - +
21B ASN* 1.3 60.8 + - - +
23B GLN* 3.1 2.6 + - - +
24B ILE* 2.9 31.5 + - + +
69B LEU* 3.8 37.7 - - + +
72B LEU* 3.9 10.1 - - + -
73B GLN* 3.4 32.3 - - + +
117B LEU* 3.8 21.5 - - + -
129B LEU* 3.9 25.8 - - + -
133B ILE* 4.8 0.9 - - + -
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.0 26.1 + - - +
18B ALA* 3.1 11.2 + - - +
20B ILE* 1.3 76.1 - - - +
22B ARG* 1.3 61.2 + - + +
24B ILE* 3.3 14.6 + - - +
25B ASN* 3.1 21.7 + - - +
73B GLN* 3.2 13.2 + - - +
79B ARG 3.2 19.0 + - - +
80B ILE* 3.6 4.5 - - - +
81B PHE* 3.0 51.4 + - + +
83B GLN* 5.3 4.3 - - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 4.5 2.6 + - - +
18B ALA* 2.9 27.8 + - - +
19B ALA* 3.4 38.5 - - - +
20B ILE 3.2 0.2 - - - -
21B ASN* 1.3 77.6 - - + +
23B GLN* 1.3 58.0 + - - +
25B ASN* 3.4 7.7 + - - +
26B LEU* 3.0 27.1 + - - +
83B GLN* 5.3 14.4 - - - +
120B LEU* 5.3 3.2 - - - +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 2.9 16.6 + - - +
20B ILE* 3.1 5.1 + - - +
22B ARG* 1.3 74.8 - - - +
24B ILE* 1.3 66.7 + - - +
26B LEU* 3.1 13.1 + - - +
27B GLU* 2.9 46.1 + - - +
69B LEU* 3.6 23.8 - - + -
110B VAL* 4.0 2.6 - - - +
113B SER* 2.8 39.9 + - - -
114B LEU* 3.4 27.2 - - + +
117B LEU* 3.9 17.0 - - + +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 2.9 25.7 + - + +
21B ASN* 3.3 23.3 + - - +
23B GLN* 1.3 75.9 - - - +
25B ASN* 1.3 62.9 + - - +
27B GLU* 3.2 4.2 + - - +
28B LEU* 3.0 32.4 + - + +
66B ALA* 4.2 4.3 - - - +
69B LEU* 3.6 28.5 - - + +
70B MET* 3.7 38.4 - - + +
73B GLN* 4.5 0.4 - - + -
80B ILE* 4.5 9.2 - - + -
81B PHE 6.0 0.7 - - - +
82B LEU* 3.8 27.4 - - + -
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 3.1 11.7 + - - +
22B ARG 3.6 8.7 + - - +
24B ILE* 1.3 78.1 - - - +
26B LEU* 1.3 68.4 + - - +
28B LEU* 3.3 9.3 + - - +
29B TYR* 2.9 27.2 + - - +
83B GLN* 3.0 44.9 + - + +
84B ASP 2.9 26.9 + - - +
85B ILE* 4.4 6.2 - - - +
86B GLN* 5.7 4.0 - - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG 3.0 14.5 + - - +
23B GLN* 3.1 17.9 + - - +
25B ASN* 1.3 80.0 - - - +
27B GLU* 1.3 57.5 + - - +
29B TYR* 3.2 23.1 + - + +
30B ALA* 2.9 27.0 + - - +
106B LEU* 5.8 1.3 - - + -
109B ASN* 4.7 4.3 - - + +
110B VAL* 4.0 28.9 - - + +
113B SER* 3.1 34.1 - - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 2.9 38.3 + - - +
24B ILE 3.9 3.4 - - - +
26B LEU* 1.3 75.0 - - - +
28B LEU* 1.3 65.9 + - - +
30B ALA* 3.2 3.7 + - - +
31B SER* 2.9 22.5 + - - -
62B GLU* 2.6 43.4 - - - +
65B HIS* 3.7 10.6 - - - +
66B ALA* 3.9 15.7 - - + +
69B LEU* 3.6 16.6 - - + +
110B VAL* 3.8 15.2 - - - +
114B LEU* 4.0 1.6 - - - +
137B TYR* 3.8 18.4 - - - -
201B FE 2.7 10.5 - - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.0 36.4 + - + +
25B ASN* 3.7 7.2 - - - +
27B GLU* 1.3 75.2 - - - +
29B TYR* 1.3 57.8 + - - +
31B SER* 3.3 7.6 + - - -
32B TYR* 3.0 26.7 + - - +
63B ARG* 4.8 24.0 - - + +
66B ALA* 3.6 19.7 - - + -
67B GLU* 6.4 0.9 - - + -
70B MET* 5.3 5.6 - - - -
82B LEU* 4.4 13.9 - - + -
83B GLN 5.8 1.8 - - - +
85B ILE* 3.7 37.9 - - + +
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN* 2.9 19.9 + - - +
26B LEU* 3.4 26.5 - - + +
28B LEU* 1.3 74.7 - - - +
30B ALA* 1.3 61.4 + - - +
32B TYR* 3.1 3.0 + - + +
33B VAL* 2.9 47.1 + - + +
85B ILE* 3.9 10.9 - - + +
86B GLN* 3.4 39.3 - - + +
87B LYS 3.9 11.6 + - - -
88B PRO* 4.2 0.7 - - + -
89B ASP* 4.1 26.0 + - - -
106B LEU* 4.0 21.7 - - + +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 2.9 13.9 + - - +
27B GLU* 3.6 4.5 - - - +
29B TYR* 1.3 75.5 - - - +
31B SER* 1.3 61.7 + - - +
33B VAL* 3.4 2.5 + - - +
34B TYR* 3.0 32.0 + - + -
62B GLU* 3.4 29.4 - - + +
106B LEU* 4.3 24.9 - - + -
107B GLU* 5.3 0.7 - - - +
110B VAL* 4.4 13.7 - - + -
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU 2.9 13.6 + - - -
28B LEU* 3.3 13.0 - - - +
29B TYR 3.1 0.2 - - - -
30B ALA* 1.3 76.6 - - - +
32B TYR* 1.3 55.7 + - - +
34B TYR 3.3 0.3 + - - -
35B LEU* 2.9 25.1 + - - +
59B SER* 3.0 40.4 + - - +
62B GLU* 3.6 8.2 - - - +
63B ARG* 3.5 23.6 - - - +
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU 3.0 13.8 + - - +
29B TYR* 3.1 8.0 + - - +
31B SER* 1.3 73.5 + - - +
33B VAL* 1.3 65.6 + - - +
35B LEU* 3.3 23.8 + - + +
36B SER* 3.0 24.9 + - - -
85B ILE* 3.7 21.5 - - + -
86B GLN 3.1 26.9 - - - +
87B LYS* 3.7 18.6 - - + +
88B PRO* 3.9 11.6 - - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 2.9 53.7 + - + +
30B ALA 3.7 4.5 - - - +
32B TYR* 1.3 77.0 - - - +
34B TYR* 1.3 63.5 + - - +
36B SER* 3.1 3.3 + - - -
37B MET* 3.0 52.5 + - + +
88B PRO* 3.7 19.3 - - + -
93B TRP* 4.2 12.3 - - + -
106B LEU* 4.0 22.7 - - + -
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 3.0 25.4 + - - +
33B VAL* 1.3 75.1 - - - +
35B LEU* 1.3 63.3 + - - +
37B MET* 3.4 8.1 + - - -
38B SER* 2.9 24.6 + - - -
55B PHE* 3.3 49.7 - + - +
58B GLN* 3.5 26.8 + - + +
59B SER* 3.5 11.7 - - - +
62B GLU* 3.7 22.9 - - + -
103B ALA* 3.9 22.0 + - + +
106B LEU* 4.0 13.7 - - + -
107B GLU* 2.6 43.7 + - - +
148B LEU* 4.0 5.4 - - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER 2.9 16.7 + - - +
32B TYR* 3.6 28.3 - - + +
33B VAL 3.2 0.2 - - - -
34B TYR* 1.3 76.4 - - - +
36B SER* 1.3 62.9 + - - +
38B SER* 3.2 5.6 + - - -
39B TYR* 3.1 55.9 + - + +
56B LEU* 4.1 14.8 - - + -
59B SER* 3.6 13.8 - - - +
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.0 20.0 + - - -
33B VAL 3.1 3.8 + - - -
35B LEU* 1.3 77.6 - - - +
37B MET* 1.3 63.5 + - - +
39B TYR* 3.5 3.0 + - - +
40B TYR* 3.0 22.7 + - - +
88B PRO* 3.9 17.3 - - - -
90B GLU 3.7 9.5 + - - -
91B ASP* 4.6 5.9 + - - +
93B TRP* 2.9 18.1 + - - -
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.0 32.6 + - + +
34B TYR* 3.7 13.5 - - - +
36B SER* 1.3 75.5 - - - +
38B SER* 1.3 64.5 + - - +
40B TYR* 3.1 8.3 + - - +
41B PHE* 3.0 26.3 + - + -
55B PHE* 4.0 33.0 - - + -
93B TRP* 3.6 55.2 - - + +
99B ALA* 3.6 27.1 - - + +
102B ALA* 3.6 10.8 - - + -
103B ALA* 3.9 8.5 - - - +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR 2.9 17.4 + - - -
35B LEU* 3.2 6.9 + - - -
37B MET* 1.3 77.0 - - - +
39B TYR* 1.3 69.8 + - - +
41B PHE 3.0 15.1 + - - -
42B ASP* 3.3 7.1 + - - +
52B ALA* 2.8 41.7 + - - +
55B PHE* 3.7 6.9 - - - +
56B LEU* 3.5 25.5 - - - +
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.1 44.6 + - + +
36B SER* 4.3 3.1 - - - +
38B SER* 1.3 81.9 - - - +
40B TYR* 1.3 65.5 + - - +
42B ASP* 3.4 38.3 + - + +
43B ARG* 3.6 12.0 + - - +
56B LEU* 4.4 18.1 - - + +
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A RFT 5.5 1.6 + - - -
36B SER 3.0 15.6 + - - +
37B MET 3.1 7.3 + - - +
39B TYR* 1.3 77.8 - - - +
41B PHE* 1.3 93.3 + + - +
43B ARG* 3.2 48.5 + - - +
46B VAL* 3.6 35.0 - - + +
91B ASP 4.3 4.7 - - - +
92B ASP* 3.1 23.7 + - - -
93B TRP* 3.5 26.0 - - + -
94B GLU* 3.2 36.8 + - - -
95B SER* 4.2 2.6 - - - -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 3.0 24.9 + - + -
38B SER 3.0 6.7 + - - +
40B TYR* 1.3 91.8 - + - +
42B ASP* 1.3 55.1 + - - +
43B ARG 3.3 1.8 - - - -
46B VAL* 3.5 23.6 - - + -
47B ALA* 3.4 6.3 + - - -
48B LEU* 2.9 55.1 + - + +
49B LYS* 5.0 0.3 - - - -
51B PHE* 3.5 25.1 - + + -
52B ALA* 3.7 14.5 - - - +
55B PHE* 4.0 11.9 - + - -
93B TRP* 4.8 0.2 - - + -
95B SER* 3.4 25.1 - - - -
96B GLY* 3.5 25.4 - - - -
99B ALA* 3.6 19.3 - - + -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 2.7 43.3 + - - +
38B SER 3.3 9.3 + - - +
39B TYR* 3.6 38.1 - - + +
40B TYR 3.2 0.4 - - - -
41B PHE* 1.3 73.9 - - - +
43B ARG* 1.3 57.0 + - - +
47B ALA* 4.7 1.8 - - - +
49B LYS* 6.3 0.7 - - - +
52B ALA* 4.6 8.5 - - + -
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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