Contacts of the helix formed by residues 1 - 31 (chain B) in PDB entry 2WY2
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 ALA 1 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 4.3 20.7 - - + -
2B GLU* 1.3 68.6 - - + +
3B GLU 3.5 1.1 - - - +
4B LEU* 4.1 25.1 - - + +
5B GLU* 2.4 62.7 + - - +
65B GLU* 5.3 7.2 - - - +
73B VAL* 5.2 8.5 - - - +
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Residues in contact with GLU 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 6.1 0.2 - - - +
1B ALA* 1.3 79.6 - - + +
3B GLU* 1.3 68.3 + - + +
5B GLU* 3.8 2.5 + - - +
6B GLU* 3.0 26.5 + - - +
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Residues in contact with GLU 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 3.5 0.4 - - - +
2B GLU* 1.3 82.9 - - + +
4B LEU* 1.3 64.3 + - + +
6B GLU* 2.8 9.3 + - - +
7B VAL* 2.4 49.9 + - + +
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Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 3.4 25.7 + - + +
3B GLU* 1.3 79.4 - - + +
5B GLU* 1.3 56.9 + - - +
7B VAL* 3.6 6.8 - - + +
8B VAL* 2.8 36.1 + - - +
58B LEU* 3.6 30.7 - - + -
65B GLU* 5.1 7.4 - - - +
71B SER* 4.3 18.4 - - - +
73B VAL* 4.7 11.4 - - + -
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Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 4.0 20.8 - - - +
1B ALA 2.4 52.4 + - - +
2B GLU 3.8 1.8 - - - +
4B LEU* 1.3 67.3 - - - +
6B GLU* 1.3 63.7 + - - +
8B VAL* 3.3 8.5 + - + +
9B MET* 3.1 32.9 + - + +
73B VAL* 5.3 7.9 - - + -
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU 3.0 20.0 + - - +
3B GLU* 2.8 10.9 + - - +
5B GLU* 1.3 70.2 - - - +
7B VAL* 1.3 66.2 + - + +
9B MET* 3.3 19.5 + - + +
10B GLY* 3.0 18.2 + - - -
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 2.4 53.9 + - + +
4B LEU* 3.6 9.4 - - + +
6B GLU* 1.3 66.1 - - + +
8B VAL* 1.3 60.6 + - - +
10B GLY* 3.1 3.6 + - - -
11B LEU* 2.8 32.7 + - + +
54B VAL* 4.1 13.2 - - + -
58B LEU* 3.8 31.0 - - + -
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 2.8 27.3 + - - +
5B GLU* 3.5 7.4 - - - +
7B VAL* 1.3 77.4 - - + +
9B MET* 1.3 53.2 + - + +
11B LEU* 3.0 11.3 + - + +
12B ILE* 2.7 53.4 + - + +
58B LEU* 5.6 4.0 - - + -
73B VAL* 3.4 36.8 - - + +
74B LEU* 5.8 0.2 - - - -
76B HIS* 4.3 22.2 - - + -
77B ALA* 4.5 12.8 - - + +
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Residues in contact with MET 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU* 3.1 26.1 + - + +
6B GLU* 3.4 20.6 - - + +
7B VAL 3.2 0.2 - - - -
8B VAL* 1.3 75.7 - - + +
10B GLY* 1.3 58.5 + - - +
12B ILE* 3.3 7.5 + - - +
13B ILE* 2.8 39.2 + - + +
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Residues in contact with GLY 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 3.0 13.6 + - - -
7B VAL* 3.1 4.4 + - - -
9B MET* 1.3 76.3 - - - +
11B LEU* 1.3 52.7 + - - +
13B ILE* 3.3 6.4 + - - +
14B ASN* 2.7 37.5 + - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 2.8 27.0 + - + +
8B VAL* 3.0 10.3 + - + +
10B GLY* 1.3 73.3 - - - +
12B ILE* 1.3 52.6 + - - +
14B ASN* 3.5 6.2 - - + +
15B SER* 2.7 37.6 + - - -
51B ALA* 3.7 38.6 - - + +
54B VAL* 4.0 13.7 - - + -
55B GLN* 5.0 2.5 - - - +
58B LEU* 3.7 30.1 - - + -
77B ALA* 3.8 27.8 - - + -
81B LEU* 4.4 13.5 - - + +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 2.7 35.1 + - + +
9B MET* 3.6 7.0 - - - +
11B LEU* 1.3 71.8 - - - +
13B ILE* 1.3 62.6 + - + +
15B SER* 2.6 19.7 + - - -
16B GLY* 2.8 12.5 + - - -
76B HIS* 3.3 33.7 - - + +
77B ALA* 4.3 3.8 - - - -
80B HIS* 3.1 50.5 + - + +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET* 2.8 26.4 + - + +
10B GLY* 3.6 6.7 - - - +
12B ILE* 1.3 81.1 - - + +
14B ASN* 1.3 53.1 + - - +
16B GLY* 3.1 2.0 + - - -
17B GLN* 2.7 44.3 + - + +
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY 2.7 21.9 + - - +
11B LEU* 3.5 10.3 - - + +
13B ILE* 1.3 74.4 - - - +
15B SER* 1.3 58.6 + - - +
17B GLN* 3.2 11.0 + - - +
18B ALA* 2.8 28.7 + - - +
47B ALA* 3.7 35.7 + - - +
48B LEU* 5.9 0.2 - - - -
50B GLU* 4.2 15.8 + - - +
51B ALA* 3.9 16.0 - - + +
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 2.7 17.3 + - - -
12B ILE 2.6 21.8 + - - -
14B ASN* 1.3 72.6 - - - +
16B GLY* 1.3 64.8 + - - +
18B ALA* 3.2 7.4 + - - +
19B ARG* 3.0 15.2 + - - +
48B LEU* 5.0 1.8 - - - -
51B ALA* 5.8 0.2 - - - -
80B HIS* 3.5 34.9 + - - +
81B LEU* 4.1 13.4 - - - +
84B SER* 2.9 31.2 + - - -
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Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE 2.8 9.6 + - - -
13B ILE* 3.5 3.4 - - - -
15B SER* 1.3 84.9 + - - +
17B GLN* 1.3 55.6 + - - +
19B ARG* 3.3 13.4 + - - +
20B SER* 2.9 28.3 + - - -
80B HIS* 5.8 1.6 - - - -
84B SER* 4.8 0.2 - - - -
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 2.7 30.6 + - + +
14B ASN* 3.6 12.4 - - - +
16B GLY* 1.3 71.9 - - - +
18B ALA* 1.3 54.3 + - - +
20B SER* 3.1 9.4 + - - +
21B LEU* 2.8 56.7 + - + +
47B ALA* 6.3 0.4 - - + -
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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 ASN 2.8 13.8 + - - +
15B SER 3.3 9.6 - - - +
17B GLN* 1.3 76.0 - - - +
19B ARG* 1.3 57.1 + - - +
21B LEU* 3.2 5.8 + - - -
22B ALA* 2.8 16.6 + - - +
44B SER* 2.7 29.6 + - - +
47B ALA* 4.6 8.4 - - + +
48B LEU* 3.3 39.7 - - + -
84B SER* 4.7 1.6 - - - -
88B ARG* 5.9 0.9 - - - -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 5.3 9.0 - - - +
85A MET* 3.9 27.5 - - - +
86A LEU* 4.3 28.2 - - - +
89A GLU* 4.4 17.9 + - - +
15B SER 3.0 12.5 + - - +
16B GLY* 3.6 12.5 + - - +
18B ALA* 1.3 75.6 - - - +
20B SER* 1.3 59.7 + - - +
22B ALA* 2.9 10.1 + - + +
23B TYR* 2.8 32.7 + - + +
84B SER* 4.2 17.0 + - - +
87B ALA* 4.8 11.4 - - + -
88B ARG* 6.0 0.2 - - - -
91B ILE* 5.3 4.3 - - + -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 2.9 14.1 + - - -
17B GLN* 3.3 14.7 - - - +
19B ARG* 1.3 77.8 - - - +
21B LEU* 1.3 60.4 + - - +
23B TYR* 3.4 7.1 + - - +
24B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 2.8 41.8 + - + +
18B ALA* 4.5 2.2 - - - -
20B SER* 1.3 73.9 - - - +
22B ALA* 1.3 53.7 + - - +
24B ALA* 3.1 6.3 + - + +
25B ALA* 2.6 36.2 + - - +
40B MET* 3.9 31.8 - - + +
43B GLN* 5.0 14.4 - - + +
44B SER* 3.3 30.1 - - - +
47B ALA* 5.1 6.5 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 2.8 13.8 + - - +
19B ARG* 2.9 12.3 + - - +
21B LEU* 1.3 75.2 - - - +
23B TYR* 1.3 63.7 + - - +
25B ALA* 2.9 11.2 + - - +
26B LEU 2.9 18.7 + - - -
41B MET* 6.0 0.9 - - - +
44B SER* 3.4 5.3 + - - +
88B ARG* 3.9 26.7 - - + +
91B ILE* 3.6 30.6 - - + +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.7 23.8 - - + +
93A GLU* 3.3 26.1 + - - -
19B ARG* 2.8 21.4 + - + +
20B SER* 3.8 7.0 - - - +
22B ALA* 1.3 72.9 - - - +
24B ALA* 1.3 61.2 + - + +
26B LEU* 3.1 14.3 + - + +
27B LYS* 2.8 44.1 + - + +
30B LYS* 5.0 7.2 + - - -
91B ILE* 4.2 9.5 - - + +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 2.9 19.2 + - - +
21B LEU* 3.3 7.6 - - + +
23B TYR* 1.3 80.4 - - + +
25B ALA* 1.3 64.5 + - - +
27B LYS* 3.1 12.0 + - - +
28B GLN* 2.9 28.5 + - + +
40B MET* 3.6 18.6 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 2.6 17.1 + - - +
22B ALA* 3.1 14.1 - - - +
24B ALA* 1.3 73.3 - - - +
26B LEU* 1.3 62.6 + - - +
28B GLN* 3.2 8.4 + - - +
29B ALA* 3.1 15.9 + - - +
37B ALA* 3.5 18.0 - - - +
40B MET* 3.5 28.4 - - + +
41B MET* 4.0 17.0 - - + +
91B ILE* 5.3 0.2 - - + -
95B ILE* 4.0 4.9 - - + -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.2 46.0 - - + +
22B ALA 2.9 11.4 + - - +
23B TYR* 3.3 16.2 - - + +
25B ALA* 1.3 77.6 - - - +
27B LYS* 1.3 63.1 + - - +
29B ALA* 2.9 15.5 + - + +
30B LYS* 3.0 19.2 + - - +
91B ILE* 3.9 17.5 - - + -
94B LEU* 4.5 11.2 - - + -
95B ILE* 3.9 21.5 - - + +
98B HIS* 3.5 33.0 - - + +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 2.8 31.5 + - + +
24B ALA* 3.3 14.4 - - + +
26B LEU* 1.3 77.3 - - - +
28B GLN* 1.3 68.4 + - + +
30B LYS* 3.1 23.4 + - + +
31B GLN* 3.1 42.8 + - + +
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 2.9 21.0 + - - +
25B ALA* 3.2 11.6 + - - +
27B LYS* 1.3 81.8 - - - +
29B ALA* 1.3 64.1 + - - +
31B GLN* 3.0 21.9 + - - +
33B ASP* 2.9 39.4 + - - +
36B ALA* 3.3 25.9 - - + +
37B ALA 3.8 17.7 - - - +
40B MET* 4.7 8.5 - - + -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.1 7.6 + - - +
26B LEU* 2.9 13.8 + - + +
28B GLN* 1.3 80.3 - - - +
30B LYS* 1.3 53.9 + - - +
32B GLY* 2.7 25.4 + - - +
33B ASP 4.4 4.9 - - - +
34B PHE* 4.9 7.9 - - + -
37B ALA* 4.1 6.4 - - + +
95B ILE* 4.0 29.4 - - + -
98B HIS* 4.3 21.1 - - + +
103B ALA 4.2 8.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 2.9 35.6 + - - -
96A GLU* 3.5 29.5 + - - +
100A LYS* 3.6 27.9 + - - +
23B TYR* 5.0 7.7 + - - -
26B LEU* 3.0 27.1 + - - +
27B LYS* 3.1 17.2 + - + +
29B ALA* 1.3 75.7 - - - +
31B GLN* 1.3 61.4 + - + +
32B GLY* 3.2 1.0 + - - -
98B HIS* 4.3 16.6 - - - +
103B ALA* 6.1 0.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 3.1 41.3 - - + +
28B GLN* 3.0 18.3 + - - +
30B LYS* 1.3 77.3 - - + +
32B GLY* 1.3 60.2 + - - +
33B ASP* 3.3 19.7 + - - +
----------------------------------------------------------
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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