Contacts of the helix formed by residues 5 - 35 (chain B) in PDB entry 2GS4
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 5 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 4.1 5.2 - - - -
126A GLN* 4.0 10.5 - - - +
4B LYS* 1.3 93.0 - - + +
6B ILE* 1.3 59.6 + - - +
7B GLU* 3.2 10.6 + - - +
8B ASP* 2.9 42.9 + - - +
9B VAL* 3.1 15.2 + - - +
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.7 24.0 - - + -
123A LEU* 4.9 9.9 - - + -
126A GLN* 2.8 52.6 + - + +
5B THR* 1.3 74.2 - - - +
7B GLU* 1.3 63.0 + - - +
9B VAL* 3.1 10.0 + - - +
10B PHE* 3.0 20.3 + - - +
123B LEU* 4.2 18.1 - - + +
126B GLN* 5.8 0.7 - - + -
127B LEU* 3.5 33.2 - - + +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 3.1 10.2 + - - +
6B ILE* 1.3 82.4 - - - +
8B ASP* 1.3 57.5 + - - +
10B PHE* 3.3 3.8 + - + +
11B ILE* 3.0 41.6 + - + +
67B ASN* 2.4 44.0 + - - +
68B LEU* 3.1 20.5 - - + +
127B LEU* 4.0 13.9 - - + +
129B TYR* 3.0 15.6 + - + +
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Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 5.6 0.7 - - + -
4B LYS* 2.5 32.4 + - - +
5B THR* 2.9 26.9 + - - +
7B GLU* 1.3 78.8 - - - +
9B VAL* 1.3 63.4 + - + +
11B ILE* 3.5 11.5 + - - +
12B HIS* 3.0 24.1 + - - +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 3.8 32.8 - - + +
122A THR* 3.5 38.6 - - + -
123A LEU* 4.1 22.7 - - + -
5B THR 3.1 4.1 + - - +
6B ILE* 3.1 9.4 + - - +
8B ASP* 1.3 78.5 - - + +
10B PHE* 1.3 57.2 + - - +
12B HIS* 3.2 8.2 + - - +
13B LEU* 2.9 41.7 + - + +
123B LEU* 4.3 7.9 - - + -
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE 3.0 15.5 + - - +
7B GLU* 3.6 4.0 - - + +
9B VAL* 1.3 78.5 - - - +
11B ILE* 1.3 58.2 + - - +
13B LEU* 3.3 2.3 + - - +
14B LEU* 2.8 43.6 + - + +
61B VAL* 4.0 11.9 - - + -
68B LEU* 3.8 39.3 - - + -
120B LEU* 3.4 33.2 - - + -
123B LEU* 3.8 29.1 - - + +
124B ALA* 3.9 14.1 - - + -
127B LEU* 3.7 13.2 - - + -
129B TYR* 4.1 12.3 - + - -
132B ALA* 4.7 0.4 - - + -
136B LEU* 3.9 17.5 - - + -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 3.0 41.4 + - + +
8B ASP* 3.9 11.4 - - - +
10B PHE* 1.3 77.6 - - - +
12B HIS* 1.3 59.0 + - - +
14B LEU* 3.9 5.9 - - + +
15B SER* 2.8 38.8 + - - +
67B ASN 4.2 5.4 - - - +
68B LEU* 3.7 28.5 - - + -
69B LYS* 3.6 35.6 - - + +
71B LYS* 3.9 24.2 - - - +
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Residues in contact with HIS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 6.3 0.4 - - - -
115A ALA* 3.9 30.9 + - + +
119A THR* 3.7 22.1 + - - -
8B ASP 3.0 19.2 + - - +
9B VAL* 3.2 6.3 + - - +
11B ILE* 1.3 78.0 - - - +
13B LEU* 1.3 76.7 - - + +
15B SER* 3.4 5.9 + - - -
16B ASP* 3.1 28.0 + - + +
71B LYS* 5.9 1.8 - - - +
73B MSE 3.8 31.5 - - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.1 9.6 - - + -
119A THR* 4.7 12.6 - - + +
9B VAL* 2.9 28.1 + - + +
10B PHE 3.9 0.4 - - - +
12B HIS* 1.3 90.1 - - + +
14B LEU* 1.3 64.1 + - - +
16B ASP* 3.3 9.9 + - + +
17B THR* 3.0 26.3 + - - -
119B THR* 4.0 17.5 - - + -
120B LEU* 3.6 17.9 - - + -
123B LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 2.8 33.1 + - + +
11B ILE* 3.9 5.4 - - + +
13B LEU* 1.3 72.5 - - - +
15B SER* 1.3 58.7 + - - +
17B THR* 3.3 2.6 + - - -
18B TYR* 2.9 28.8 + - - +
58B ILE* 3.8 25.4 - - + +
61B VAL* 3.9 21.3 - - + -
62B VAL* 3.8 29.2 - - + -
68B LEU* 5.1 3.4 - - + -
69B LYS 5.1 3.4 - - - +
70B ILE* 3.9 6.1 - - + -
120B LEU* 3.5 27.7 - - + +
136B LEU* 4.2 17.3 - - + -
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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 ILE* 2.8 24.4 + - - +
12B HIS 3.6 0.2 - - - -
14B LEU* 1.3 78.0 - - - +
16B ASP* 1.3 61.9 + - - +
18B TYR* 3.3 5.6 + - - +
19B SER* 3.1 21.5 + - - -
69B LYS 4.1 0.3 + - - -
70B ILE* 3.6 14.1 - - - -
71B LYS* 2.8 45.6 + - - +
73B MSE 3.6 22.4 - - - +
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 5.1 3.6 + - - -
12B HIS* 3.1 22.5 + - - +
13B LEU* 3.5 15.2 - - + +
15B SER* 1.3 76.7 - - - +
17B THR* 1.3 57.8 + - - +
19B SER* 3.2 2.3 + - - -
20B ALA* 2.9 24.3 + - - +
73B MSE 3.6 19.3 - - - +
74B LYS 4.3 2.3 - - - +
75B CYS* 3.1 50.1 - - - +
77B ALA* 5.6 0.2 - - - +
112B TYR* 3.4 9.9 + - - -
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 3.0 16.9 + - - -
14B LEU 3.8 3.8 - - - -
16B ASP* 1.3 73.6 - - - +
18B TYR* 1.3 60.5 + - - +
20B ALA* 3.2 7.6 + - - +
21B GLU* 2.8 32.1 + - + +
58B ILE* 4.3 3.4 - - + -
112B TYR* 6.1 0.8 - - - -
113B GLU* 4.5 7.5 + - - +
116B SER* 3.8 18.3 + - - -
117B TYR* 3.4 45.8 - - + +
120B LEU* 3.6 16.5 - - + +
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Residues in contact with TYR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 2.9 14.7 + - - +
15B SER* 3.4 11.4 - - - +
17B THR* 1.3 77.8 - - - +
19B SER* 1.3 64.3 + - - +
21B GLU* 3.4 2.9 + - - +
22B LYS* 3.0 52.1 + - + +
55B ILE* 3.7 30.3 - - + +
58B ILE* 4.0 28.7 - - + +
59B ASP* 3.8 19.2 + - - -
70B ILE* 3.9 33.4 - - + -
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER 3.1 9.0 + - - -
16B ASP* 3.4 9.4 - - - -
18B TYR* 1.3 82.9 - - - +
20B ALA* 1.3 62.7 + - - +
22B LYS* 3.1 8.1 + - - +
23B GLN* 2.9 35.1 + - - +
73B MSE 3.1 24.5 + - - -
74B LYS* 3.5 3.1 - - - +
75B CYS 2.9 24.9 + - - -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 2.9 13.5 + - - +
17B THR* 3.4 11.7 - - - +
19B SER* 1.3 76.4 + - - +
21B GLU* 1.3 56.0 + - - +
23B GLN* 3.3 5.8 + - - +
24B LEU* 2.9 28.2 + - - +
75B CYS* 3.9 17.2 - - - +
78B MSE 3.7 24.3 - - + +
112B TYR* 4.6 2.7 - - + -
113B GLU* 3.8 20.6 - - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 2.8 23.9 + - + +
18B TYR* 3.8 2.7 - - - +
20B ALA* 1.3 72.3 - - - +
22B LYS* 1.3 63.0 + - - +
24B LEU* 3.0 22.4 + - - +
25B THR* 3.0 15.9 + - - +
51B THR* 3.2 19.5 - - + +
54B GLN* 3.5 23.8 - - + +
55B ILE* 3.5 23.1 - - + -
58B ILE* 4.2 7.2 - - + -
113B GLU* 3.2 22.4 - - - +
117B TYR* 2.9 32.6 + - - +
143B GLU* 5.2 2.1 - - - +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.0 49.0 + - + +
19B SER* 3.5 9.4 - - - +
21B GLU* 1.3 75.3 - - - +
23B GLN* 1.3 60.8 + - - +
25B THR* 2.5 27.2 + - + +
26B ARG* 3.3 26.9 + - - +
52B HIS* 6.3 1.3 - - + -
55B ILE* 3.8 27.1 - - + -
----------------------------------------------------------
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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 SER* 2.9 34.4 + - - +
20B ALA 3.5 6.5 - - - +
22B LYS* 1.3 75.0 - - - +
24B LEU* 1.3 64.1 + - - +
26B ARG* 3.1 37.3 + - - +
27B ALA 3.2 8.5 + - - -
74B LYS* 4.4 12.0 - - + +
75B CYS* 2.8 30.7 + - - +
78B MSE 3.8 7.1 - - + +
79B GLU* 3.3 35.7 + - - +
82B ILE* 3.7 18.6 - - + +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 2.9 13.2 + - - +
21B GLU* 3.0 23.8 + - - +
23B GLN* 1.3 77.6 - - - +
25B THR* 1.3 62.6 + - - +
27B ALA* 4.2 11.0 - - + -
28B LEU* 2.9 55.5 + - + +
31B LEU* 5.9 1.8 - - + -
47B HIS* 4.3 14.8 - - + +
51B THR* 4.4 4.3 - - + +
78B MSE 4.0 26.0 - - + -
82B ILE* 4.1 6.5 - - + +
109B VAL* 3.9 28.7 - - + -
113B GLU* 4.8 5.8 - - + -
143B GLU* 5.4 0.7 - - - +
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU 3.0 13.5 + - - +
22B LYS* 2.5 21.1 + - + +
24B LEU* 1.3 77.6 - - - +
26B ARG* 1.3 68.7 + - - +
29B ALA* 3.3 11.1 + - - +
48B LEU* 3.2 30.9 - - + +
51B THR* 3.7 19.3 - - + -
52B HIS* 3.7 34.4 - - + +
55B ILE* 3.8 11.9 - - + -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 3.3 32.5 + - - +
23B GLN* 3.1 37.9 + - - +
25B THR* 1.3 82.8 + - - +
27B ALA* 1.3 63.3 + - - +
29B ALA* 3.3 8.4 + - - +
30B LYS* 3.2 20.6 + - - +
33B ARG* 5.0 0.7 + - - -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN 3.2 3.0 + - - -
24B LEU* 3.8 12.3 - - + +
26B ARG* 1.3 79.6 - - - +
28B LEU* 1.3 56.8 + - - +
30B LYS* 3.2 10.4 + - - +
31B LEU* 2.8 40.5 + - + +
82B ILE* 3.6 46.0 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 2.9 45.1 + - + +
25B THR 4.1 0.9 - - - +
27B ALA* 1.3 69.6 - - - +
29B ALA* 1.3 66.1 + - - +
31B LEU* 3.9 12.4 - - + +
32B ALA* 3.0 25.1 + - - +
44B PHE* 4.0 42.3 - - + +
47B HIS* 3.7 31.2 - - + +
48B LEU* 3.8 15.0 - - + +
51B THR* 3.6 24.7 - - - +
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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 THR 3.3 11.0 + - - +
26B ARG* 3.3 11.5 + - - +
28B LEU* 1.3 79.7 - - - +
30B LYS* 1.3 62.2 + - - +
32B ALA* 3.6 5.4 + - - +
33B ARG* 3.3 41.1 + - - +
45B HIS* 6.0 0.7 - - - -
48B LEU* 4.2 19.9 - - + +
----------------------------------------------------------
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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
----------------------------------------------------------
26B ARG 3.2 7.7 + - - +
27B ALA* 3.2 11.2 + - - +
28B LEU 3.2 0.2 - - - -
29B ALA* 1.3 79.2 - - - +
31B LEU* 1.3 64.1 + - + +
33B ARG* 3.2 24.8 + - - +
34B ALA* 3.1 20.3 + - + +
86B ASN* 2.7 41.9 + - - +
89B ILE* 4.1 21.3 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 5.9 2.0 - - + -
27B ALA* 2.8 31.7 + - + +
28B LEU* 3.4 17.7 + - + +
30B LYS* 1.3 73.3 - - + +
32B ALA* 1.3 62.6 + - - +
34B ALA* 3.1 13.3 + - - +
35B THR* 3.4 16.8 + - - +
44B PHE* 3.7 38.6 - - + -
85B ALA* 3.9 19.3 - - + -
86B ASN* 6.3 0.2 - - - +
89B ILE* 4.5 8.5 - - + -
102B LEU* 3.7 36.4 - - + +
106B ALA* 5.6 3.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU 3.0 18.0 + - - +
29B ALA* 3.7 8.1 - - - +
30B LYS 3.3 0.2 - - - -
31B LEU* 1.3 77.1 - - - +
33B ARG* 1.3 61.0 + - + +
35B THR* 3.8 4.1 - - - +
41B SER* 2.7 47.1 + - - +
44B PHE* 3.9 12.7 - - + +
45B HIS* 4.1 18.2 - - + +
----------------------------------------------------------
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG 5.0 0.8 + - - -
29B ALA* 3.3 26.4 + - - +
30B LYS* 3.2 35.7 + - - +
31B LEU 3.1 0.4 - - - -
32B ALA* 1.3 78.4 - - + +
34B ALA* 1.3 58.9 + - - +
35B THR 3.4 2.1 - - - +
94B LYS* 3.0 24.6 + - - -
----------------------------------------------------------
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 3.1 16.0 + - + +
31B LEU* 3.1 7.5 + - - +
33B ARG* 1.3 79.1 - - - +
35B THR* 1.3 57.7 + - - +
89B ILE* 3.7 35.2 - - + -
94B LYS* 3.6 6.2 - - - +
98B ARG* 3.0 37.5 + - - +
102B LEU* 4.6 4.5 - - + -
----------------------------------------------------------
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 3.4 15.7 + - - +
32B ALA 3.8 4.2 - - - +
33B ARG 3.4 1.9 - - - +
34B ALA* 1.3 78.9 - - - +
36B SER* 1.3 61.8 + - - +
37B ASN* 3.1 14.6 + - - +
40B LEU* 3.7 9.3 - - - +
41B SER* 3.6 39.5 - - - +
44B PHE* 4.2 6.5 - - + -
94B LYS* 3.6 10.4 + - - -
98B ARG* 4.9 1.6 - - - +
99B ASP* 2.6 29.3 + - - -
102B LEU* 4.5 5.8 - - - -
----------------------------------------------------------
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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).
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