Contacts of the helix formed by residues 4 - 29 (chain G) in PDB entry 3FKS
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 LYS 4 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN 5.4 0.2 + - - -
333A GLY* 5.0 11.7 + - - -
335A ASP* 5.2 10.7 - - - +
316D ASP* 5.0 12.6 - - - +
318D THR* 4.6 22.6 - - - +
2G THR* 3.6 6.9 - - + +
3G LEU* 1.3 89.3 - - + +
5G GLU* 1.3 57.3 + - - +
6G VAL 3.1 2.5 - - - -
7G GLU* 2.7 51.0 + - - +
8G MET* 2.9 31.2 + - + +
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Residues in contact with GLU 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C GLY 5.8 0.2 - - - +
334C GLY 5.5 2.4 - - - +
1G ALA 5.8 1.8 - - - +
2G THR* 3.4 35.0 + - + +
4G LYS* 1.3 78.6 - - - +
6G VAL* 1.3 59.0 + - + +
8G MET* 3.8 14.4 - - + +
9G ARG* 3.0 62.9 + - + +
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Residues in contact with VAL 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA 3.6 25.1 - - - +
2G THR 3.2 19.0 + - - +
3G LEU 4.1 8.3 - - - +
5G GLU* 1.3 78.3 - - + +
7G GLU* 1.3 60.3 + - - +
9G ARG* 4.1 10.9 - - - +
10G LEU* 3.3 23.3 + - - +
251G TYR* 4.9 13.0 - - + +
254G LEU* 3.7 24.9 - - + -
255G TYR* 4.4 21.1 - - + +
258G THR* 4.2 18.8 - - + +
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Residues in contact with GLU 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASP* 5.9 3.1 - - - +
3G LEU 4.6 2.1 - - - +
4G LYS* 2.7 42.3 + - - +
6G VAL* 1.3 78.9 - - - +
8G MET* 1.3 60.1 + - - +
9G ARG 3.2 1.1 - - - -
10G LEU* 3.2 8.3 + - + +
11G LYS* 3.0 50.9 + - + +
255G TYR* 3.8 37.6 + - + -
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Residues in contact with MET 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LYS* 2.9 36.3 + - + +
5G GLU* 3.8 13.2 - - + +
7G GLU* 1.3 74.0 - - - +
9G ARG* 1.3 65.8 + - + +
10G LEU 3.3 0.2 - - - -
11G LYS* 3.7 17.2 - - + +
12G SER* 3.2 24.9 + - - -
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Residues in contact with ARG 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F ASP* 4.3 16.8 + - - -
5G GLU* 3.0 51.4 + - + +
6G VAL* 4.4 10.0 - - - +
8G MET* 1.3 79.8 - - + +
10G LEU* 1.3 63.5 + - - +
11G LYS 3.2 0.4 - - - -
12G SER* 3.4 17.7 + - - +
13G ILE* 3.6 17.9 + - - +
247G MET* 6.1 0.2 - - - +
251G TYR* 3.0 48.4 + - + -
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Residues in contact with LEU 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G VAL 3.3 16.5 + - - +
7G GLU* 3.2 10.7 + - + +
9G ARG* 1.3 78.7 - - - +
11G LYS* 1.3 62.7 + - + +
13G ILE* 3.8 5.0 - - - +
14G LYS* 2.9 49.5 + - + +
248G ILE* 4.4 9.9 - - - +
251G TYR* 3.8 18.1 - - + +
252G SER* 3.5 38.6 - - - +
255G TYR* 4.1 16.2 - - + -
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Residues in contact with LYS 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLU* 3.0 43.0 + - + +
8G MET* 3.7 16.4 - - + +
9G ARG 3.2 0.4 - - - -
10G LEU* 1.3 79.1 - - + +
12G SER* 1.3 57.6 + - - +
13G ILE 2.9 10.7 + - - -
14G LYS* 4.3 4.9 - - + -
15G ASN* 3.1 35.0 + - - +
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Residues in contact with SER 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ASP* 5.3 1.3 - - - -
8G MET 3.2 12.9 + - - -
9G ARG* 3.4 16.1 + - - +
11G LYS* 1.3 76.7 - - - +
13G ILE* 1.3 71.0 + - - +
16G ILE* 2.9 30.5 - - - +
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Residues in contact with ILE 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F ASP* 6.1 4.3 - - + -
390F ILE* 4.4 15.0 - - + -
9G ARG* 3.6 15.2 + - + +
10G LEU* 4.1 4.5 - - - +
11G LYS 2.9 0.4 - - - -
12G SER* 1.3 107.8 + - - +
14G LYS* 1.3 61.1 + - - +
15G ASN 3.3 1.8 - - - -
16G ILE* 3.6 8.7 - - + +
17G GLU* 2.9 26.5 + - - +
244G ALA* 4.5 1.8 - - - +
247G MET* 3.7 43.1 - - + -
248G ILE* 3.6 21.8 - - + +
251G TYR* 6.1 2.0 - - + -
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Residues in contact with LYS 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 2.9 33.2 + - + +
11G LYS* 4.0 5.4 - - - +
13G ILE* 1.3 79.5 - - - +
15G ASN* 1.3 65.7 + - - +
17G GLU* 3.5 26.4 + - - +
18G LYS* 3.6 4.7 + - - +
248G ILE* 3.7 41.7 + - + +
249G ASN* 5.5 4.0 - - - +
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Residues in contact with ASN 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ASP* 3.7 17.2 - - - +
11G LYS* 3.1 23.3 + - - +
14G LYS* 1.3 84.7 - - - +
16G ILE* 1.3 61.4 + - - +
17G GLU 3.2 1.1 - - - -
18G LYS* 3.7 22.2 + - - +
19G ILE* 3.2 27.2 + - - +
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ASP* 3.0 39.3 - - - +
390D ILE* 5.7 9.6 - - + -
390F ILE* 4.4 27.4 - - + -
391F LEU* 6.4 0.7 - - + -
12G SER* 2.9 34.3 - - - +
13G ILE* 3.4 8.9 + - + +
14G LYS 3.4 0.2 - - - -
15G ASN* 1.3 75.5 - - - +
17G GLU* 1.3 65.2 + - - +
18G LYS 3.3 0.2 - - - -
19G ILE* 3.2 13.0 - - + +
20G THR* 3.2 32.0 - - + +
244G ALA* 4.6 2.2 - - + +
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Residues in contact with GLU 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ILE 2.9 16.9 + - - +
14G LYS* 3.5 18.3 + - - +
15G ASN 3.2 0.2 - - - -
16G ILE* 1.3 79.7 - - - +
18G LYS* 1.3 70.1 + - - +
20G THR* 3.3 12.8 + - - -
21G LYS* 3.5 29.9 + - - +
241G SER* 4.3 10.7 - - - +
244G ALA* 3.5 28.5 - - + +
248G ILE* 3.6 33.4 - - + +
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Residues in contact with LYS 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG 6.0 0.2 + - - -
401A GLU* 5.9 6.6 + - + +
404A ALA* 4.8 19.3 - - + +
14G LYS 3.6 6.9 + - - +
15G ASN* 3.7 22.3 + - - +
16G ILE 3.3 0.2 - - - -
17G GLU* 1.3 89.9 + - - +
19G ILE* 1.3 61.4 + - - +
21G LYS* 3.2 17.8 + - - +
22G THR* 2.7 37.4 + - - -
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Residues in contact with ILE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA* 5.8 8.3 - - + +
386D ASP* 5.4 9.6 - - + +
387D ILE* 3.5 33.4 - - + -
390D ILE* 5.2 16.4 - - + -
15G ASN 3.2 12.9 + - - +
16G ILE* 3.2 31.4 - - + +
18G LYS* 1.3 81.4 - - - +
20G THR* 1.3 70.8 + - + +
22G THR* 3.0 36.2 - - + +
23G MET* 3.1 24.3 + - + +
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Residues in contact with THR 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D ILE* 5.9 5.2 - - + -
390F ILE* 5.1 5.6 - - + -
391F LEU* 5.1 9.0 - - + -
16G ILE* 3.2 23.9 + - + +
17G GLU* 3.3 12.3 + - - -
19G ILE* 1.3 84.3 - - + +
21G LYS* 1.3 59.7 + - - +
24G LYS* 3.1 25.1 + - - +
83G LEU* 6.3 0.2 - - + -
237G MET* 3.5 28.3 - - + +
240G ALA* 3.9 26.6 + - + -
241G SER* 3.5 16.5 + - - -
244G ALA* 4.6 0.6 - - + +
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Residues in contact with LYS 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 3.5 31.9 + - - +
18G LYS* 3.2 17.5 + - - +
19G ILE 3.2 0.6 - - - -
20G THR* 1.3 81.6 + - - +
22G THR* 1.3 60.4 + - - +
24G LYS* 3.5 13.2 + - + +
25G ILE* 3.2 34.8 + - + +
241G SER* 4.0 17.7 - - - +
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Residues in contact with THR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA* 4.8 15.3 - - + +
405A PHE* 4.0 27.6 + - - -
407A GLN 6.6 0.2 - - - -
18G LYS* 2.7 18.5 + - - -
19G ILE* 3.0 42.6 - - + +
21G LYS* 1.3 78.0 - - - +
23G MET* 1.3 64.7 + - + +
24G LYS 3.3 0.2 - - - -
25G ILE* 3.8 10.4 + - - +
26G VAL* 3.1 28.0 + - + +
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Residues in contact with MET 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLN 5.9 6.1 - - - -
387D ILE* 4.2 23.3 - - + -
390D ILE* 4.3 11.2 - - + -
391D LEU* 3.5 31.9 - - + -
395D GLU* 5.2 5.6 - - + -
19G ILE* 3.1 19.6 + - + +
21G LYS 3.3 0.2 - - - -
22G THR* 1.3 84.0 - - + +
24G LYS* 1.3 60.3 + - - +
25G ILE 3.2 0.9 - - - -
26G VAL* 3.6 12.2 - - + +
27G ALA* 2.9 29.3 + - - +
81G LYS* 6.1 1.6 - - - -
83G LEU* 4.9 2.5 - - - -
233G ARG* 4.9 6.1 - - - -
237G MET* 3.3 39.7 - - - +
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Residues in contact with LYS 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E ASP* 5.2 13.3 - - - +
20G THR 3.1 19.1 + - - +
21G LYS* 3.6 15.3 - - + +
22G THR 3.3 0.2 - - - -
23G MET* 1.3 76.9 - - - +
25G ILE* 1.3 62.7 + - + +
27G ALA* 3.4 5.5 + - - +
28G SER* 2.8 36.1 + - - -
234G ARG* 3.7 40.3 - - + +
237G MET* 4.1 14.1 - - + +
238G ASP* 3.1 46.4 - - - +
241G SER* 4.7 5.2 - - - +
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Residues in contact with ILE 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 4.1 30.7 - - + -
390E ILE* 4.0 20.0 - - + -
21G LYS* 3.2 27.1 + - + +
22G THR* 3.9 10.1 - - - +
23G MET 3.2 0.4 - - - -
24G LYS* 1.3 81.3 - - + +
26G VAL* 1.3 56.9 + - - +
28G SER* 4.2 5.2 - - - -
29G THR* 2.6 44.1 + - + -
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Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 4.6 17.7 - - + -
407A GLN 4.9 13.0 - - - +
410A SER* 4.8 5.2 - - - +
22G THR* 3.1 18.8 + - + +
23G MET* 3.4 15.2 + - + +
24G LYS 3.4 0.4 - - - -
25G ILE* 1.3 77.0 - - - +
27G ALA* 1.3 58.6 + - - +
29G THR* 3.6 10.0 - - + +
30G ARG* 3.0 62.0 + - - +
233G ARG* 6.5 0.7 - - - -
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G MET 2.9 17.5 + - - +
24G LYS 3.8 3.6 - - - +
26G VAL* 1.3 77.8 - - - +
28G SER* 1.3 61.1 + - - +
30G ARG* 3.7 3.5 + - - +
31G LEU* 3.4 5.9 + - - +
230G ILE* 3.1 37.4 - - + +
233G ARG* 3.8 20.6 - - + +
234G ARG* 3.7 28.6 - - - +
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E ILE* 5.6 6.1 - - - +
390E ILE* 4.0 19.9 - - - +
391E LEU* 5.9 2.9 - - - +
24G LYS* 2.8 25.4 + - - -
25G ILE* 3.1 5.8 + - - -
27G ALA* 1.3 78.5 - - - +
29G THR* 1.3 59.2 + - - +
30G ARG 3.2 0.7 - - - -
31G LEU* 3.4 24.1 - - - +
32G SER 4.5 0.9 + - - -
234G ARG* 3.8 25.3 + - - +
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Residues in contact with THR 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 6.4 0.7 - - + -
411A ASP 5.9 2.9 - - - +
413A ASP* 5.4 9.4 + - - +
390E ILE* 3.3 32.0 - - - +
25G ILE* 2.6 32.0 + - + +
26G VAL* 3.6 13.7 - - + +
28G SER* 1.3 71.6 - - - +
30G ARG* 1.3 60.2 + - + +
31G LEU 3.3 2.7 - - - -
32G SER* 3.0 19.8 + - - -
33G LYS* 5.8 0.2 - - - +
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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