Contacts of the helix formed by residues 2 - 31 (chain D) in PDB entry 1GCL
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 MET 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 3.1 40.6 - - + -
1C ARG* 2.8 53.9 - - - +
2C MET* 4.1 17.5 - - + +
5C ILE* 5.0 7.1 - - + +
1D ARG* 1.4 74.8 - - + +
3D LYS* 1.3 62.7 + - - +
4D GLN 2.9 5.6 - - - -
5D ILE* 3.1 27.8 + - + +
6D GLU* 3.7 5.2 + - - +
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Residues in contact with LYS 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ARG* 4.8 5.3 - - - +
1D ARG 5.1 0.4 - - - +
2D MET* 1.3 75.6 - - - +
4D GLN* 1.4 64.8 + - + +
6D GLU* 3.3 5.3 + - + +
7D ASP* 2.6 49.8 + - - +
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Residues in contact with GLN 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 3.6 30.5 + - - +
0D ACE 4.2 9.2 - - - +
1D ARG* 3.1 51.0 + - - +
3D LYS* 1.4 79.7 - - + +
5D ILE* 1.3 52.2 + - - +
7D ASP* 2.9 10.2 + - - +
8D LYS* 2.7 41.4 + - + +
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Residues in contact with ILE 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 3.3 42.8 - - + +
5A ILE* 3.8 25.1 - - + -
6A GLU* 4.0 17.7 - - + -
9A LEU* 3.3 23.9 - - + +
5C ILE* 3.5 26.7 - - + -
1D ARG 4.2 14.1 - - - +
2D MET* 3.1 16.3 + - + +
4D GLN* 1.3 76.1 - - - +
6D GLU* 1.3 58.1 + - - +
7D ASP 3.1 0.2 - - - -
8D LYS* 5.1 0.4 - - - -
9D LEU* 3.0 27.0 + - + +
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Residues in contact with GLU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ARG* 4.5 2.6 - - + +
4C GLN* 4.0 8.0 + - - +
5C ILE* 3.0 40.9 + - + +
8C LYS* 3.6 15.1 - - - +
2D MET 3.7 4.5 + - - +
3D LYS* 3.3 8.6 + - + +
5D ILE* 1.3 77.3 - - - +
7D ASP* 1.3 60.4 + - - +
8D LYS 3.5 0.2 - - - -
9D LEU* 2.8 26.7 - - - +
10D GLU* 3.0 50.4 + - - +
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Residues in contact with ASP 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 2.6 44.0 + - - +
4D GLN* 3.1 11.2 - - - +
6D GLU* 1.3 78.1 - - - +
8D LYS* 1.3 63.5 + - + +
9D LEU 3.3 0.7 - - - -
10D GLU* 4.2 7.3 + - - +
11D GLU* 3.5 21.9 + - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 3.3 44.8 + - + +
7A ASP* 4.8 1.8 + - - -
9A LEU* 4.4 13.2 - - + -
10A GLU* 2.9 48.1 + - - +
13A LEU* 3.8 23.5 - - + +
4D GLN* 2.7 19.0 + - + +
5D ILE 4.3 4.0 - - - +
7D ASP* 1.3 82.1 - - + +
9D LEU* 1.4 47.9 + - - +
11D GLU* 2.8 15.5 - - - +
12D ILE* 2.7 38.8 + - - +
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 27.1 - - + -
5C ILE* 4.2 25.4 - - + +
8C LYS* 4.5 6.1 - - + -
9C LEU* 4.2 10.3 - - + -
12C ILE* 3.9 23.7 - - + +
5D ILE* 3.0 21.7 + - + +
6D GLU* 2.8 44.0 - - - +
7D ASP 3.3 0.2 - - - -
8D LYS* 1.4 72.0 - - - +
10D GLU* 1.3 68.4 + - - +
11D GLU 2.9 1.3 - - - -
12D ILE* 3.0 6.0 + - + +
13D LEU* 2.8 31.7 + - + +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 4.3 9.8 + - - -
6D GLU* 3.0 42.5 + - + +
7D ASP* 4.2 8.0 + - - +
9D LEU* 1.3 72.7 - - - +
11D GLU* 1.4 50.6 + - - +
13D LEU* 2.9 24.4 - - - +
14D SER* 2.9 36.3 + - - +
17D TYR* 5.6 0.2 - - - -
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 2.9 35.4 - - + +
17A TYR* 4.4 8.8 + - - -
7D ASP 3.5 15.2 + - - +
8D LYS* 2.8 18.5 - - - +
10D GLU* 1.4 75.6 - - - +
12D ILE* 1.3 61.4 + - - +
13D LEU 3.1 1.3 - - - -
14D SER* 4.3 5.8 - - - -
15D LYS* 3.1 44.5 + - - +
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Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.2 51.4 - - + +
12A ILE* 3.8 18.2 - - + -
13A LEU* 3.4 17.7 - - + -
16A LEU* 3.6 22.6 - - + +
12C ILE* 3.8 35.4 - - + -
8D LYS 2.7 21.0 + - - +
9D LEU* 3.0 9.4 + - + +
11D GLU* 1.3 71.1 - - - +
13D LEU* 1.3 68.4 + - - +
15D LYS 3.6 0.5 + - - -
16D LEU* 3.3 18.5 + - - +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 4.1 19.5 - - + +
11C GLU* 3.4 39.0 - - + +
12C ILE* 4.3 17.0 - - + -
15C LYS* 3.7 5.8 + - - +
9D LEU* 2.8 15.5 + - + +
10D GLU* 2.9 52.9 - - - +
12D ILE* 1.3 74.5 - - - +
14D SER* 1.3 62.3 + - - +
15D LYS 3.0 1.0 + - - -
16D LEU* 3.0 6.3 + - - -
17D TYR* 3.0 47.0 + - + +
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU 2.9 19.9 + - - -
11D GLU* 3.9 9.1 - - - -
13D LEU* 1.3 71.5 - - - +
15D LYS* 1.3 74.8 + - - +
17D TYR* 3.0 24.7 + - - +
18D HIS* 3.0 18.4 + - - +
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.5 7.4 - - + -
16A LEU* 3.7 22.2 - - + -
17A TYR* 4.4 21.1 - - + -
20A GLU* 3.7 28.5 - - - +
11D GLU* 3.1 33.0 + - - +
12D ILE 3.7 8.7 - - - +
13D LEU 3.0 1.2 + - - -
14D SER* 1.3 80.3 - - - +
16D LEU* 1.3 50.9 + - - +
17D TYR 2.9 4.0 - - - -
18D HIS* 2.5 32.6 + - + +
19D ILE* 2.7 21.3 + - + +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.0 12.8 - - + -
12C ILE* 4.0 17.7 - - + +
15C LYS* 3.3 44.5 - - + +
16C LEU* 3.6 39.5 - - + +
19C ILE* 3.8 14.6 - - + +
12D ILE 3.3 10.0 + - - +
13D LEU* 3.0 6.0 + - - +
15D LYS* 1.3 79.0 - - - +
17D TYR* 1.4 56.3 + - - +
19D ILE* 3.5 24.0 - - + +
20D GLU* 3.0 29.5 + - - +
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Residues in contact with TYR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 4.6 5.8 + - - -
15C LYS* 2.8 33.0 - - - -
13D LEU* 3.0 40.3 + - + +
14D SER* 3.3 22.2 - - - +
15D LYS 2.9 1.2 - - - -
16D LEU* 1.4 75.6 - - - +
18D HIS* 1.3 66.8 + - - +
20D GLU* 2.8 38.4 - - - +
21D ASN* 3.4 7.1 + - - +
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Residues in contact with HIS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.0 43.4 + - + +
27A LYS* 6.0 0.7 - - - -
14D SER 3.0 8.7 + - - +
15D LYS* 2.5 20.2 + - + +
17D TYR* 1.3 73.3 - - - +
19D ILE* 1.3 61.5 + - - +
21D ASN* 3.3 4.6 + - - +
22D GLU* 2.9 43.3 + - + +
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.2 12.8 - - + +
19A ILE* 4.1 22.4 - - + -
20A GLU* 4.1 26.0 - - + +
23A LEU* 4.0 19.3 - - + -
19C ILE* 4.0 24.5 - - + -
15D LYS* 2.7 25.6 + - + +
16D LEU* 3.5 28.5 - - + +
18D HIS* 1.3 70.2 - - - +
20D GLU* 1.4 63.9 + - - +
22D GLU* 2.8 22.2 + - - +
23D LEU* 3.0 22.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS* 4.4 21.2 + - + +
18C HIS* 6.1 5.4 - - + -
19C ILE* 5.7 4.0 - - + -
22C GLU* 4.8 7.1 - - - +
16D LEU 3.0 21.0 + - - +
17D TYR* 2.8 26.3 - - - +
19D ILE* 1.4 73.9 - - - +
21D ASN* 1.3 74.0 + - - +
23D LEU* 3.5 9.0 + - - +
24D ALA* 3.1 21.5 + - - +
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR 4.4 4.5 - - - +
18D HIS* 3.3 7.4 + - - +
19D ILE 3.3 0.4 - - - -
20D GLU* 1.3 96.5 + - - +
22D GLU* 1.3 54.4 + - - +
23D LEU 3.1 2.5 - - - -
24D ALA* 3.2 12.9 - - + +
25D ARG* 2.7 36.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.3 19.5 - - - +
23A LEU* 3.0 38.7 - - + +
24A ALA* 4.6 5.1 - - - +
27A LYS* 3.6 26.5 + - - +
18D HIS* 2.9 47.4 + - + +
19D ILE* 2.8 17.5 + - - +
21D ASN* 1.3 72.5 - - - +
23D LEU* 1.3 52.6 + - - +
25D ARG* 3.1 8.2 - - - +
26D ILE* 2.6 41.4 + - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 24.2 - - + -
19C ILE* 3.3 50.3 - - + +
22C GLU* 3.9 21.3 - - + +
23C LEU* 3.7 22.9 - - + -
26C ILE* 3.8 16.7 - - + +
19D ILE* 3.0 17.2 + - + +
20D GLU* 3.7 8.3 - - - +
22D GLU* 1.3 76.8 - - - +
24D ALA* 1.3 54.7 + - - +
26D ILE* 3.0 5.1 + - + +
27D LYS* 2.7 41.4 + - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU 3.1 9.3 + - - +
21D ASN* 2.9 27.2 + - + +
23D LEU* 1.3 75.1 - - - +
25D ARG* 1.3 58.6 + - - +
27D LYS* 3.2 16.5 + - - +
28D LYS* 2.8 43.3 + - + +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 2.9 48.4 - - + +
21D ASN 2.7 12.6 + - - +
22D GLU 3.1 9.9 - - - +
24D ALA* 1.3 77.0 - - - +
26D ILE* 1.4 58.8 + - - +
28D LYS* 3.1 8.7 + - - +
29D LEU* 2.8 42.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.5 52.0 - - + +
26A ILE* 4.3 22.0 - - + -
27A LYS* 4.3 16.4 - - + -
30A LEU* 5.0 5.8 - - + -
26C ILE* 3.9 24.0 - - + -
22D GLU 2.6 30.4 + - - +
23D LEU* 3.0 11.6 + - + +
25D ARG* 1.4 71.9 - - - +
27D LYS* 1.4 60.9 + - - +
29D LEU* 3.3 8.6 + - + +
30D LEU* 3.0 31.6 + - + +
----------------------------------------------------------
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C HIS* 5.4 2.2 + - - -
22C GLU* 2.8 46.4 + - + +
25C ARG* 4.6 24.9 - - + +
26C ILE* 4.5 11.6 - - + +
29C LEU* 4.1 22.2 - - + +
23D LEU 2.7 22.4 + - - +
24D ALA* 3.5 13.2 - - - +
26D ILE* 1.4 70.1 - - - +
28D LYS* 1.3 62.8 + - + +
30D LEU* 3.1 9.2 + - - +
31D GLY 2.7 36.5 + - - -
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 5.9 2.8 - - - +
24D ALA* 2.8 31.8 + - + +
25D ARG* 3.6 7.2 - - - +
27D LYS* 1.3 83.9 - - - +
29D LEU* 1.3 68.5 - - + +
31D GLY* 2.8 23.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE 5.2 0.4 - - - +
27A LYS* 3.4 50.3 - - + +
30A LEU* 4.3 27.1 - - + +
31A GLY* 5.5 4.5 - - - -
25D ARG* 2.8 36.2 + - + +
26D ILE* 3.4 12.3 - - + +
28D LYS* 1.3 72.8 - - + +
30D LEU* 1.3 61.1 + - - +
31D GLY 3.7 0.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.0 24.0 - - + -
26C ILE* 4.3 21.1 - - + +
29C LEU* 4.0 43.6 - - + +
30C LEU* 3.9 37.5 - - + -
26D ILE* 3.0 22.4 + - + +
27D LYS 3.3 8.3 - - - +
28D LYS 3.0 0.6 - - - -
29D LEU* 1.3 77.3 - - - +
31D GLY* 1.3 56.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 3.8 22.0 + - - -
29C LEU* 4.8 5.9 - - - +
27D LYS* 2.7 18.5 + - - -
28D LYS* 2.8 25.1 + - - -
29D LEU 3.7 0.4 + - - -
30D LEU* 1.3 76.1 - - - +
----------------------------------------------------------
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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