Contacts of the helix formed by residues 5 - 33 (chain A) in PDB entry 2L6W
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 PRO 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY 4.7 5.6 - - - +
3A SER 3.9 4.0 - - - +
4A LEU* 1.3 93.8 - - + +
6A PHE* 1.3 62.1 + - + +
7A LYS* 2.9 26.4 + - + -
8A VAL* 3.3 25.3 + - + +
9A VAL* 3.3 14.1 + - - +
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Residues in contact with PHE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY 4.9 7.1 - - - +
4A LEU 3.8 1.4 + - - -
5A PRO* 1.3 73.0 - - + +
7A LYS* 1.3 89.1 + - + +
8A VAL 3.3 0.4 - - - -
9A VAL* 3.7 13.0 - - + -
10A VAL* 2.9 43.8 + - + +
1B GLY* 4.5 27.1 - - - -
6B PHE* 4.9 17.3 - - + -
9B VAL* 6.1 1.6 - - + -
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 2.9 19.9 - - + -
6A PHE* 1.3 109.8 - - + +
8A VAL* 1.3 64.0 + - + +
10A VAL* 4.1 2.5 - - - +
11A ILE* 3.1 36.9 + - + +
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.8 7.4 - - + -
5A PRO* 3.3 24.4 + - + +
7A LYS* 1.3 76.2 - - + +
9A VAL* 1.3 67.0 + - + +
11A ILE* 4.0 7.4 - - + +
12A SER* 3.0 28.0 + - - -
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.7 11.7 - - + +
5A PRO 3.3 20.0 - - - +
6A PHE* 3.3 13.4 + - + +
8A VAL* 1.3 77.4 - - + +
10A VAL* 1.3 58.8 + - + +
12A SER* 3.6 5.2 - - - -
13A ALA* 2.9 28.6 + - - +
6B PHE* 4.5 7.2 - - + +
9B VAL* 3.5 20.4 - - + +
10B VAL* 3.5 40.2 - - + +
13B ALA* 4.5 3.0 - - + +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 2.9 38.1 + - + +
7A LYS* 4.1 3.4 - - - +
9A VAL* 1.3 73.0 - - - +
11A ILE* 1.3 70.3 + - + +
13A ALA* 2.9 2.9 + - - +
14A ILE* 2.9 46.9 + - + +
1B GLY* 4.7 13.5 - - - +
9B VAL* 3.5 24.5 - - + -
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.1 28.6 + - + +
8A VAL* 4.1 5.6 - - + +
10A VAL* 1.3 79.3 - - + +
12A SER* 1.3 61.0 + - - +
14A ILE* 4.2 4.6 - - - +
15A LEU* 3.2 29.0 + - + +
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Residues in contact with SER 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.0 25.6 + - - -
9A VAL* 3.6 5.6 - - - -
11A ILE* 1.3 76.6 - - - +
13A ALA* 1.3 64.5 + - - +
15A LEU* 3.9 6.7 - - - +
16A ALA* 3.1 24.8 + - - +
13B ALA* 4.3 11.8 - - - +
17B LEU* 5.0 6.9 - - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL 2.9 17.4 + - - +
10A VAL 3.5 2.9 - - - +
12A SER* 1.3 72.4 - - - +
14A ILE* 1.3 71.4 + - + +
16A ALA* 3.2 4.2 + - - +
17A LEU* 3.0 22.8 + - - +
9B VAL* 3.7 33.0 - - + +
12B SER* 4.7 9.5 + - - +
13B ALA* 3.7 16.1 - - + +
16B ALA* 4.9 1.9 - - - +
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 2.9 42.0 + - + +
11A ILE* 4.2 5.4 - - - +
13A ALA* 1.3 73.7 - - + +
15A LEU* 1.3 65.8 + - - +
17A LEU* 3.0 24.5 + - + +
18A VAL* 3.0 27.0 + - + +
9B VAL* 6.5 0.2 - - + -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.2 23.2 + - + +
12A SER* 3.9 5.4 - - - +
14A ILE* 1.3 78.5 - - - +
16A ALA* 1.3 59.6 + - - +
18A VAL* 2.9 30.0 + - + +
19A VAL* 3.0 27.7 + - + +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER 3.1 18.8 + - - +
13A ALA* 3.6 3.6 - - - +
15A LEU* 1.3 77.7 - - - +
17A LEU* 1.3 58.9 + - - +
19A VAL* 3.0 26.6 - - + +
20A LEU* 3.4 10.6 + - - +
13B ALA 4.3 1.1 - - - +
16B ALA* 3.3 32.3 - - + +
17B LEU* 3.5 23.3 - - + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 3.0 11.2 + - - +
14A ILE* 3.0 21.6 + - + +
16A ALA* 1.3 76.9 - - - +
18A VAL* 1.3 61.8 + - + +
20A LEU* 3.6 16.2 + - + +
21A THR* 3.5 16.5 + - - +
12B SER* 5.4 9.9 - - - +
16B ALA* 4.4 8.0 - - + +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.0 26.9 + - + +
15A LEU* 2.9 17.4 + - + +
17A LEU* 1.3 76.9 - - + +
19A VAL* 1.3 66.1 + - + +
21A THR* 3.1 17.1 + - - -
22A ILE* 3.1 25.4 + - + +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.0 24.1 + - + +
16A ALA* 3.0 35.0 - - - +
18A VAL* 1.3 78.5 - - + +
20A LEU* 1.3 56.0 + - - +
22A ILE* 3.5 10.7 - - + +
23A ILE* 2.9 32.2 + - - +
17B LEU* 6.3 0.2 - - + -
20B LEU* 3.7 33.3 - - + +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 3.4 8.5 + - - +
17A LEU* 3.7 17.5 - - + +
18A VAL 3.2 0.8 - - - -
19A VAL* 1.3 80.3 - - - +
21A THR* 1.3 59.0 + - - +
23A ILE* 3.0 16.6 - - + +
24A SER* 3.2 15.3 + - - -
16B ALA* 4.5 1.3 - - + +
19B VAL* 3.6 30.7 - - + -
20B LEU* 3.7 17.9 - - + -
23B ILE* 3.6 33.7 - - + -
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 3.5 11.3 + - - -
18A VAL* 3.1 11.1 + - - -
20A LEU* 1.3 77.0 - - - +
22A ILE* 1.3 64.4 + - + +
24A SER* 3.7 5.1 - - - -
25A LEU* 2.9 30.3 + - + +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.1 27.9 + - + +
19A VAL* 3.2 11.9 + - + +
21A THR* 1.3 79.4 - - + +
23A ILE* 1.3 66.7 + - - +
25A LEU* 3.1 27.2 + - + +
26A ILE* 3.3 22.5 + - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL 2.9 16.5 + - - +
20A LEU* 3.0 23.6 - - + +
22A ILE* 1.3 78.5 - - - +
24A SER* 1.3 65.6 + - - +
26A ILE* 3.6 13.1 + - + +
27A ILE* 3.3 17.4 + - - +
20B LEU* 3.5 37.0 - - + +
23B ILE* 3.4 20.4 - - + -
24B SER* 3.6 29.2 - - - +
27B ILE* 4.2 9.4 - - + +
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.2 22.4 + - - -
21A THR* 3.7 8.1 - - - -
22A ILE 3.1 0.4 - - - -
23A ILE* 1.3 82.8 - - - +
25A LEU* 1.3 62.9 + - - +
27A ILE* 3.1 13.8 + - - +
28A LEU* 3.0 23.3 + - - +
23B ILE* 4.7 4.7 - - - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 2.9 17.4 + - + +
22A ILE* 3.1 23.5 + - + +
24A SER* 1.3 77.4 - - - +
26A ILE* 1.3 68.1 + - + +
28A LEU* 3.3 19.2 + - + +
29A ILE* 3.2 36.5 + - + +
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.4 23.3 - - + +
23A ILE* 3.8 10.5 - - + +
24A SER 3.2 0.4 - - - -
25A LEU* 1.3 85.7 - - + +
27A ILE* 1.3 57.0 + - + +
29A ILE* 4.2 3.4 - - - +
30A MET* 2.9 51.3 + - + +
27B ILE* 5.8 3.6 - - + -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE 3.3 13.0 - - - +
24A SER* 3.1 9.3 + - - +
26A ILE* 1.3 73.6 - - - +
28A LEU* 1.3 67.2 + - - +
30A MET* 3.6 6.6 - - - +
31A LEU* 2.9 30.4 + - + +
23B ILE* 3.5 26.7 - - + +
26B ILE* 5.7 7.0 - - + -
27B ILE* 3.4 38.1 - - + -
30B MET* 4.6 21.8 - - + -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 3.0 13.0 + - - +
25A LEU* 3.3 25.3 + - + +
27A ILE* 1.3 76.9 - - - +
29A ILE* 1.3 64.1 + - + +
31A LEU* 3.8 2.9 - - - +
32A TRP* 2.9 30.9 + - + +
37A ARG* 6.0 4.5 - - - +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.2 28.3 + - + +
26A ILE* 4.3 2.9 - - - +
28A LEU* 1.3 85.7 - - + +
30A MET* 1.3 67.8 + - - +
32A TRP* 3.1 40.1 + - + +
33A GLN* 3.2 19.8 + - + +
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Residues in contact with MET 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 2.9 44.4 + - + +
27A ILE* 3.6 6.7 - - + +
29A ILE* 1.3 79.7 - - - +
31A LEU* 1.3 60.7 + - - +
33A GLN* 3.4 8.5 + - - +
34A LYS* 3.2 41.9 + - + +
27B ILE* 4.0 30.5 - - + -
30B MET* 4.3 14.6 - - + -
31B LEU* 5.7 10.3 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 2.9 23.3 + - + +
28A LEU* 4.2 2.7 - - - +
30A MET* 1.3 72.2 - - - +
32A TRP* 1.3 60.0 + - - +
33A GLN 3.1 2.2 - - - -
34A LYS* 3.0 16.0 + - + -
35A LYS* 3.0 63.0 + - + +
30B MET* 5.1 19.5 - - + -
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Residues in contact with TRP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 2.9 22.3 + - + +
29A ILE* 3.1 38.6 + - + +
31A LEU* 1.3 77.9 - - - +
33A GLN* 1.3 92.6 + - - +
34A LYS 3.4 0.4 - - - -
35A LYS 4.6 8.2 - - - +
36A PRO* 5.3 3.1 - - - +
37A ARG* 3.1 58.0 - - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.2 20.9 + - + +
30A MET* 3.4 4.7 + - - +
31A LEU 3.1 0.8 - - - -
32A TRP* 1.3 131.9 + - + +
34A LYS* 1.3 62.9 + - + +
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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