Contacts of the helix formed by residues 3 - 27 (chain S) in PDB entry 2D2C
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 3 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2S MET* 1.3 81.1 + - - +
4S GLU* 1.3 76.6 + - - +
5S GLU 2.9 2.5 + - - -
6S MET* 3.3 14.5 + - + +
7S LEU* 3.0 39.9 + - + +
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Residues in contact with GLU 4 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P GLU* 3.6 24.2 - - - +
35P GLU* 3.4 25.0 - - - +
51P LYS* 5.4 2.3 + - - -
2S MET 5.2 2.9 - - - +
3S THR* 1.3 83.7 + - - +
5S GLU* 1.3 87.4 - - + +
7S LEU* 3.3 13.5 - - - +
8S TYR* 3.3 20.8 + - - +
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Residues in contact with GLU 5 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLU* 3.2 33.1 - - + +
2R ILE* 4.8 2.4 - - + +
2S MET* 3.5 37.7 - - - +
3S THR 2.9 1.0 + - - -
4S GLU* 1.3 98.8 - - + +
6S MET* 1.3 58.5 + - + +
8S TYR* 2.8 34.9 - - - -
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Residues in contact with MET 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O TRP* 4.3 6.7 - - + -
1R MET* 3.7 16.4 - - + +
2R ILE* 3.1 45.1 - - - +
4R GLY* 4.1 6.1 - - - -
5R ALA* 2.7 42.2 - - + +
8R TYR* 4.3 16.6 - - + -
2S MET 4.0 13.5 - - - +
3S THR* 3.5 15.0 - - + +
5S GLU* 1.3 73.7 - - + +
7S LEU* 1.3 74.8 + - - +
8S TYR 3.0 2.5 - - - -
9S ALA* 2.5 25.3 + - - +
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Residues in contact with LEU 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ALA* 4.1 2.7 - - - -
3S THR* 3.0 39.2 + - + +
4S GLU* 3.3 11.7 - - - +
6S MET* 1.3 90.5 - - - +
8S TYR* 1.3 60.2 + - + +
10S ALA* 3.4 10.5 - - - +
11S LEU* 3.1 26.1 - - + +
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Residues in contact with TYR 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R ILE* 5.2 2.5 - - + -
4S GLU 3.3 8.2 + - - +
5S GLU 2.8 22.2 - - - -
6S MET 3.0 1.2 - - - -
7S LEU* 1.3 78.8 - - + +
9S ALA* 1.3 82.5 + - + +
10S ALA 3.1 5.4 - - - -
11S LEU* 2.7 20.2 - - + +
12S LEU* 2.6 43.9 - - + +
10T PHE* 5.6 7.8 - - - -
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Residues in contact with ALA 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R ILE* 3.0 37.5 - - + -
5R ALA* 3.7 5.9 - - + +
6R VAL* 4.4 7.3 - - + +
6S MET 2.5 12.5 + - - +
8S TYR* 1.3 84.7 - - + +
10S ALA* 1.3 64.7 - - - +
12S LEU* 3.1 25.2 - - + +
13S SER* 3.3 11.4 + - - -
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Residues in contact with ALA 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R ALA* 2.9 33.8 - - + +
8R TYR* 5.3 2.2 - - + -
9R ILE* 2.7 38.2 - - + +
6S MET 2.9 3.8 + - - -
7S LEU* 3.4 12.3 - - - +
8S TYR 3.1 1.0 - - - -
9S ALA* 1.3 78.5 - - - +
11S LEU* 1.3 58.9 + - + +
12S LEU 2.5 14.9 + - - -
13S SER* 2.9 6.2 + - - -
14S PHE 3.2 0.3 + - - -
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Residues in contact with LEU 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ILE* 3.1 20.4 - - + +
7S LEU* 3.1 26.9 - - + +
8S TYR* 2.7 37.7 - - + +
10S ALA* 1.3 79.0 - - + +
12S LEU* 1.3 68.9 + - - +
14S PHE* 3.9 7.4 - - + -
15S GLY* 2.9 16.5 + - - -
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Residues in contact with LEU 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8S TYR* 2.6 42.2 + - + +
9S ALA* 3.1 28.7 - - + +
10S ALA 2.5 4.2 + - - -
11S LEU* 1.3 80.9 - - - +
13S SER* 1.3 67.1 + - - +
15S GLY* 3.0 3.6 + - - -
16S LEU* 2.9 33.1 - - + +
14T GLY* 6.0 3.8 - - - -
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Residues in contact with SER 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R ALA 4.4 0.3 + - - -
6R VAL* 4.9 5.9 - - - -
9R ILE* 2.9 23.2 - - - +
10R VAL* 3.7 16.6 - - - +
9S ALA 3.6 5.9 + - - -
10S ALA 2.9 4.7 + - - -
12S LEU* 1.3 81.0 - - - +
14S PHE* 1.3 61.6 + - - -
15S GLY 2.6 1.2 + - - -
16S LEU* 2.5 43.2 + - - +
17S ILE* 3.3 10.2 + - - +
13T LEU* 6.6 0.4 - - - -
17T PHE* 5.3 9.0 - - - -
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Residues in contact with PHE 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ILE* 3.0 42.2 - - + +
10R VAL 5.2 0.7 - - - +
12R ILE* 4.1 11.0 - - + -
13R ALA* 3.2 44.9 - - + -
16R PHE* 4.9 10.1 - + + -
1101R BCR 4.9 4.5 - - + -
10S ALA 3.2 0.4 + - - -
11S LEU* 3.7 9.2 - - + +
13S SER* 1.3 82.1 + - - +
15S GLY* 1.3 62.0 + - - +
17S ILE* 2.8 26.9 - - - +
18S PHE* 3.8 34.8 - + - -
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Residues in contact with GLY 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S LEU 2.9 13.5 + - - -
12S LEU 3.6 4.5 - - - -
13S SER 2.6 5.9 + - - -
14S PHE* 1.3 75.0 - - - +
16S LEU* 1.3 51.5 + - - +
17S ILE 2.7 15.5 + - - -
18S PHE* 2.7 28.0 + - - +
19S VAL* 3.2 12.0 + - - +
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Residues in contact with LEU 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S LEU* 2.9 47.3 - - + +
13S SER* 2.5 15.6 + - - +
15S GLY* 1.3 71.1 - - - -
17S ILE* 1.3 61.8 + - + -
18S PHE 3.1 0.4 - - - -
19S VAL* 3.2 33.6 - - + +
20S GLY 3.1 19.1 + - - -
14T GLY* 4.0 28.0 - - - +
17T PHE* 4.8 9.1 - - + -
21T TYR* 3.7 15.0 + - - +
4U LEU* 6.1 1.8 - - + -
7U VAL* 4.5 16.2 - - + -
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Residues in contact with ILE 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R VAL* 4.3 15.5 - - + -
13R ALA* 4.1 10.3 - - + -
1101R BCR 3.5 46.7 - - + -
13S SER 3.3 15.0 - - - +
14S PHE* 2.8 28.5 - - - +
15S GLY 2.7 0.4 + - - -
16S LEU* 1.3 78.5 - - - +
18S PHE* 1.3 66.0 + - + +
21S TRP* 3.0 25.1 + - - +
17T PHE* 3.7 30.3 - - + -
21T TYR* 5.9 0.2 - - - -
24T TYR* 4.6 7.9 + - - +
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Residues in contact with PHE 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R PHE* 5.6 0.7 - + - -
1101R BCR 3.3 52.9 - - + -
14S PHE* 3.8 37.0 - + - -
15S GLY* 2.7 14.0 + - - +
17S ILE* 1.3 81.8 - - + +
19S VAL* 1.3 70.6 - - - +
20S GLY 2.7 3.6 + - - -
21S TRP* 2.8 35.7 + + + -
22S GLY* 2.8 13.2 + - - -
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Residues in contact with VAL 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S GLY 3.7 5.4 - - - +
16S LEU* 3.2 49.4 - - + +
18S PHE* 1.3 79.3 - - - +
20S GLY* 1.3 62.5 + - - +
22S GLY* 4.0 1.0 + - - -
23S LEU* 3.4 24.5 + - + +
21T TYR* 4.0 11.7 - - + +
4U LEU* 6.2 4.7 - - + -
7U VAL* 4.8 12.6 - - + -
11U VAL* 5.7 2.9 - - + -
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Residues in contact with GLY 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S LEU 3.1 6.9 + - - -
18S PHE 2.7 3.0 + - - -
19S VAL* 1.3 76.4 - - - +
21S TRP* 1.3 66.2 + - - +
22S GLY 2.8 4.0 + - - -
23S LEU* 2.8 16.0 + - - +
24S GLY 2.9 11.4 + - - -
21T TYR* 3.4 37.3 - - - -
24T TYR* 3.3 7.5 - - - -
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Residues in contact with TRP 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ILE* 4.7 19.3 - - + +
22R ILE* 5.2 6.1 - - + -
1101R BCR 3.5 50.9 - - + -
17S ILE 3.0 22.2 + - - +
18S PHE* 2.8 30.4 + + + +
20S GLY* 1.3 70.8 - - - +
22S GLY* 1.3 67.9 + - - +
24S GLY* 3.4 1.9 + - - -
25S VAL* 3.1 34.3 + - + +
24T TYR* 3.1 28.4 - + + -
26T ARG* 5.6 1.7 - - - +
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Residues in contact with GLY 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S PHE 2.8 13.4 + - - -
19S VAL 4.5 1.6 - - - -
20S GLY 2.8 4.0 + - - -
21S TRP* 1.3 76.4 - - - +
23S LEU* 1.3 52.2 + - - -
25S VAL* 2.4 38.0 + - - +
26S LEU* 2.9 11.2 + - - -
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Residues in contact with LEU 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S VAL* 3.4 22.4 - - + +
20S GLY* 2.8 6.7 + - - +
22S GLY* 1.3 68.0 - - - -
24S GLY* 1.3 66.4 + - - +
26S LEU* 2.6 37.7 + - + +
27S LEU* 2.6 27.9 + - + +
18T TYR* 6.2 1.8 - - + -
21T TYR* 4.4 23.3 - - + -
11U VAL* 4.6 18.6 - - + -
12U VAL* 6.3 2.7 - - + -
15U TRP* 4.5 22.0 - - + +
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Residues in contact with GLY 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S GLY 2.9 10.7 + - - -
23S LEU* 1.3 77.2 - - - +
25S VAL* 1.3 58.5 + - - +
27S LEU* 3.1 20.6 + - - +
28S LEU* 3.5 14.1 - - - +
21T TYR* 3.8 4.0 + - - +
24T TYR* 3.4 36.5 - - - +
25T LYS* 3.5 9.0 + - - +
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Residues in contact with VAL 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S TRP* 3.1 36.6 - - + +
22S GLY* 2.4 19.5 + - - +
24S GLY* 1.3 68.1 - - - -
26S LEU* 1.3 55.6 + - - +
27S LEU 3.0 2.5 - - - -
28S LEU* 2.5 52.0 + - + +
29S LYS* 3.5 3.3 + - - +
24T TYR* 5.9 1.1 - - + -
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Residues in contact with LEU 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S GLY 2.9 6.6 + - - +
23S LEU* 2.6 33.7 + - + +
25S VAL* 1.3 74.1 - - - +
27S LEU* 1.3 58.5 + - + +
28S LEU 2.9 4.9 + - - -
29S LYS* 3.3 16.8 + - + +
30S ILE* 3.5 15.7 - - + +
15U TRP* 3.2 40.2 - - + -
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Residues in contact with LEU 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU* 2.6 30.5 + - + +
24S GLY* 3.1 23.1 - - - +
26S LEU* 1.3 72.2 - - - +
28S LEU* 1.3 59.9 + - - +
30S ILE* 3.4 24.4 - - + +
31S GLN* 3.3 15.6 + - - +
21T TYR* 4.5 4.7 - - + +
22T GLN* 5.8 2.2 - - - +
25T LYS* 3.0 37.9 + - + +
15U TRP* 2.7 48.2 - - + +
18U ALA* 6.3 1.8 - - + -
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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
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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) + - + + + + + -
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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