Contacts of the helix formed by residues 12 - 36 (chain V) in PDB entry 1YHQ
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 12 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10V ASP 3.8 0.2 + - - -
11V MET* 1.3 76.9 - - - +
13V PRO* 1.3 79.0 - - - +
14V ALA* 3.2 14.8 - - + +
15V GLU* 2.8 63.0 + - + +
16V ARG* 3.1 12.8 + - - +
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Residues in contact with PRO 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V MET 4.6 0.9 - - - +
12V THR* 1.3 93.6 - - - +
14V ALA* 1.3 57.2 + - - +
16V ARG* 3.4 28.8 + - - +
17V GLU* 3.2 27.7 + - - +
63V GLU* 6.2 0.4 - - + -
65V ASP* 4.0 22.4 - - + +
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Residues in contact with ALA 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V THR* 3.1 11.2 - - + +
13V PRO* 1.3 78.4 - - - +
15V GLU* 1.3 61.8 + - + +
16V ARG 3.3 0.2 - - - -
17V GLU* 3.6 9.1 + - - +
18V ALA* 3.2 25.1 + - - +
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Residues in contact with GLU 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V ASP 5.0 1.2 - - - +
11V MET* 3.8 20.0 - - + +
12V THR* 2.8 47.6 + - + +
14V ALA* 1.3 78.6 - - + +
16V ARG* 1.3 59.6 + - - +
18V ALA* 3.6 5.9 + - - +
19V GLU* 2.9 29.5 + - - +
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Residues in contact with ARG 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V ILE* 3.1 32.8 + - + +
9V ARG 4.4 4.6 + - - -
11V MET* 3.6 32.8 + - + -
12V THR 3.1 8.2 + - - +
13V PRO* 3.4 27.9 - - - +
14V ALA 3.3 0.2 - - - -
15V GLU* 1.3 74.5 - - - +
17V GLU* 1.3 57.1 + - - +
19V GLU* 3.3 6.9 + - - +
20V LEU* 2.7 35.1 + - - +
56V ILE* 3.7 16.9 - - + +
59V ILE* 3.8 9.7 - - - +
60V GLN* 4.3 16.2 - - + +
63V GLU* 3.4 33.4 + - - +
65V ASP 2.8 38.0 + - - -
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Residues in contact with GLU 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V PRO 3.2 18.6 + - - +
14V ALA* 3.8 8.9 - - - +
15V GLU 3.3 0.2 - - - -
16V ARG* 1.3 74.2 - - - +
18V ALA* 1.3 66.4 + - - +
20V LEU* 3.0 14.5 + - - +
21V ASP* 2.9 32.6 + - - +
60V GLN* 4.0 20.1 - - - +
65V ASP* 5.1 7.6 - - - +
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Residues in contact with ALA 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V ALA 3.2 15.3 + - - +
15V GLU* 3.8 6.7 - - - +
17V GLU* 1.3 78.7 - - - +
19V GLU* 1.3 58.3 + - - +
21V ASP* 3.4 8.1 + - - +
22V ASP* 3.0 36.3 + - - +
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Residues in contact with GLU 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V LEU* 4.3 9.4 - - + +
11V MET* 4.0 24.9 - - + +
15V GLU 2.9 19.2 + - - +
16V ARG* 3.5 5.4 - - - +
18V ALA* 1.3 74.1 - - - +
20V LEU* 1.3 60.0 + - - +
22V ASP* 3.2 15.2 + - - +
23V LEU* 2.9 53.7 + - - +
56V ILE* 3.5 18.6 - - + -
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Residues in contact with LEU 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V ARG 2.7 20.4 + - - +
17V GLU* 3.0 13.9 + - - +
19V GLU* 1.3 73.9 - - - +
21V ASP* 1.3 59.5 + - - +
23V LEU* 3.0 4.7 + - - +
24V LYS* 2.8 46.0 + - - +
53V ILE* 3.7 36.1 - - + +
56V ILE* 4.0 24.0 - - + -
57V LYS* 4.2 16.6 - - + +
60V GLN* 3.3 26.7 - - - +
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Residues in contact with ASP 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V GLU* 2.9 24.3 + - - +
18V ALA* 3.7 7.6 - - - +
20V LEU* 1.3 77.5 - - - +
22V ASP* 1.3 61.7 + - - +
24V LYS* 3.6 14.3 + - - +
25V THR* 3.0 27.2 + - - -
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Residues in contact with ASP 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V ALA* 3.0 25.2 + - - +
19V GLU* 3.4 22.6 - - - +
20V LEU 3.1 0.2 - - - -
21V ASP* 1.3 76.3 - - - +
23V LEU* 1.3 64.7 + - + +
25V THR* 3.2 8.4 + - - -
26V GLU* 3.1 20.1 + - - +
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Residues in contact with LEU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V LEU* 4.2 5.2 - - + -
19V GLU* 2.9 28.4 + - - +
20V LEU 3.5 6.5 - - - +
22V ASP* 1.3 77.2 - - + +
24V LYS* 1.3 63.7 + - - +
26V GLU* 3.0 11.5 + - - +
27V LEU* 2.9 22.7 + - - +
49V LEU* 3.5 27.0 - - + +
52V ALA* 3.5 30.7 - - + -
53V ILE* 3.9 16.6 - - + +
56V ILE* 3.4 32.8 - - + -
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Residues in contact with LYS 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680 U 5.1 4.8 + - - -
1S SER 5.6 1.6 + - - -
3S ASP* 3.5 29.8 + - - +
20V LEU* 2.8 40.9 + - + +
21V ASP* 3.9 15.5 + - - +
22V ASP 3.4 0.2 - - - -
23V LEU* 1.3 73.7 - - - +
25V THR* 1.3 58.4 + - - +
27V LEU* 3.3 7.8 - - + +
28V LEU* 2.9 28.2 + - - +
53V ILE* 4.0 21.3 - - + +
57V LYS* 4.6 21.2 - - - +
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Residues in contact with THR 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S GLN* 4.4 22.3 + - - +
21V ASP 3.0 12.2 + - - -
22V ASP* 3.2 11.3 + - - -
23V LEU 3.1 0.8 - - - -
24V LYS* 1.3 75.8 - - - +
26V GLU* 1.3 65.8 + - - +
27V LEU 3.1 1.3 - - - -
28V LEU* 3.7 5.7 - - + +
29V ASN* 2.8 48.9 + - - +
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Residues in contact with GLU 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V ASP 3.1 11.4 + - - +
23V LEU* 3.0 14.7 + - - +
25V THR* 1.3 76.6 - - - +
27V LEU* 1.3 57.4 + - - +
29V ASN* 3.3 8.1 + - + +
30V ALA* 2.9 29.9 + - + +
45V ARG* 3.3 41.3 + - - +
49V LEU* 3.6 28.1 - - + +
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Residues in contact with LEU 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V LEU 2.9 12.0 + - - +
24V LYS* 3.3 11.7 - - + +
26V GLU* 1.3 77.7 - - - +
28V LEU* 1.3 57.7 + - - +
30V ALA* 3.1 3.9 + - - +
31V ARG* 2.9 76.0 + - - +
46V ILE* 4.0 21.3 - - + +
49V LEU* 3.3 28.2 - - + +
50V ARG* 4.2 8.7 - - + -
53V ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S ILE* 3.8 25.8 - - + +
6S LYS 3.5 26.7 - - - +
7S HIS* 4.7 2.5 - - - +
8S PRO* 5.1 2.3 - - + +
44S GLN* 3.3 35.0 - - + +
45S TYR* 4.2 18.4 - - + +
24V LYS 2.9 18.0 + - - +
25V THR* 3.2 6.7 + - + +
27V LEU* 1.3 75.6 - - - +
29V ASN* 1.3 62.1 + - - +
31V ARG* 3.4 8.5 + - - +
32V ALA* 3.0 28.6 + - + +
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Residues in contact with ASN 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45S TYR* 5.9 0.2 - - - -
81S ILE* 3.0 33.0 - - + +
25V THR* 2.8 45.2 + - - +
26V GLU* 3.8 6.5 - - + +
28V LEU* 1.3 79.9 - - - +
30V ALA* 1.3 57.6 + - - +
32V ALA* 3.6 6.6 - - - +
33V VAL* 3.1 34.2 + - + +
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Residues in contact with ALA 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V GLU* 2.9 18.8 + - + +
27V LEU* 3.1 8.3 + - - +
29V ASN* 1.3 74.8 - - - +
31V ARG* 1.3 60.5 + - - +
33V VAL* 3.1 8.0 + - - +
34V GLN* 2.9 28.7 + - - +
41V GLU* 5.9 0.9 - - - +
46V ILE* 4.6 23.3 - - + +
49V LEU* 4.7 5.4 - - + -
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Residues in contact with ARG 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560 G 5.2 5.8 + - - -
3S ASP* 5.9 0.8 + - - -
6S LYS* 4.4 15.1 + - - +
7S HIS* 4.0 19.6 - - + +
27V LEU* 2.9 57.0 + - + +
28V LEU* 3.9 7.7 - - - +
30V ALA* 1.3 76.0 - - - +
32V ALA* 1.3 56.9 + - - +
34V GLN* 3.6 15.8 - - - +
35V ALA* 3.0 26.3 + - - +
46V ILE* 4.2 17.9 - - + +
50V ARG* 4.1 23.4 - - - +
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Residues in contact with ALA 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8S PRO* 3.5 36.0 - - + +
10S VAL* 5.2 0.3 - - - +
81S ILE* 4.6 20.2 - - + -
28V LEU* 3.0 17.6 + - + +
29V ASN* 3.6 10.1 - - - +
30V ALA 3.1 0.2 - - - -
31V ARG* 1.3 76.0 - - - +
33V VAL* 1.3 64.9 + - + +
34V GLN 3.1 0.2 - - - -
35V ALA* 3.1 4.2 + - - +
36V ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S ILE* 4.8 16.8 - - - -
29V ASN* 3.1 16.7 + - + +
30V ALA* 3.5 9.9 - - - +
32V ALA* 1.3 76.3 - - - +
34V GLN* 1.3 58.5 - - - +
36V ALA* 3.5 7.5 + - - +
38V GLY* 2.8 45.2 + - - +
40V PRO* 3.9 23.1 - - + -
41V GLU* 4.7 8.3 - - + +
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Residues in contact with GLN 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570 C 3.1 47.1 + - - +
580 C 4.3 10.4 + - - -
30V ALA 2.9 16.0 + - - +
31V ARG* 3.6 12.9 - - - +
32V ALA 3.1 0.2 - - - -
33V VAL* 1.3 76.9 - - - +
35V ALA* 1.3 59.1 + - - +
37V GLY* 2.9 20.1 + - - -
38V GLY 4.4 0.9 - - - -
41V GLU* 3.5 24.9 + - - +
46V ILE* 4.0 20.8 - - + +
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Residues in contact with ALA 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S HIS* 3.8 15.5 - - + +
8S PRO* 3.4 26.0 - - + +
10S VAL* 2.9 16.9 - - + +
31V ARG 3.0 18.0 + - - +
32V ALA* 3.1 8.7 + - - +
34V GLN* 1.3 77.0 - - - +
36V ALA* 1.3 56.6 + - - +
37V GLY 3.0 3.6 + - - -
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Residues in contact with ALA 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S VAL* 3.3 24.4 - - + +
81S ILE 6.5 1.1 - - - -
32V ALA 3.0 13.9 + - - +
33V VAL* 3.9 7.9 - - - +
34V GLN 3.2 0.6 - - - -
35V ALA* 1.3 75.1 - - - +
37V GLY* 1.3 56.3 + - - +
38V GLY* 2.9 11.5 + - - +
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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