Contacts of the helix formed by residues 12 - 38 (chain V) in PDB entry 1OCR
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 LEU 12 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O LEU* 3.5 25.9 - - + +
40R ASP* 3.3 5.0 + - - +
41R LEU* 5.0 3.1 - - - +
42R VAL* 4.0 12.6 - - + +
74R LYS 4.4 9.0 - - - +
75R ALA 4.8 0.7 - - - +
78R HIS* 3.4 32.7 - - + +
81R ILE* 3.7 22.0 - - + -
8V GLN* 3.5 24.0 - - + +
9V MET 3.8 21.1 - - - +
11V GLY* 1.3 77.3 - - - +
13V LEU* 1.3 61.8 + - - +
15V ARG* 3.6 23.6 + - - +
16V ARG* 3.1 17.8 + - - +
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Residues in contact with LEU 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328N HIS* 3.8 28.7 - - + +
329N GLY* 3.4 29.6 - - - +
48O THR* 4.0 19.7 - - + -
50O LEU* 3.6 33.3 - - + +
51O THR 4.5 2.0 - - - +
52O HIS* 3.6 22.0 - - + -
40R ASP* 2.9 19.2 + - - +
12V LEU* 1.3 76.2 - - - +
14V ALA* 1.3 66.0 + - - +
16V ARG* 2.9 11.2 + - - +
17V LEU* 2.9 21.3 + - - +
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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
----------------------------------------------------------
328N HIS* 5.4 3.1 - - - -
40R ASP* 3.1 13.0 + - - +
11V GLY* 4.0 7.9 - - - +
13V LEU* 1.3 79.2 - - - +
15V ARG* 1.3 65.5 + - - +
17V LEU* 3.0 10.6 + - + +
18V ARG* 2.9 48.8 + - - +
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Residues in contact with ARG 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R HIS* 4.6 19.1 + - + -
8V GLN* 3.5 37.7 - - - +
10V ARG 5.9 0.2 - - - -
11V GLY 2.9 20.0 + - - +
12V LEU* 3.7 20.0 - - - +
14V ALA* 1.3 78.9 - - - +
16V ARG* 1.3 61.8 + - - +
18V ARG* 3.6 15.8 + - - +
19V PHE* 3.4 18.9 + - - +
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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
----------------------------------------------------------
328N HIS* 6.4 0.4 - - - -
44O LEU* 2.9 40.8 + - + +
45O MET* 5.0 2.6 - - - +
47O THR* 2.7 39.6 + - - -
48O THR* 3.5 35.8 + - - +
50O LEU* 4.7 7.0 - - + -
78R HIS* 6.3 0.9 - - + -
12V LEU 3.1 13.4 + - - +
13V LEU* 2.9 14.5 + - - +
15V ARG* 1.3 75.9 - - - +
17V LEU* 1.3 68.6 + - - +
19V PHE* 3.4 4.3 + - - +
20V HIS* 3.2 45.4 + - + +
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Residues in contact with LEU 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328N HIS* 3.8 28.3 - - + +
44O LEU* 4.3 13.5 - - + -
45O MET* 3.8 30.1 - - + -
13V LEU 2.9 11.8 + - - +
14V ALA* 3.5 10.5 - - - +
16V ARG* 1.3 80.3 - - - +
18V ARG* 1.3 64.6 + - - +
19V PHE 3.0 0.5 + - - -
20V HIS 3.2 0.5 + - - -
21V ILE* 2.9 39.4 + - + +
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Residues in contact with ARG 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V ALA* 2.9 43.4 + - - +
15V ARG* 3.7 12.6 - - - +
17V LEU* 1.3 78.1 - - - +
19V PHE* 1.3 62.0 + - - +
21V ILE* 3.8 17.1 - - - +
22V VAL* 4.1 8.7 - - - +
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Residues in contact with PHE 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V ARG 3.4 8.8 + - - +
16V ARG* 3.4 7.7 + - - +
17V LEU 3.0 1.0 + - - -
18V ARG* 1.3 78.8 - - - +
20V HIS* 1.3 93.9 + + - +
22V VAL* 2.9 24.7 + - + +
23V GLY* 3.5 8.6 + - - -
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Residues in contact with HIS 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O TYR* 3.7 16.8 + + - +
44O LEU* 3.4 41.7 - - + +
16V ARG* 3.2 33.4 + - + +
17V LEU 3.2 1.6 + - - -
19V PHE* 1.3 104.9 - + - +
21V ILE* 1.3 52.7 + - - +
23V GLY* 2.9 4.5 + - - +
24V ALA* 2.7 35.3 + - - +
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Residues in contact with ILE 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O ILE* 3.4 33.2 - - + -
44O LEU* 4.5 3.3 - - + +
17V LEU* 2.9 34.7 + - + +
18V ARG* 3.8 15.9 - - - +
19V PHE 3.1 0.4 + - - -
20V HIS* 1.3 75.7 - - - +
22V VAL* 1.3 70.5 + - + +
24V ALA* 3.4 2.1 + - + +
25V PHE* 3.2 44.7 + - + -
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Residues in contact with VAL 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 ARG 4.1 9.6 - - - +
19V PHE* 2.9 16.4 + - + +
20V HIS 2.9 0.8 - - - -
21V ILE* 1.3 81.1 - - + +
23V GLY* 1.3 67.7 + - - +
24V ALA 3.0 1.3 - - - -
25V PHE* 3.0 7.9 + - - +
26V MET* 2.9 41.1 + - + +
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Residues in contact with GLY 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O TYR* 3.5 12.6 - - - -
19V PHE* 3.5 9.2 + - - -
20V HIS* 2.9 9.4 + - - -
22V VAL* 1.3 80.3 - - - +
24V ALA* 1.3 61.4 + - - +
26V MET* 3.6 9.8 - - - +
27V VAL* 3.1 31.1 + - - +
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Residues in contact with ALA 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 3.8 9.1 - - + +
40O TYR* 3.3 39.5 - - + -
41O ILE* 4.0 20.2 - - + -
20V HIS 2.7 16.0 + - - +
21V ILE* 3.5 8.5 - - + +
22V VAL 3.0 0.2 - - - -
23V GLY* 1.3 70.9 - - - +
25V PHE* 1.3 59.6 + - + +
27V VAL* 3.5 2.4 + - - +
28V SER* 3.0 32.2 + - - -
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Residues in contact with PHE 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU* 5.8 3.6 - - + -
37O LEU* 4.2 31.9 - - + -
64O ILE* 6.4 1.8 - - + -
68O LEU* 4.7 22.7 - - + -
21V ILE* 3.2 35.5 + - + +
22V VAL* 3.0 9.6 + - - +
24V ALA* 1.3 77.1 - - - +
26V MET* 1.3 77.6 + - + +
28V SER* 3.2 6.2 + - - -
29V LEU* 2.9 40.4 + - + +
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Residues in contact with MET 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V VAL* 2.9 35.9 + - + +
23V GLY* 3.6 11.7 - - - +
25V PHE* 1.3 86.3 - - + +
27V VAL* 1.3 63.1 + - + +
29V LEU* 3.6 14.7 + - + +
30V GLY* 3.0 19.2 + - - -
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Residues in contact with VAL 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O SER* 5.4 4.3 - - - +
40O TYR* 3.7 28.9 - - + -
23V GLY 3.1 18.6 + - - +
24V ALA 3.9 3.6 - - - +
26V MET* 1.3 74.6 - - + +
28V SER* 1.3 66.9 + - - +
30V GLY* 3.0 10.9 + - - -
31V PHE* 3.2 38.0 + - + -
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Residues in contact with SER 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU* 3.4 29.2 - - - +
36O SER* 3.4 14.8 + - - -
37O LEU* 3.0 39.1 + - - +
40O TYR* 5.4 0.2 - - - +
24V ALA 3.0 16.6 + - - -
25V PHE* 3.6 5.4 - - - -
27V VAL* 1.3 79.1 - - - +
29V LEU* 1.3 62.4 + - - +
30V GLY 3.3 0.2 + - - -
31V PHE* 3.5 3.8 + - - +
32V ALA* 3.2 20.6 + - - +
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Residues in contact with LEU 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU* 4.3 23.6 - - + -
25V PHE* 2.9 32.9 + - + +
26V MET* 4.2 15.3 - - + +
28V SER* 1.3 73.8 - - - +
30V GLY* 1.3 58.6 + - - +
32V ALA* 3.8 6.5 - - + -
33V THR* 2.9 44.9 + - + +
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Residues in contact with GLY 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 MET 3.0 11.5 + - - -
27V VAL* 3.0 9.8 + - - -
29V LEU* 1.3 73.3 - - - +
31V PHE* 1.3 64.1 + - - +
33V THR* 3.0 8.9 + - - -
34V PHE* 2.8 26.4 + - - +
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Residues in contact with PHE 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O PHE* 4.9 18.8 - + + +
36O SER* 4.4 22.9 - - - +
27V VAL* 3.2 41.4 + - + -
28V SER 3.9 6.1 - - - +
30V GLY* 1.3 73.7 - - - +
32V ALA* 1.3 57.9 + - - +
34V PHE* 3.5 13.8 - + - +
35V TYR* 2.9 30.3 + - - +
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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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29O MET* 3.5 44.4 - - + +
32O PHE* 5.2 0.9 - - - -
33O LEU* 4.0 19.4 - - + +
28V SER 3.2 14.9 + - - +
29V LEU* 3.8 8.5 - - + +
30V GLY 3.2 1.0 - - - -
31V PHE* 1.3 81.3 - - - +
33V THR* 1.3 63.1 + - + +
35V TYR* 3.2 2.8 + - - +
36V LYS* 3.0 17.5 + - - +
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Residues in contact with THR 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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29O MET* 5.4 0.7 - - - -
29V LEU* 2.9 32.5 + - + +
30V GLY* 3.0 12.0 + - - -
32V ALA* 1.3 73.2 - - + +
34V PHE* 1.3 64.6 + - - +
36V LYS* 3.2 11.7 + - + +
37V PHE* 3.0 42.4 + - + -
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Residues in contact with PHE 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V GLY 2.8 19.4 + - - +
31V PHE* 3.5 13.5 - + - +
33V THR* 1.3 77.7 + - - +
35V TYR* 1.3 72.6 + + + +
37V PHE* 5.3 2.5 - - - -
38V ALA* 2.9 47.8 + - + +
39V VAL* 5.8 2.9 - - + -
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Residues in contact with TYR 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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24O HIS* 5.0 2.1 + - - -
25O ASP* 2.8 56.0 + - + -
28O LEU* 3.4 31.6 - - + +
29O MET* 4.2 11.0 - - + -
32O PHE* 3.5 26.2 - + + -
31V PHE 2.9 13.4 + - - +
32V ALA* 3.2 9.4 + - - +
34V PHE* 1.3 83.8 - + + +
36V LYS* 1.3 68.3 + - - +
39V VAL* 2.9 57.7 + - + +
40V ALA* 3.1 3.9 + - + -
43V ARG* 4.2 1.0 + - - -
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Residues in contact with LYS 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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29O MET* 4.0 24.2 - - + +
32V ALA 3.0 13.5 + - - +
33V THR* 3.2 14.1 - - + +
34V PHE 3.1 0.2 - - - -
35V TYR* 1.3 77.6 - - - +
37V PHE* 1.3 76.8 + - + +
40V ALA* 2.8 23.9 + - + +
41V GLU* 2.7 56.5 + - + -
44V LYS* 5.4 4.2 - - - +
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Residues in contact with PHE 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V THR* 3.0 36.0 + - + +
34V PHE* 4.5 1.6 - - - +
36V LYS* 1.3 96.0 - - + +
38V ALA* 1.3 62.3 + - - +
39V VAL 3.3 0.5 + - - -
41V GLU* 3.6 26.4 - - + +
42V LYS* 3.7 16.5 + - - +
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Residues in contact with ALA 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34V PHE* 2.9 50.1 + - + +
37V PHE* 1.3 74.6 - - - +
39V VAL* 1.3 66.1 + - + +
42V LYS* 3.8 19.0 + - - +
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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) + - + + + + + -
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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