Contacts of the helix formed by residues 26 - 49 (chain V) in PDB entry 3J9X
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 ASN 26 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V ASN 4.5 2.2 - - - +
23V ALA 3.1 16.2 + - - +
24V PHE 3.0 1.2 + - - -
25V SER* 1.3 78.6 + - - +
27V PRO* 1.4 68.2 - - - +
28V THR* 2.9 24.0 + - - -
29V VAL* 2.7 36.9 + - + -
30V ALA* 2.8 11.9 + - - -
32W THR* 4.0 19.2 + - + +
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Residues in contact with PRO 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U PRO* 3.5 33.0 - - + +
28U THR* 5.5 1.1 - - + -
31U SER* 3.5 19.5 - - - +
25V SER 3.2 7.1 - - - +
26V ASN* 1.4 91.9 - - - +
28V THR* 1.3 61.4 + - - +
30V ALA* 4.0 2.2 - - + +
31V SER* 2.8 29.8 + - - -
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Residues in contact with THR 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U PRO* 5.7 0.4 - - - -
26V ASN* 2.8 13.9 + - - -
27V PRO* 1.3 75.8 - - - +
29V VAL* 1.3 60.4 + - - +
31V SER* 3.1 4.7 + - - -
32V THR* 2.5 47.6 + - - +
26W ASN* 4.8 4.5 - - - +
28W THR* 3.1 33.3 - - + +
29W VAL* 4.6 0.7 - - + -
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Residues in contact with VAL 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V ALA 3.3 28.9 - - - +
24V PHE* 3.8 9.9 - - - -
26V ASN* 2.7 14.8 + - + +
28V THR* 1.3 70.5 - - - +
30V ALA* 1.3 64.8 + - - +
32V THR* 3.4 0.3 + - - -
33V ILE* 3.1 44.1 + - + +
28W THR* 4.3 1.3 - - - +
29W VAL* 3.9 29.8 - - + +
32W THR* 3.8 29.8 - - + +
33W ILE* 4.9 6.5 - - + -
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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
----------------------------------------------------------
30U ALA* 3.6 29.4 - - + -
34U LEU* 4.6 2.9 - - + -
24V PHE* 3.3 35.6 + - + +
25V SER 4.9 0.7 - - - -
26V ASN 2.8 12.6 + - - +
27V PRO* 4.0 4.0 - - + +
29V VAL* 1.3 78.5 - - - +
31V SER* 1.3 57.4 + - - +
33V ILE* 4.0 0.3 - - - +
34V LEU* 2.9 37.5 + - + +
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Residues in contact with SER 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U SER 3.5 24.5 - - - -
27U PRO* 3.5 24.4 - - - +
27V PRO 2.8 19.9 + - - -
28V THR* 3.1 8.1 + - - +
30V ALA* 1.3 77.2 - - - +
32V THR* 1.3 58.4 + - - +
34V LEU* 4.6 0.4 - - - -
35V SER* 2.6 42.8 + - - -
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Residues in contact with THR 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28V THR* 2.5 34.9 + - - +
29V VAL 3.7 3.1 - - - -
31V SER* 1.3 78.5 + - - +
33V ILE* 1.3 63.5 + - - +
35V SER* 3.2 3.7 + - - -
36V ASN* 3.1 35.1 + - - +
23W ALA* 3.6 34.3 - - + +
26W ASN* 4.0 15.6 + - + +
29W VAL* 3.7 15.3 - - + +
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Residues in contact with ILE 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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2107 T 5.7 2.5 - - - +
1308 T 3.7 38.1 - - - +
1318 A 4.7 6.3 - - - +
24V PHE* 4.2 14.8 - - + -
29V VAL* 3.1 33.6 + - + +
30V ALA 4.0 1.8 - - - +
32V THR* 1.3 78.8 - - - +
34V LEU* 1.3 58.8 + - - +
36V ASN* 3.1 3.3 + - - +
37V VAL* 3.0 29.5 + - + +
20W LYS* 4.0 23.6 - - + -
23W ALA* 3.8 21.3 - - + -
29W VAL* 4.9 7.6 - - + -
33W ILE* 5.3 5.4 - - + -
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Residues in contact with LEU 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298 A 4.9 7.0 - - + -
1308 T 4.6 14.1 - - - +
21U PHE* 4.1 21.6 - - + -
24U PHE* 3.4 41.5 - - + +
25U SER* 3.9 25.8 - - - -
30U ALA* 4.5 0.2 - - + -
24V PHE* 4.0 23.1 - - + -
30V ALA* 2.9 27.0 + - + +
31V SER 4.3 0.7 - - - +
33V ILE* 1.3 77.4 - - - +
35V SER* 1.3 52.7 + - - +
37V VAL* 3.4 8.3 + - + +
38V SER* 2.6 37.3 + - - -
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Residues in contact with SER 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U SER* 4.6 8.7 - - - -
31V SER* 2.6 27.6 + - - -
32V THR* 3.2 6.2 + - - -
34V LEU* 1.3 78.8 - - - +
36V ASN* 1.3 69.7 + - - +
38V SER* 3.4 20.4 + - - -
39V PRO* 4.1 3.5 - - - +
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Residues in contact with ASN 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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32V THR* 3.1 22.9 + - - +
33V ILE 3.1 6.0 + - - +
35V SER* 1.3 85.2 + - - +
37V VAL* 1.3 58.8 + - - +
38V SER 3.3 0.9 + - - -
39V PRO* 3.6 12.3 - - - +
40V VAL* 4.3 1.9 - - - +
19W ALA* 3.4 30.2 + - + +
22W ASN* 4.0 9.7 - - - +
23W ALA* 3.4 31.5 - - + +
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Residues in contact with VAL 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298 A 4.1 21.1 - - - +
1308 T 3.9 6.5 - - - +
21U PHE* 4.6 9.0 - - + -
33V ILE* 3.0 20.7 + - + +
34V LEU* 3.5 17.0 - - + +
36V ASN* 1.3 76.1 - - - +
38V SER* 1.3 65.4 + - - +
39V PRO* 3.5 1.3 - - - -
40V VAL* 3.3 8.2 + - + -
41V ALA* 2.8 23.5 + - + +
16W LYS* 4.9 7.6 - - + -
19W ALA* 3.7 22.2 - - + +
20W LYS* 3.7 27.1 - - + -
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Residues in contact with SER 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U PHE* 3.6 21.8 - - - -
22U ASN* 5.5 2.5 + - - -
25U SER* 4.6 5.0 + - - -
34V LEU 2.6 21.3 + - - -
35V SER* 3.4 15.9 - - - -
37V VAL* 1.3 81.5 - - - +
39V PRO* 1.4 68.7 - - - +
41V ALA* 2.9 15.1 + - - +
42V GLN* 3.0 25.4 + - - +
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Residues in contact with PRO 39 (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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35V SER 4.1 4.5 - - - +
36V ASN 3.6 13.0 - - - +
37V VAL 3.5 1.3 - - - -
38V SER* 1.4 97.4 - - - +
40V VAL* 1.3 68.3 + - + +
42V GLN* 3.4 20.9 + - - +
43V GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (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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1298 A 4.8 1.8 - - - +
36V ASN 4.3 13.9 - - - +
37V VAL* 3.5 11.7 - - + +
38V SER 3.0 0.6 + - - -
39V PRO* 1.3 77.2 - - + +
41V ALA* 1.3 67.2 + - - +
43V GLN* 3.1 8.9 + - - +
44V ASN* 3.1 33.0 + - - +
12W GLN* 5.2 1.3 - - - +
15W ALA* 4.0 28.9 - - + +
16W LYS* 3.9 32.8 - - + +
19W ALA* 4.3 5.8 - - + -
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Residues in contact with ALA 41 (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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1288 T 4.2 2.5 - - - +
1298 A 3.7 35.4 - - - -
17U TRP* 4.1 17.2 - - + -
21U PHE* 4.3 11.9 - - + -
37V VAL 2.8 13.4 + - - +
38V SER 3.3 8.7 - - - +
40V VAL* 1.3 77.0 - - - +
42V GLN* 1.3 57.7 + - - +
44V ASN* 3.1 2.4 + - - +
45V PHE* 2.8 31.7 + - - +
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Residues in contact with GLN 42 (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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14U TYR* 3.7 11.9 + - - +
17U TRP* 4.3 10.5 - - + -
18U GLN* 3.2 41.1 - - - +
21U PHE* 5.8 0.7 - - + -
22U ASN* 4.7 2.0 + - - -
38V SER* 3.0 20.8 + - - +
39V PRO* 3.5 28.9 - - - +
40V VAL 3.1 0.4 - - - -
41V ALA* 1.3 76.2 - - - +
43V GLN* 1.3 57.2 + - - +
45V PHE* 3.7 0.9 - - - +
46V GLN* 2.9 43.3 + - - +
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Residues in contact with GLN 43 (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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39V PRO 3.1 9.1 + - - +
40V VAL* 3.1 12.4 + - - +
42V GLN* 1.3 79.7 - - - +
44V ASN* 1.3 60.5 + - - +
46V GLN* 3.4 14.6 + - - +
47V THR* 2.6 61.2 + - - +
12W GLN* 5.3 9.0 - - + +
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Residues in contact with ASN 44 (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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1288 T 3.5 30.0 - - - +
1298 A 3.0 21.6 + - - -
40V VAL* 3.1 23.8 + - - +
41V ALA 3.6 3.1 - - - +
43V GLN* 1.3 75.4 - - - +
45V PHE* 1.3 65.0 + - - +
47V THR* 3.4 4.5 + - - -
48V ASN* 3.1 22.3 + - - +
8W ARG* 3.6 23.8 - - - +
12W GLN* 2.9 34.5 + - - +
16W LYS* 5.0 4.6 - - - +
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Residues in contact with PHE 45 (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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2237 A 5.2 5.2 - - - -
1278 A 4.6 10.5 - + - -
1288 T 3.6 22.6 - - - -
10U TYR* 4.1 2.0 - + - -
13U ARG* 4.5 6.5 - - + -
14U TYR* 3.4 43.7 - + + -
17U TRP* 3.5 61.7 - + + -
41V ALA 2.8 16.6 + - - +
42V GLN 3.7 2.9 - - - +
44V ASN* 1.3 76.8 - - - +
46V GLN* 1.3 63.9 + - - +
49V VAL* 3.0 65.4 + - + +
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Residues in contact with GLN 46 (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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10U TYR* 3.3 21.0 + - - +
14U TYR* 2.9 39.0 + - + -
42V GLN* 2.9 30.6 + - - +
43V GLN* 3.7 15.1 + - - +
45V PHE* 1.3 77.7 - - - +
47V THR* 1.3 62.7 + - - +
50V PRO* 3.1 21.7 - - - +
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Residues in contact with THR 47 (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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43V GLN* 2.6 42.6 + - - +
44V ASN* 3.7 6.5 - - - -
45V PHE 3.2 0.4 - - - -
46V GLN* 1.3 79.6 - - - +
48V ASN* 1.3 74.6 + - - +
50V PRO* 3.7 6.4 - - - +
51V LYS* 3.4 23.9 - - - +
12W GLN* 4.6 13.7 + - - +
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Residues in contact with ASN 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278 A 3.8 20.6 - - - +
1288 T 3.1 20.4 + - - -
44V ASN 3.1 10.6 + - - +
47V THR* 1.3 87.0 - - - +
49V VAL* 1.3 62.9 + - - +
50V PRO* 3.4 1.8 - - - -
51V LYS* 3.0 34.4 + - + +
52V PHE* 3.1 27.5 - - + -
88V ASN* 4.9 4.7 + - - -
7W SER 3.9 14.2 + - - +
8W ARG* 3.4 15.2 - - - +
12W GLN* 5.2 2.2 - - - +
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Residues in contact with VAL 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278 A 3.9 28.0 - - + +
10U TYR* 3.8 10.1 - - + -
13U ARG* 3.7 26.9 + - - +
45V PHE* 3.0 63.8 + - + +
48V ASN* 1.3 70.7 - - - +
50V PRO* 1.4 60.3 - - + +
51V LYS 3.0 4.3 - - - -
52V PHE* 2.8 30.0 + - - +
53V THR 3.2 6.4 + - - -
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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