Contacts of the helix formed by residues 26 - 49 (chain j) 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 j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22j ASN 3.6 2.7 + - - +
23j ALA 3.1 15.4 + - - +
24j PHE 3.0 1.4 + - - -
25j SER* 1.3 78.2 + - - +
27j PRO* 1.4 67.1 - - - +
28j THR* 2.9 23.5 + - - -
29j VAL* 2.7 37.1 + - + -
30j ALA* 2.8 11.7 + - - -
32k THR* 4.0 19.1 + - + +
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Residues in contact with PRO 27 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27i PRO* 3.5 32.6 - - + +
28i THR* 5.5 1.3 - - + -
31i SER* 3.5 18.8 - - - +
25j SER 3.2 7.1 - - - +
26j ASN* 1.4 91.2 - - - +
28j THR* 1.3 60.4 + - - +
30j ALA* 4.0 2.4 - - + +
31j SER* 2.8 30.0 + - - -
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Residues in contact with THR 28 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27i PRO* 5.7 0.2 - - - -
26j ASN* 2.8 13.8 + - - -
27j PRO* 1.3 75.2 - - - +
29j VAL* 1.3 60.2 + - + +
31j SER* 3.1 5.1 + - - +
32j THR* 2.5 47.4 + - - +
26k ASN* 4.8 4.3 - - - +
28k THR* 3.1 32.9 - - + +
29k VAL* 4.6 0.4 - - + -
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Residues in contact with VAL 29 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23j ALA 3.3 30.3 - - - +
24j PHE* 3.8 10.3 - - - -
26j ASN* 2.7 14.8 + - + +
28j THR* 1.3 71.1 - - - +
30j ALA* 1.3 65.3 + - - +
32j THR* 3.7 0.3 - - - -
33j ILE* 3.1 43.7 + - + +
28k THR 4.3 1.3 - - - +
29k VAL* 3.9 29.6 - - + +
32k THR* 3.8 30.1 - - + +
33k ILE* 4.9 6.7 - - + -
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Residues in contact with ALA 30 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30i ALA* 3.6 28.9 - - + -
34i LEU* 4.6 2.7 - - + -
24j PHE* 3.3 35.6 + - + +
25j SER 4.9 0.7 - - - -
26j ASN 2.8 12.8 + - - +
27j PRO* 4.0 4.5 - - + +
29j VAL* 1.3 77.3 - - - +
31j SER* 1.3 57.1 + - - +
33j ILE* 4.0 0.7 - - - +
34j LEU* 2.9 37.5 + - + +
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Residues in contact with SER 31 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25i SER 3.5 24.0 - - - -
27i PRO* 3.5 24.9 - - - +
27j PRO 2.8 21.0 + - - -
28j THR* 3.1 8.1 + - - +
30j ALA* 1.3 75.7 - - - +
32j THR* 1.3 57.2 + - - +
34j LEU* 4.6 0.2 - - - -
35j SER* 2.6 42.4 + - - -
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Residues in contact with THR 32 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28j THR* 2.5 35.0 + - - +
29j VAL 3.7 3.4 - - - -
31j SER* 1.3 77.8 + - - +
33j ILE* 1.3 64.1 + - - +
35j SER* 3.2 3.6 + - - -
36j ASN* 3.1 35.3 + - - +
22k ASN 5.2 0.2 - - - +
23k ALA* 3.6 34.1 - - + +
26k ASN* 4.0 14.4 + - + +
29k VAL* 3.7 15.7 - - + +
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Residues in contact with ILE 33 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267 T 5.7 2.2 - - - +
2148 T 3.7 38.6 - - - +
2158 A 4.7 6.3 - - - +
24j PHE* 4.2 15.7 - - + -
29j VAL* 3.1 33.9 + - + +
30j ALA 4.0 1.3 - - - +
32j THR* 1.3 78.1 - - - +
34j LEU* 1.3 60.3 + - - +
36j ASN* 3.1 2.9 + - - +
37j VAL* 3.0 29.7 + - + +
20k LYS* 4.0 22.9 - - + -
23k ALA* 3.8 21.8 - - + -
29k VAL* 4.9 7.4 - - + -
33k ILE* 5.3 5.2 - - + -
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Residues in contact with LEU 34 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2138 A 4.9 7.4 - - + +
2148 T 4.6 14.1 - - - +
21i PHE* 4.1 21.2 - - + -
24i PHE* 3.4 41.3 - - + +
25i SER* 3.9 25.8 - - - -
30i ALA* 4.5 0.2 - - + -
24j PHE* 4.0 23.3 - - + -
30j ALA* 2.9 27.0 + - + +
31j SER 4.3 0.4 - - - +
33j ILE* 1.3 77.8 - - - +
35j SER* 1.3 52.1 + - - +
37j VAL* 3.4 8.3 + - + +
38j SER* 2.6 37.3 + - - -
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Residues in contact with SER 35 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25i SER* 4.6 8.4 - - - -
31j SER* 2.6 27.0 + - - -
32j THR* 3.2 6.8 + - - -
34j LEU* 1.3 78.6 - - - +
36j ASN* 1.3 69.0 + - - +
38j SER* 3.4 20.5 + - - -
39j PRO* 4.1 3.6 - - - +
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Residues in contact with ASN 36 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32j THR* 3.1 23.3 + - - +
33j ILE 3.1 5.6 + - - +
35j SER* 1.3 85.8 + - - +
37j VAL* 1.3 59.8 + - - +
38j SER 3.3 1.0 + - - -
39j PRO* 3.6 12.1 - - - +
40j VAL* 4.3 1.6 - - - +
19k ALA* 3.4 30.2 + - + +
22k ASN* 4.0 10.6 - - - +
23k ALA* 3.4 31.3 - - + +
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Residues in contact with VAL 37 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2138 A 4.1 20.6 - - - +
2148 T 3.9 5.8 - - - +
21i PHE* 4.6 9.0 - - + -
33j ILE* 3.0 20.9 + - + +
34j LEU* 3.5 17.5 - - + +
36j ASN* 1.3 76.0 - - - +
38j SER* 1.3 66.2 + - - +
39j PRO* 3.5 1.6 - - - -
40j VAL* 3.9 7.9 - - + -
41j ALA* 2.8 24.1 + - + +
16k LYS* 4.9 8.3 - - + -
19k ALA* 3.7 22.7 - - + -
20k LYS* 3.7 26.5 - - + -
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Residues in contact with SER 38 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21i PHE* 3.6 21.6 - - - -
22i ASN* 5.5 2.5 + - - -
25i SER* 4.6 5.0 + - - -
34j LEU 2.6 21.5 + - - -
35j SER* 3.4 16.1 - - - -
37j VAL* 1.3 80.7 - - - +
39j PRO* 1.4 72.1 - - - +
41j ALA* 2.9 11.1 + - - +
42j GLN* 3.0 25.5 + - - +
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Residues in contact with PRO 39 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35j SER 4.1 3.6 - - - +
36j ASN 3.6 12.8 - - - +
37j VAL 3.5 1.6 - - - -
38j SER* 1.4 98.0 - - - +
40j VAL* 1.3 67.5 + - + +
42j GLN* 3.4 19.4 + - - +
43j GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2138 A 4.8 1.8 - - - +
36j ASN 4.3 5.4 - - - +
37j VAL* 3.5 11.4 - - + +
38j SER 3.0 0.6 - - - -
39j PRO* 1.3 78.5 - - + +
41j ALA* 1.3 68.2 + - - +
43j GLN* 3.1 9.7 + - - +
44j ASN* 3.1 32.2 + - - +
12k GLN* 5.2 1.3 - - - +
15k ALA* 4.0 29.6 - - + +
16k LYS* 3.9 33.2 - - + +
19k ALA* 4.3 14.4 - - + -
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Residues in contact with ALA 41 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2128 T 4.2 3.4 - - - +
2138 A 3.7 34.7 - - - -
17i TRP* 4.1 17.0 - - + -
21i PHE* 4.3 12.6 - - + -
37j VAL 2.8 13.4 + - - +
38j SER 3.3 8.7 - - - +
40j VAL* 1.3 76.1 - - - +
42j GLN* 1.3 57.9 + - - +
44j ASN* 3.1 2.1 + - - +
45j PHE* 2.8 31.4 + - - +
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Residues in contact with GLN 42 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14i TYR* 3.7 12.0 + - - +
17i TRP* 4.3 10.5 - - + -
18i GLN* 3.2 39.8 - - - +
21i PHE* 5.8 0.4 - - + -
22i ASN* 4.7 2.2 + - - -
38j SER* 3.0 20.1 + - - +
39j PRO* 3.5 28.4 - - - +
40j VAL 3.1 0.2 - - - -
41j ALA* 1.3 76.8 - - - +
43j GLN* 1.3 57.7 + - - +
45j PHE* 3.7 0.9 - - - +
46j GLN* 2.9 42.7 + - - +
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Residues in contact with GLN 43 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F SER* 5.2 5.7 + - - -
12F GLN* 6.2 2.2 - - - +
43G GLN* 3.1 41.2 - - - +
39j PRO 3.1 9.6 + - - +
40j VAL* 3.1 11.8 + - - +
42j GLN* 1.3 79.9 - - - +
44j ASN* 1.3 59.8 + - - +
46j GLN* 3.4 14.8 + - - +
47j THR* 2.6 62.2 + - - +
12k GLN* 5.3 8.3 - - + +
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Residues in contact with ASN 44 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1287 T 5.5 0.2 + - - -
2128 T 3.5 29.6 - - - +
2138 A 3.0 21.0 + - - -
40j VAL* 3.1 22.9 + - - +
41j ALA 3.1 3.1 + - - +
43j GLN* 1.3 76.1 - - - +
45j PHE* 1.3 65.5 + - - +
47j THR* 3.7 4.4 - - - -
48j ASN* 3.1 23.0 + - - +
8k ARG* 3.6 24.5 - - - +
12k GLN* 2.9 33.7 + - - +
16k LYS* 5.0 4.9 - - - +
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Residues in contact with PHE 45 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1397 A 5.2 4.9 - - - -
2118 A 4.6 10.1 - + - -
2128 T 3.6 23.0 - - - -
10i TYR* 4.1 2.2 - + - -
13i ARG* 4.5 6.7 - - + -
14i TYR* 3.4 42.6 - + + -
17i TRP* 3.5 60.6 - + + -
41j ALA 2.8 16.2 + - - +
42j GLN 3.7 3.1 - - - +
44j ASN* 1.3 77.6 - - - +
46j GLN* 1.3 65.0 + - - +
49j VAL* 3.0 65.0 + - + +
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Residues in contact with GLN 46 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F SER* 4.3 26.9 + - - +
10i TYR* 3.3 20.7 + - - +
14i TYR* 2.9 39.1 + - + -
42j GLN* 2.9 33.1 + - - +
43j GLN* 3.7 15.3 + - - +
45j PHE* 1.3 77.4 - - - +
47j THR* 1.3 62.2 - - - +
50j PRO* 3.1 21.8 - - - +
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Residues in contact with THR 47 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 5.8 4.5 - - - -
11F SER* 5.0 6.1 + - - -
43j GLN* 2.6 42.1 + - - +
44j ASN* 3.7 6.5 - - - -
45j PHE 3.2 0.2 - - - -
46j GLN* 1.3 80.4 - - - +
48j ASN* 1.3 73.4 + - - +
50j PRO* 3.7 6.4 - - - +
51j LYS* 3.4 23.2 - - - +
12k GLN* 4.6 13.9 + - - +
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Residues in contact with ASN 48 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2118 A 3.8 19.5 - - - +
2128 T 3.1 20.2 + - - -
44j ASN 3.1 11.5 + - - +
47j THR* 1.3 87.2 - - - +
49j VAL* 1.3 62.6 + - - +
50j PRO* 3.4 1.1 - - - -
51j LYS* 3.0 34.4 + - + +
52j PHE* 3.1 27.2 - - + -
88j ASN* 4.9 5.0 + - - -
7k SER 3.9 13.4 + - - +
8k ARG* 3.4 16.0 - - - +
12k GLN* 5.2 2.0 - - - +
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Residues in contact with VAL 49 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2118 A 3.9 28.5 - - + +
10i TYR* 3.8 9.4 - - + -
13i ARG* 3.7 27.3 + - - +
45j PHE* 3.0 63.8 + - + +
48j ASN* 1.3 70.4 - - - +
50j PRO* 1.4 61.3 - - + +
51j LYS 3.0 4.7 - - - -
52j PHE* 2.8 31.2 + - - +
53j 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