Contacts of the helix formed by residues 39 - 62 (chain J) in PDB entry 5OA3
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 39 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6422 U 3.2 39.0 + - + +
6432 A 2.3 33.5 + - - -
32J ILE* 3.9 12.8 - - - +
37J LEU* 4.5 0.5 - - - +
38J ARG* 1.3 89.5 + - + +
40J LYS* 1.3 63.3 + - - +
41J ARG* 3.1 22.0 - - - +
42J GLU* 3.0 26.4 + - - +
43J VAL 4.0 1.6 + - - -
34e ARG* 4.3 7.6 - - - +
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Residues in contact with LYS 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6412 A 3.2 20.6 - - - +
6422 U 3.2 10.0 + - - +
25J LEU* 3.0 50.5 + - - +
28J GLU* 3.4 36.7 + - + +
29J LEU* 4.3 8.5 - - - +
32J ILE* 3.7 17.6 - - + +
39J ASN* 1.3 73.7 - - - +
41J ARG* 1.3 62.4 + - - +
42J GLU 3.2 0.2 - - - -
43J VAL* 3.3 7.2 + - + +
44J TRP* 3.0 47.7 + - + +
34e ARG* 3.2 26.0 - - - +
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Residues in contact with ARG 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5212 A 5.6 5.2 + - - +
5222 A 3.8 13.1 - - - +
6412 A 5.2 0.2 + - - -
6422 U 2.9 36.8 + - - +
6432 A 4.0 10.9 + - - -
6442 G 3.4 30.9 + - - -
6452 C 4.9 6.9 + - - -
13J TYR* 3.4 51.4 + - + +
38J ARG* 5.9 0.4 - - - +
39J ASN* 3.0 17.1 - - - +
40J LYS* 1.3 78.5 - - - +
42J GLU* 1.3 55.0 + - - +
44J TRP* 3.2 16.6 + - + +
45J ARG* 2.8 34.3 + - + +
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Residues in contact with GLU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5222 A 3.8 9.9 + - - -
37J LEU* 3.5 22.3 - - + +
38J ARG* 2.9 47.4 + - - +
39J ASN* 3.0 17.4 + - - +
41J ARG* 1.3 78.9 - - - +
43J VAL* 1.3 62.9 + - - +
45J ARG* 3.0 38.6 + - - +
46J VAL* 3.0 29.8 + - + +
109J ARG* 4.9 1.6 - - - +
127J ARG* 3.4 20.1 + - - -
146J SER* 4.4 8.9 + - - +
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Residues in contact with VAL 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J GLU* 4.1 32.1 - - + +
31J LEU* 4.1 23.3 - - + -
32J ILE* 3.9 22.9 - - + -
37J LEU* 3.6 23.1 - - + -
39J ASN 4.5 1.6 - - - +
40J LYS* 3.3 11.9 + - - +
42J GLU* 1.3 75.0 - - - +
44J TRP* 1.3 62.8 + - + +
45J ARG 3.3 0.2 + - - -
46J VAL* 3.4 6.3 + - - +
47J LYS* 2.9 36.9 + - + +
102J ILE* 4.8 5.2 - - + +
106J LEU* 5.7 2.7 - - + -
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Residues in contact with TRP 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6412 A 4.4 27.4 - - - -
6422 U 5.0 0.7 - - - -
13J TYR* 4.0 17.6 - + + +
14J VAL 3.6 15.9 + - - +
15J THR* 3.5 34.3 - - + -
16J PRO* 3.5 29.5 - - + +
24J ARG* 4.2 11.4 - - - -
28J GLU* 3.3 32.9 + - - -
40J LYS* 3.0 27.3 + - + +
41J ARG* 3.2 21.3 + - + +
43J VAL* 1.3 79.4 - - + +
45J ARG* 1.3 56.8 + - - +
47J LYS* 3.6 10.5 - - + +
48J PHE* 2.9 29.5 + - - +
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Residues in contact with ARG 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5212 A 2.5 47.2 + - - -
5222 A 3.2 28.3 + - - -
12J THR* 3.4 37.7 - - + +
13J TYR* 3.8 5.3 - - + +
41J ARG* 2.8 19.6 + - + +
42J GLU* 3.0 30.9 + - - +
44J TRP* 1.3 74.4 - - - +
46J VAL* 1.3 70.6 + - + +
48J PHE* 3.1 4.3 + - - +
49J THR* 2.9 31.7 + - + +
146J SER* 3.6 28.3 + - - -
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Residues in contact with VAL 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 5.8 1.3 - - + -
42J GLU* 3.0 17.9 + - + +
43J VAL* 3.7 7.9 - - - +
45J ARG* 1.3 79.5 - - + +
47J LYS* 1.3 63.1 + - - +
49J THR* 2.4 30.6 + - - +
50J LEU* 3.0 7.6 + - - +
102J ILE* 3.7 17.0 - - + +
105J PHE* 3.9 22.4 - - + -
106J LEU* 3.5 35.0 - - + -
109J ARG* 5.5 6.7 - - + +
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Residues in contact with LYS 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 U 4.0 26.9 + - - -
16J PRO* 5.7 3.0 - - - +
24J ARG* 4.7 9.9 - - - +
27J GLN* 4.9 11.1 + - - +
28J GLU* 3.4 25.0 + - + +
31J LEU* 6.3 0.4 - - + -
43J VAL* 2.9 26.3 + - + +
44J TRP* 3.6 11.7 - - + +
46J VAL* 1.3 77.7 - - - +
48J PHE* 1.3 56.8 + - - +
50J LEU* 3.5 8.8 + - + +
51J ALA* 2.9 28.5 + - - +
102J ILE* 3.4 28.0 - - + +
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Residues in contact with PHE 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ARG* 6.0 1.6 - - - -
11J LYS 3.8 21.8 - - - -
12J THR* 3.1 23.3 - - + +
13J TYR* 4.1 6.3 - - - -
14J VAL* 3.5 31.2 - - + +
44J TRP 2.9 19.3 + - - +
45J ARG 3.4 3.1 - - - +
47J LYS* 1.3 74.1 - - - +
49J THR* 1.3 68.2 + - + +
51J ALA* 3.1 10.7 + - + +
52J LYS* 2.9 64.5 + - + +
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Residues in contact with THR 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J THR* 5.2 4.5 - - + +
45J ARG* 2.9 30.6 + - + +
46J VAL* 2.4 31.7 + - - +
48J PHE* 1.3 85.1 - - + +
50J LEU* 1.3 65.4 + - - +
52J LYS* 3.3 19.1 + - - +
53J ILE* 3.4 18.7 + - - +
105J PHE* 4.5 13.6 - - - -
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Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J VAL 3.0 7.1 + - - +
47J LYS* 3.7 14.1 - - + +
49J THR* 1.3 81.7 + - - +
51J ALA* 1.3 62.1 + - + +
53J ILE* 3.2 17.1 + - + +
54J ARG* 2.9 48.5 + - + +
100J LEU* 3.7 26.0 - - + +
101J LYS* 3.7 27.4 - - - +
102J ILE* 4.4 11.2 - - + +
105J PHE* 3.7 24.2 - - + -
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Residues in contact with ALA 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 U 3.7 31.8 + - - +
47J LYS 2.9 18.0 + - - +
48J PHE* 3.1 14.6 + - + +
50J LEU* 1.3 80.0 - - + +
52J LYS* 1.3 66.6 + - - +
54J ARG* 3.3 7.2 + - - +
55J LYS* 2.9 23.9 + - - +
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Residues in contact with LYS 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8162 A 5.7 2.2 - - - +
8172 G 5.6 4.8 + - - +
10J ARG* 4.4 26.6 - - - +
12J THR* 6.2 0.6 - - - +
48J PHE* 2.9 60.8 + - + +
49J THR* 3.6 16.5 - - - +
51J ALA* 1.3 73.6 - - - +
53J ILE* 1.3 66.0 + - + +
55J LYS* 3.1 13.6 + - - +
56J ALA* 2.9 23.5 + - - +
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Residues in contact with ILE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J THR* 3.4 16.6 - - - +
50J LEU* 3.2 8.3 - - + +
52J LYS* 1.3 76.3 - - + +
54J ARG* 1.3 59.2 + - + +
56J ALA* 3.1 9.3 + - - +
57J ALA* 2.9 26.9 + - - +
77J LEU* 4.0 18.0 - - + +
80J ARG* 5.8 4.3 - - - +
81J LEU* 3.7 33.0 - - + -
97J ILE* 3.8 14.8 - - + -
100J LEU* 5.9 1.1 - - + -
105J PHE* 3.5 35.7 - - + -
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Residues in contact with ARG 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 U 4.0 16.3 + - - +
199C PRO* 4.7 2.4 - - - +
200C ARG 2.6 29.5 + - - -
201C GLY* 3.3 22.8 + - - -
202C THR* 3.3 23.8 - - - +
50J LEU* 2.9 44.1 + - + +
51J ALA* 3.3 8.7 + - - +
53J ILE* 1.3 78.4 - - + +
55J LYS* 1.3 57.4 + - - +
57J ALA* 3.8 1.3 - - - +
58J ARG* 2.9 39.1 + - - +
97J ILE* 4.9 6.3 - - + +
98J LEU* 3.9 40.6 + - + +
100J LEU* 4.6 9.0 + - + -
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Residues in contact with LYS 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 U 5.8 2.4 + - - +
4172 C 6.0 1.6 - - - +
8162 A 5.9 4.8 - - - -
51J ALA 2.9 13.8 + - - +
52J LYS* 3.1 14.6 + - - +
54J ARG* 1.3 74.3 - - - +
56J ALA* 1.3 66.3 + - - +
58J ARG* 3.3 32.1 + - - +
59J GLU* 3.0 50.4 + - - +
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Residues in contact with ALA 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8172 G 4.4 17.3 - - - +
52J LYS 2.9 12.5 + - - +
53J ILE* 3.4 11.9 - - - +
55J LYS* 1.3 79.1 - - - +
57J ALA* 1.3 57.3 + - - +
59J GLU* 3.2 6.7 + - - +
60J LEU* 2.9 35.1 + - + +
73J GLU* 5.5 6.7 - - - +
77J LEU* 4.7 11.2 - - + -
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Residues in contact with ALA 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J ILE 2.9 15.8 + - - +
54J ARG 3.8 4.0 - - - +
56J ALA* 1.3 72.7 - - - +
58J ARG* 1.3 66.9 + - - +
60J LEU* 3.0 9.6 + - - +
61J LEU* 3.0 29.5 + - + +
77J LEU* 4.5 7.4 - - + +
94J LEU* 4.2 18.4 - - + -
97J ILE* 4.2 14.1 - - + -
98J LEU* 3.8 19.7 - - + -
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Residues in contact with ARG 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 U 4.8 14.1 + - - -
22 A 4.9 7.1 + - - -
4182 A 5.9 0.8 + - - -
170C TRP* 4.8 9.9 - - + -
199C PRO* 3.6 30.9 - - + +
202C THR* 4.3 19.8 - - - +
223C TYR* 4.3 12.7 + - - -
54J ARG* 2.9 33.6 + - - +
55J LYS* 3.6 31.0 - - - +
57J ALA* 1.3 76.8 - - - +
59J GLU* 1.3 68.2 + - + +
60J LEU 3.5 0.5 + - - -
61J LEU* 3.5 10.8 + - - +
62J THR* 3.4 21.0 + - + +
98J LEU* 4.6 11.6 - - + +
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Residues in contact with GLU 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4192 G 6.1 0.9 - - - -
55J LYS* 3.0 48.3 + - - +
56J ALA* 3.5 5.2 - - - +
58J ARG* 1.3 85.4 + - + +
60J LEU* 1.3 64.6 + - - +
62J THR* 3.4 19.9 + - + +
63J LEU* 4.2 9.5 - - - +
69J ARG* 4.9 5.7 + - - +
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Residues in contact with LEU 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J ALA* 2.9 19.6 + - + +
57J ALA* 3.0 11.9 + - - +
59J GLU* 1.3 81.2 - - - +
61J LEU* 1.3 60.7 + - - +
62J THR 3.1 2.5 - - - -
63J LEU* 3.0 32.5 + - + +
69J ARG* 4.3 15.5 - - + +
70J ARG* 3.7 21.4 - - + +
73J GLU* 4.0 32.5 - - + +
74J GLY* 3.8 34.3 - - - +
77J LEU* 5.1 7.4 - - + -
94J LEU* 4.6 18.4 - - + -
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Residues in contact with LEU 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C TRP* 4.6 22.9 - - + -
172C ASN* 5.1 8.7 - - - +
57J ALA 3.0 17.0 + - - +
58J ARG* 3.5 6.4 + - - +
60J LEU* 1.3 76.0 - - - +
62J THR* 1.3 61.9 + - - +
63J LEU 3.2 7.5 - - - +
70J ARG* 3.3 28.1 + - - +
94J LEU* 3.6 27.6 - - + -
95J ASP* 3.8 28.9 - - + +
98J LEU* 4.3 23.8 - - + -
97W ARG* 5.1 4.7 + - - -
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Residues in contact with THR 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C TRP* 5.0 10.3 - - + -
58J ARG* 3.4 19.1 - - + +
59J GLU* 3.4 21.1 + - + +
61J LEU* 1.3 78.4 - - - +
63J LEU* 1.3 65.9 + - - +
64J ASP 4.0 0.5 + - - -
87W GLU* 3.8 28.8 + - - +
97W ARG* 4.3 25.0 + - - +
117W ARG* 5.3 6.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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