Contacts of the helix formed by residues 57 - 81 (chain G) in PDB entry 2J28
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 TYR 57 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ARG* 6.3 0.7 - - + -
55G ASP* 2.8 52.9 + - + +
56G GLY* 1.3 75.8 - - - +
58G ALA* 1.3 71.9 + - - +
59G ASP 4.8 1.8 - - - +
60G GLY* 2.7 18.2 + - - +
61G TRP* 2.9 9.9 + - - +
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Residues in contact with ALA 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B U 6.0 5.8 - - - +
1036B G 5.9 2.7 - - - +
56G GLY 4.0 1.4 + - - -
57G TYR* 1.3 72.9 - - - +
59G ASP* 1.3 59.3 + - + +
60G GLY 2.5 13.3 + - - -
61G TRP* 3.1 11.0 + - - +
62G ALA* 3.7 10.7 + - - +
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Residues in contact with ASP 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757B A 3.0 27.3 + - - +
57G TYR* 3.5 3.0 - - + +
58G ALA* 1.3 78.6 - - - +
60G GLY* 1.3 54.8 + - - +
62G ALA* 5.6 2.2 - - - -
63G GLN* 2.7 33.9 - - - +
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Residues in contact with GLY 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ALA* 6.0 6.2 - - - +
51G PHE* 4.4 1.6 - - - -
53G PRO* 3.7 16.7 - - - +
55G ASP 4.3 8.5 - - - -
57G TYR* 2.7 18.0 + - - +
58G ALA 2.5 8.3 + - - -
59G ASP* 1.3 76.7 - - - +
61G TRP* 1.3 62.2 + - - +
62G ALA 3.6 0.4 - - - -
63G GLN* 3.4 16.3 - - - +
64G ALA 3.9 1.9 + - - -
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Residues in contact with TRP 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749B A 6.1 4.7 - - - -
4G ALA* 6.5 0.7 - - + -
53G PRO* 3.2 37.7 - - + -
55G ASP 4.5 4.6 + - - -
56G GLY* 5.1 11.2 - - - -
57G TYR 2.9 13.1 + - - +
58G ALA* 4.0 3.6 - - - +
60G GLY* 1.3 73.8 - - - +
62G ALA* 1.3 61.5 + - - +
63G GLN 3.0 1.3 - - - -
64G ALA* 2.8 34.3 + - + +
65G GLY 3.9 0.9 + - - -
68G ARG* 5.4 12.2 + - - -
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748B A 2.8 31.8 + - + +
2749B A 3.3 42.6 - - - +
2757B A 5.2 3.0 - - - +
58G ALA 3.7 8.7 + - - +
59G ASP* 5.6 1.8 - - - +
61G TRP* 1.3 75.0 - - - +
63G GLN* 1.3 62.3 + - - +
64G ALA 2.8 10.4 + - - -
65G GLY 3.0 5.2 + - - +
66G THR* 3.5 5.9 + - - -
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Residues in contact with GLN 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757B A 3.2 29.3 + - - +
2758B A 3.0 31.5 + - - +
37G ASN* 3.1 36.6 - - + +
51G PHE* 3.7 10.5 - - + -
59G ASP* 2.7 41.8 + - - +
60G GLY* 3.4 15.4 - - - +
61G TRP 3.0 0.4 - - - -
62G ALA* 1.3 79.3 - - - +
64G ALA* 1.3 60.6 + - - +
66G THR* 4.4 3.3 - - - +
67G ALA* 3.3 20.3 + - - +
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Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G PHE* 3.4 31.0 - - + -
53G PRO* 4.0 9.6 - - + -
60G GLY 3.9 1.0 + - - -
61G TRP* 2.8 22.3 + - + +
62G ALA 2.8 0.4 - - - -
63G GLN* 1.3 78.5 - - - +
65G GLY* 1.3 56.8 + - - +
67G ALA* 2.8 3.3 + - - +
68G ARG* 2.6 54.4 + - - +
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Residues in contact with GLY 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748B A 3.4 26.3 + - - +
2749B A 5.8 0.2 - - - -
4G ALA 5.3 0.7 - - - -
5G LYS* 5.1 2.7 - - - +
61G TRP 3.9 1.0 + - - -
62G ALA* 3.0 5.5 + - - +
64G ALA* 1.3 80.6 - - - +
66G THR* 1.3 61.4 + - - +
67G ALA 2.9 1.7 + - - -
68G ARG* 3.3 24.6 + - - +
69G ALA* 3.3 23.0 + - - +
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Residues in contact with THR 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747B G 2.9 28.2 + - - +
2748B A 2.9 17.1 + - - -
2757B A 2.6 39.4 + - + +
2758B A 4.0 24.0 - - + +
62G ALA 3.5 6.9 + - - -
63G GLN* 4.6 4.3 - - - +
64G ALA 3.4 0.8 - - - -
65G GLY* 1.3 72.1 - - - +
67G ALA* 1.3 58.9 + - - +
69G ALA* 4.2 1.1 - - - +
70G LEU* 3.0 33.1 + - + +
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Residues in contact with ALA 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.6 14.4 - - + -
37G ASN* 4.8 4.3 - - - +
51G PHE* 3.2 31.4 - - + -
63G GLN 3.3 11.1 + - - +
64G ALA 2.8 10.3 + - - +
66G THR* 1.3 77.0 - - - +
68G ARG* 1.3 55.4 + - - +
69G ALA 2.7 15.6 + - - -
70G LEU* 3.0 10.2 + - - -
71G LEU* 2.9 23.9 - - - +
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Residues in contact with ARG 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749B A 4.7 4.8 + - - -
4G ALA* 3.1 31.1 + - - +
5G LYS* 2.6 77.4 + - + +
6G ALA* 5.1 0.9 - - - +
8G VAL* 4.1 8.7 - - + +
50G THR* 5.5 4.0 - - - +
51G PHE* 3.5 31.4 - - + +
61G TRP* 5.4 11.7 + - - -
64G ALA* 2.6 27.7 + - - +
65G GLY* 3.4 24.4 - - - +
67G ALA* 1.3 71.7 - - - +
69G ALA* 1.3 56.6 + - - +
71G LEU* 4.3 10.5 - - - +
72G ASN* 3.4 16.6 + - - +
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747B G 3.6 13.7 - - - +
2748B A 3.5 25.1 - - - +
5G LYS* 4.5 12.1 - - + +
65G GLY 3.3 11.7 + - - +
66G THR 4.2 1.8 - - - +
67G ALA 2.7 2.4 + - - -
68G ARG* 1.3 79.0 - - - +
70G LEU* 1.3 66.0 + - + +
71G LEU 3.3 0.4 - - - -
72G ASN* 3.1 6.7 + - - +
73G SER* 2.9 27.9 + - - +
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2746B U 4.0 4.5 - - - +
2747B G 3.5 34.5 - - - +
2758B A 3.6 26.2 - - + +
34G ARG* 3.1 51.4 + - + +
66G THR* 3.0 29.3 + - + +
67G ALA* 3.0 6.7 + - - +
69G ALA* 1.3 77.4 - - - +
71G LEU* 1.3 67.9 + - + +
73G SER* 3.1 10.0 + - - -
74G MET* 3.0 24.5 + - - +
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Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 5.3 7.9 - - + -
23G ILE* 3.6 20.4 - - + -
34G ARG* 5.4 1.8 - - - -
36G LEU* 3.4 29.6 - - + -
42G VAL* 4.1 25.6 - - + -
49G LEU* 5.5 11.4 - - + -
50G THR* 6.0 0.4 - - - +
51G PHE* 5.4 5.8 - - + +
67G ALA* 2.9 24.9 - - + +
68G ARG* 4.3 8.1 - - - +
70G LEU* 1.3 76.6 - - + +
72G ASN* 1.3 56.3 + - - +
74G MET* 2.7 44.5 + - - +
75G VAL* 3.0 11.3 + - + +
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Residues in contact with ASN 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LYS* 3.6 19.2 + - - +
7G PRO 5.2 0.9 - - - -
8G VAL* 3.8 24.2 - - + +
68G ARG 3.4 16.4 + - - +
69G ALA* 3.1 11.8 + - - +
71G LEU* 1.3 78.8 - - - +
73G SER* 1.3 56.7 + - - +
75G VAL* 3.0 11.7 + - - +
76G ILE* 2.8 49.2 + - - +
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Residues in contact with SER 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747B G 4.2 8.4 + - - -
34G ARG* 6.2 0.4 - - - -
69G ALA* 2.9 15.7 + - - +
70G LEU* 3.4 11.0 - - - -
72G ASN* 1.3 73.3 + - - +
74G MET* 1.3 56.2 + - - +
76G ILE* 3.5 13.9 - - - +
77G GLY* 2.7 32.9 + - - -
82G PHE* 4.2 6.2 - - - -
137G LYS* 4.1 33.8 + - - +
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Residues in contact with MET 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ILE* 3.6 21.5 - - - +
25G ILE* 4.2 21.0 - - + +
32G LEU* 3.7 34.7 - - + +
33G THR* 3.6 17.3 - - - +
34G ARG* 3.5 35.4 - - + +
70G LEU 3.0 15.4 + - - +
71G LEU* 2.7 27.5 + - - +
73G SER* 1.3 77.4 - - - +
75G VAL* 1.3 55.1 + - - +
77G GLY* 3.9 0.6 - - - -
78G VAL* 3.0 29.7 + - - +
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 5.6 1.6 - - + -
9G VAL* 4.2 20.9 - - + +
11G PRO* 4.9 4.5 - - + -
14G VAL* 4.1 29.2 - - + -
16G VAL* 4.9 0.2 - - + -
25G ILE* 3.4 20.6 - - + -
49G LEU* 4.7 11.9 - - + -
71G LEU* 3.6 12.3 - - + +
72G ASN* 3.0 16.1 + - - +
74G MET* 1.3 74.9 - - - +
76G ILE* 1.3 65.9 + - + +
77G GLY 3.0 1.6 - - - -
78G VAL* 3.0 19.6 - - + +
79G THR* 3.0 22.2 - - + +
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Residues in contact with ILE 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ASN* 2.8 51.4 + - - +
73G SER* 3.2 11.0 + - - +
75G VAL* 1.3 77.0 - - + +
77G GLY* 1.3 59.5 + - - +
79G THR* 3.8 8.5 - - + -
80G GLU* 3.3 31.9 + - + +
82G PHE* 4.6 16.4 - - + -
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Residues in contact with GLY 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASN* 2.5 27.0 - - - +
32G LEU* 5.9 0.7 - - - -
73G SER 2.7 20.8 + - - -
74G MET* 3.9 1.3 - - - -
76G ILE* 1.3 73.6 - - - +
78G VAL* 1.3 55.4 + - - +
80G GLU* 4.6 0.4 - - - -
81G GLY* 3.0 16.5 + - - -
82G PHE* 3.8 24.3 + - - -
135G ALA* 4.2 8.3 - - - -
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Residues in contact with VAL 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLY 5.9 0.2 - - - -
14G VAL* 5.3 5.6 - - + +
25G ILE* 4.5 13.0 - - + -
26G LYS* 3.4 31.2 - - - +
27G GLY* 3.5 15.7 - - - +
28G LYS* 3.9 5.4 + - - +
29G ASN* 2.9 42.7 + - + +
30G GLY 3.9 11.0 - - - +
32G LEU* 5.3 4.6 - - + +
74G MET 3.0 17.5 + - - +
75G VAL* 3.0 23.6 - - + +
77G GLY* 1.3 75.7 - - - +
79G THR* 1.3 67.2 + - - +
135G ALA* 5.2 1.9 - - - +
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Residues in contact with THR 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ALA 5.7 1.9 + - - -
14G VAL* 5.8 5.2 - - - -
28G LYS* 4.9 17.6 + - - +
75G VAL* 3.0 23.1 - - + +
76G ILE* 3.7 13.7 - - + +
78G VAL* 1.3 85.6 - - - +
80G GLU* 1.3 67.1 + - + +
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Residues in contact with GLU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ILE* 3.3 23.6 + - + +
79G THR* 1.3 86.9 - - + +
81G GLY* 1.3 87.1 + - - +
82G PHE* 3.2 29.7 + - - -
83G THR* 5.1 6.0 + - - +
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Residues in contact with GLY 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASN* 3.1 23.0 + - - -
77G GLY 3.0 9.1 + - - -
80G GLU* 1.3 95.6 - - - +
82G PHE* 1.3 64.6 + - - -
83G THR* 3.7 4.9 + - - +
134G GLY 4.1 1.6 - - - -
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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