Contacts of the helix formed by residues 70 - 91 (chain B) 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 GLY 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3467 T 3.5 24.7 + - - +
3477 A 4.4 11.3 + - - -
69B THR* 1.3 75.8 - - - +
71B PRO* 1.3 66.9 - - - +
72B ASN 3.0 0.2 - - - -
73B ARG* 2.9 36.7 + - - +
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Residues in contact with PRO 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3467 T 3.6 22.9 - - + +
3477 A 3.9 34.3 - - + +
38 A 5.4 5.6 - - + +
69B THR 4.4 0.2 - - - +
70B GLY* 1.3 83.4 - - - +
72B ASN* 1.3 67.1 + - - +
73B ARG 3.1 0.2 - - - -
74B ALA* 3.1 5.0 + - + +
75B ILE* 3.0 25.6 + - + +
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 3.5 15.0 - - + -
69B THR* 3.3 17.9 + - - +
70B GLY 3.0 1.0 - - - -
71B PRO* 1.3 77.2 - - - +
73B ARG* 1.3 64.6 + - - +
75B ILE* 3.3 28.3 + - + +
76B TYR* 3.0 25.4 - - + -
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3467 T 3.0 36.0 + - - +
3477 A 6.0 0.2 - - - -
60B SER* 2.7 47.4 + - - +
63B LEU* 3.5 16.3 - - + +
64B THR* 2.9 32.1 + - - +
68B ILE* 2.8 54.9 + - + +
69B THR* 3.9 8.8 - - - +
70B GLY 2.9 15.0 + - - +
72B ASN* 1.3 76.3 - - - +
74B ALA* 1.3 53.7 + - - +
76B TYR* 3.0 5.0 + - - -
77B GLN* 2.8 36.9 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3457 A 4.1 16.5 - - + +
3467 T 3.0 41.6 + - + +
38 A 4.7 5.2 - - + -
48 T 4.4 8.0 - - - +
70B GLY 3.6 0.8 + - - -
71B PRO 3.1 8.6 + - - +
73B ARG* 1.3 76.8 - - - +
75B ILE* 1.3 64.7 + - - +
77B GLN* 3.6 10.3 - - - +
78B GLY* 2.9 22.2 + - - -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48 T 5.8 1.1 - - - -
71B PRO* 3.0 15.5 + - + +
72B ASN* 3.4 33.2 - - + +
73B ARG 3.2 0.6 - - - -
74B ALA* 1.3 77.9 - - - +
76B TYR* 1.3 65.6 + - + +
78B GLY* 3.4 0.9 + - - -
79B PHE* 3.1 20.8 + - - +
107B TYR* 3.5 31.1 - - + -
111B PHE* 4.6 22.7 - - + +
112B ASN 5.9 0.4 - - - +
113B ALA* 4.1 20.0 - - + -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 4.4 2.7 - - - +
63B LEU* 3.6 29.2 - - + -
68B ILE* 4.0 18.4 - - + +
72B ASN* 3.0 27.6 - - + -
73B ARG 3.0 5.2 + - - +
75B ILE* 1.3 80.8 - - + +
77B GLN* 1.3 61.1 + - - +
79B PHE* 3.5 5.8 - - - +
80B GLY* 2.8 26.7 + - - -
112B ASN 5.0 0.2 + - - -
113B ALA* 3.9 9.6 - - + -
114B ASN* 2.9 38.1 + - - +
117B VAL* 3.7 29.8 - - + +
118B LEU* 3.7 30.3 - - + -
121B VAL* 4.2 11.8 - - + +
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3457 A 3.4 34.6 + - + +
3467 T 3.1 21.1 + - - +
55B VAL* 5.4 0.5 - - - +
56B ASN* 3.4 24.3 + - - +
59B VAL* 3.3 21.1 - - - +
60B SER* 3.5 26.3 - - - +
63B LEU* 4.0 2.1 - - + +
73B ARG 2.8 22.1 + - - +
74B ALA* 3.2 9.2 + - - +
76B TYR* 1.3 76.4 - - - +
78B GLY* 1.3 57.4 + - - +
80B GLY* 3.3 0.5 + - - -
81B LEU* 2.9 41.6 + - + +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3457 A 5.4 0.8 + - - -
48 T 5.1 3.8 - - - -
58 A 4.1 24.6 - - - +
74B ALA 2.9 15.6 + - - -
75B ILE 3.8 1.3 - - - -
77B GLN* 1.3 77.5 - - - +
79B PHE* 1.3 63.1 + - - +
81B LEU* 3.4 6.0 + - - +
82B LYS* 3.0 23.9 + - - +
107B TYR* 3.5 13.1 + - - -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE 3.1 13.3 + - - +
76B TYR 3.5 8.3 - - - +
78B GLY* 1.3 76.2 - - - +
80B GLY* 1.3 64.8 + - - +
82B LYS* 3.1 4.7 + - - +
83B VAL* 2.9 32.3 + - + +
100B ILE* 5.1 2.0 - - + -
103B LEU* 3.7 22.9 - - + -
104B LYS* 3.8 24.2 - - + -
107B TYR* 3.5 34.6 + + + -
118B LEU* 3.3 52.7 - - + -
121B VAL* 3.8 17.0 - - + -
122B VAL* 3.7 24.5 - - + -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 4.5 5.6 - - - -
59B VAL* 5.0 2.2 - - - -
76B TYR 2.8 16.5 + - - -
77B GLN* 3.8 1.3 - - - -
79B PHE* 1.3 73.2 - - - +
81B LEU* 1.3 62.0 - - - +
83B VAL* 3.1 2.8 + - - -
84B ALA* 3.0 19.9 + - - +
121B VAL* 3.5 26.9 - - - -
125B ILE* 3.1 17.2 - - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3447 T 5.5 1.6 - - - +
3457 A 5.6 3.6 - - - +
58 A 4.1 19.3 - - + +
68 T 3.4 35.7 - - - +
52B PHE* 3.5 42.8 - - + +
55B VAL* 4.5 6.0 - - + +
56B ASN* 3.4 31.6 - - - +
77B GLN* 2.9 29.0 + - + +
78B GLY* 3.8 4.3 - - - +
80B GLY* 1.3 74.6 - - - +
82B LYS* 1.3 57.0 + - - +
84B ALA* 3.2 4.1 + - - -
85B ARG 2.9 23.6 + - - -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3357 A 6.3 0.2 - - - -
3367 T 3.2 14.1 + - - -
58 A 3.7 26.7 + - - +
68 T 3.3 27.6 + - - +
106A TYR* 2.8 34.0 + - - -
78B GLY 3.0 17.8 + - - +
79B PHE* 3.1 5.4 + - - +
81B LEU* 1.3 74.3 - - - +
83B VAL* 1.3 63.8 + - - +
85B ARG* 3.3 11.6 + - - +
86B ALA* 3.1 22.0 + - - +
99B MET* 5.9 2.8 - - - -
103B LEU* 3.5 35.3 - - + +
106B TYR* 5.0 5.6 - - - -
107B TYR* 4.6 3.6 - - + -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 2.9 41.7 + - + +
80B GLY* 3.3 8.1 - - - +
82B LYS* 1.3 77.3 - - - +
84B ALA* 1.3 62.4 + - - +
86B ALA* 3.3 7.7 + - - +
87B LEU* 3.0 20.9 + - + +
96B LEU* 4.5 2.8 - - + +
100B ILE* 4.3 28.3 - - + -
103B LEU* 3.7 19.3 - - + -
122B VAL* 4.6 8.5 - - + -
125B ILE* 3.9 26.5 - - + -
126B THR* 4.5 5.8 - - + -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LYS 5.7 0.7 - - - +
52B PHE* 3.6 20.6 - - + -
55B VAL* 4.2 19.3 - - + -
80B GLY 3.0 12.6 + - - +
81B LEU* 3.2 8.9 + - - +
83B VAL* 1.3 74.5 - - - +
85B ARG* 1.3 67.4 + - - +
87B LEU* 3.1 11.9 + - + +
88B ASN* 3.0 26.2 + - - +
125B ILE* 4.4 11.7 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3357 A 3.8 35.3 + - - -
3367 T 2.9 33.7 + - - +
68 T 3.0 37.0 + - - +
78 A 3.4 29.9 + - - +
52B PHE* 3.5 11.1 - - - -
81B LEU 2.9 13.9 + - - +
82B LYS* 3.3 20.4 - - - +
84B ALA* 1.3 74.6 - - - +
86B ALA* 1.3 64.5 + - - +
88B ASN* 3.0 6.4 + - - +
89B ARG* 3.0 44.9 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3357 A 5.6 2.5 - - - -
82B LYS 3.1 9.1 + - - +
83B VAL* 3.6 9.4 - - - +
85B ARG* 1.3 77.6 - - - +
87B LEU* 1.3 59.5 + - - +
89B ARG* 4.5 2.9 - - - +
90B ILE* 2.7 46.2 + - + +
96B LEU* 3.8 17.0 - - + -
99B MET* 3.8 28.3 - - + -
100B ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.0 13.2 + - + +
84B ALA* 3.1 12.5 + - + +
86B ALA* 1.3 76.2 - - - +
88B ASN* 1.3 64.4 + - - +
91B GLY* 2.7 30.9 + - - +
92B SER* 3.6 29.4 - - - +
96B LEU* 3.6 24.6 - - + +
125B ILE* 4.5 25.6 - - + +
126B THR* 6.0 2.5 - - + -
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78 A 5.4 1.7 + - - +
48B ASN* 4.9 5.0 + - - +
51B LYS* 3.8 31.5 + - - +
52B PHE* 3.4 34.3 - - + -
84B ALA* 3.0 12.0 + - - +
85B ARG* 3.0 6.9 + - - +
87B LEU* 1.3 85.2 - - - +
89B ARG* 1.3 64.4 + - + +
90B ILE 4.8 0.3 - - - -
91B GLY 4.5 1.0 + - - -
7C SER* 4.6 13.8 - - - +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3337 A 4.6 10.3 + - - -
3347 T 3.6 28.5 + - - +
3357 A 3.3 33.0 + - - +
78 A 4.1 16.9 + - - +
88 T 4.3 16.0 + - - -
85B ARG* 3.0 45.9 + - + +
86B ALA* 4.3 1.8 - - - +
88B ASN* 1.3 81.3 - - + +
90B ILE* 1.3 60.5 + - + +
7C SER* 4.1 32.3 - - - +
60D SER* 4.5 6.6 + - - -
73D ARG* 4.6 1.6 + - - -
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3347 T 5.6 0.7 - - - +
3357 A 4.5 11.2 - - - +
86B ALA* 2.7 28.7 + - + +
88B ASN 4.8 0.7 - - - -
89B ARG* 1.3 78.4 - - - +
91B GLY* 1.3 66.8 + - - +
95B ALA* 3.6 26.5 - - + +
96B LEU* 4.0 4.9 - - + +
99B MET* 3.8 38.4 - - + -
60D SER* 4.9 1.7 + - - -
61D ALA* 5.8 0.7 - - - -
64D THR* 2.6 36.3 + - - +
69D THR* 4.4 10.5 - - + -
70D GLY 5.6 0.2 - - - +
73D ARG* 3.7 19.4 + - - +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 3.6 0.4 + - - -
87B LEU* 2.7 31.5 + - - -
88B ASN 4.5 0.6 - - - -
90B ILE* 1.3 91.3 - - - +
92B SER* 1.3 66.9 + - - +
96B LEU* 3.4 10.0 - - - +
64D THR* 3.6 0.9 - - - +
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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
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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