Contacts of the helix formed by residues 70 - 91 (chain h) 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 h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1547 T 3.5 25.4 + - - +
1557 A 4.4 2.6 + - - -
111e PHE* 3.5 19.8 - - - -
90f ILE* 5.6 0.6 - - - +
99f MET* 5.3 0.2 - - - +
69h THR* 1.3 76.8 - - - +
71h PRO* 1.3 66.3 - - - +
73h ARG* 2.9 35.8 + - - +
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Residues in contact with PRO 71 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547 T 3.6 22.9 - - + +
1557 A 3.9 33.0 - - - +
71e PRO* 3.6 19.3 - - + +
74e ALA* 4.8 2.9 - - + -
75e ILE* 3.5 37.2 - - + +
107e TYR* 6.5 1.1 - - + -
111e PHE* 4.6 6.5 - - + -
69h THR 4.4 0.4 - - - +
70h GLY* 1.3 82.0 - - - +
72h ASN* 1.3 64.9 + - - +
73h ARG 3.1 0.2 - - - -
74h ALA* 3.1 4.9 + - - +
75h ILE* 3.0 24.6 + - - +
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Residues in contact with ASN 72 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72e ASN* 3.1 25.1 - - - +
75e ILE* 3.5 12.1 - - - +
111e PHE* 3.3 24.7 + - - +
112e ASN* 4.8 8.7 + - - +
68h ILE* 3.5 15.7 - - + -
69h THR* 3.3 14.3 + - - +
70h GLY 3.0 1.0 - - - -
71h PRO* 1.3 75.6 - - - +
73h ARG* 1.3 64.8 + - - +
75h ILE* 3.3 18.4 + - + +
76h TYR* 3.0 25.7 - - + -
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Residues in contact with ARG 73 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547 T 3.0 35.2 + - - +
89f ARG 4.6 0.6 + - - -
90f ILE* 3.7 27.0 + - - +
60h SER* 2.7 47.0 + - - +
63h LEU* 3.5 16.6 - - + +
64h THR* 2.9 31.1 + - - +
68h ILE* 2.8 56.2 + - + +
69h THR* 3.9 8.1 - - - +
70h GLY 2.9 15.4 + - - +
72h ASN* 1.3 76.6 - - - +
74h ALA* 1.3 59.9 + - - +
76h TYR* 3.0 5.4 + - - -
77h GLN* 2.8 30.5 + - - +
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Residues in contact with ALA 74 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537 A 4.1 16.7 - - + +
1547 T 3.0 41.4 + - + +
1958 A 4.7 5.4 - - + -
1968 T 4.4 5.8 - - - +
71e PRO* 4.8 4.5 - - + -
70h GLY 3.6 0.8 + - - -
71h PRO 3.1 7.9 + - - +
73h ARG* 1.3 76.7 - - - +
75h ILE* 1.3 65.4 + - - +
77h GLN* 3.6 10.7 - - - +
78h GLY* 2.9 21.8 + - - -
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Residues in contact with ILE 75 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968 T 6.5 0.2 - - - -
71e PRO* 3.6 26.9 - - + +
72e ASN* 3.5 35.2 - - - +
71h PRO 3.0 14.6 + - - +
72h ASN* 3.4 22.4 - - + +
73h ARG 3.2 0.6 - - - -
74h ALA* 1.3 77.1 - - - +
76h TYR* 1.3 67.7 + - + +
78h GLY* 3.4 0.7 + - - -
79h PHE* 3.1 21.1 + - - +
107h TYR* 3.5 31.6 - - + -
111h PHE* 4.6 11.0 - - + +
112h ASN 5.9 0.4 - - - +
113h ALA* 4.1 19.7 - - + -
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Residues in contact with TYR 76 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59h VAL* 4.4 2.9 - - - +
63h LEU* 3.6 28.3 - - + -
68h ILE* 4.0 18.3 - - + +
72h ASN* 3.0 27.8 - - + -
73h ARG 3.0 5.2 + - - +
75h ILE* 1.3 80.5 - - + +
77h GLN* 1.3 61.1 + - - +
79h PHE* 3.5 6.0 - - - +
80h GLY* 2.8 26.3 + - - -
112h ASN 5.0 0.3 + - - -
113h ALA* 3.9 9.1 - - + -
114h ASN* 2.9 38.5 + - - +
117h VAL* 3.7 31.5 - - + +
118h LEU* 3.7 29.8 - - + -
121h VAL* 4.2 12.1 - - + +
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Residues in contact with GLN 77 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537 A 3.4 34.3 + - + +
1547 T 3.1 21.5 + - - +
55h VAL* 5.4 0.7 - - - +
56h ASN* 3.4 24.3 + - - +
59h VAL* 3.3 21.3 - - - +
60h SER* 3.5 25.9 - - - +
63h LEU* 4.0 2.5 - - + +
73h ARG 2.8 22.6 + - - +
74h ALA* 3.2 9.4 + - - +
76h TYR* 1.3 77.6 - - - +
78h GLY* 1.3 56.6 + - - +
80h GLY* 3.3 0.7 + - - -
81h LEU* 2.9 41.4 + - + +
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Residues in contact with GLY 78 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537 A 5.4 1.1 + - - -
1968 T 5.1 2.9 - - - -
1978 A 4.1 24.8 - - - +
74h ALA 2.9 16.0 + - - -
75h ILE 3.8 1.8 - - - -
77h GLN* 1.3 77.2 - - - +
79h PHE* 1.3 62.2 + - - +
81h LEU* 3.4 5.5 + - - +
82h LYS* 3.0 24.4 + - - +
107h TYR* 3.5 13.5 + - - -
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Residues in contact with PHE 79 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75h ILE 3.1 13.3 + - - +
76h TYR 3.5 7.6 - - - +
78h GLY* 1.3 75.8 - - - +
80h GLY* 1.3 64.6 + - - +
82h LYS* 3.1 5.7 + - - +
83h VAL* 2.9 32.4 + - + +
100h ILE* 5.1 2.2 - - + -
103h LEU* 3.7 23.3 - - + -
104h LYS* 3.8 24.0 - - + -
107h TYR* 3.5 33.2 + + + -
118h LEU* 3.3 54.1 - - + -
121h VAL* 3.8 16.8 - - + -
122h VAL* 3.7 24.5 - - + -
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Residues in contact with GLY 80 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55h VAL* 4.5 5.8 - - - -
59h VAL* 5.0 2.2 - - - -
76h TYR 2.8 16.1 + - - -
77h GLN 3.8 0.9 - - - -
79h PHE* 1.3 73.4 - - - +
81h LEU* 1.3 62.4 + - - +
83h VAL* 3.1 2.8 + - - -
84h ALA* 3.0 19.2 + - - +
121h VAL* 3.5 26.9 - - - -
125h ILE* 3.1 17.7 - - - +
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Residues in contact with LEU 81 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1527 T 5.5 1.8 - - - +
1537 A 5.6 3.4 - - - +
1978 A 4.1 19.1 - - + +
1988 T 3.4 36.7 - - - +
52h PHE* 3.5 43.1 - - + +
55h VAL* 4.5 6.0 - - + +
56h ASN* 3.4 32.3 - - - +
77h GLN* 2.9 28.9 + - + +
78h GLY* 3.8 4.9 - - - +
80h GLY* 1.3 75.0 - - - +
82h LYS* 1.3 57.8 + - - +
84h ALA* 3.2 3.9 + - - -
85h ARG 2.9 23.7 + - - -
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Residues in contact with LYS 82 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 A 4.9 0.4 + - - -
1447 T 3.2 13.5 + - - -
1978 A 3.7 26.4 + - - +
1988 T 3.3 27.8 + - - +
106g TYR* 2.8 33.5 + - - -
78h GLY 3.0 17.9 + - - +
79h PHE* 3.5 5.2 - - - +
81h LEU* 1.3 74.7 - - - +
83h VAL* 1.3 64.6 + - - +
85h ARG* 3.3 11.6 + - - +
86h ALA* 3.1 22.0 + - - +
99h MET* 5.9 2.6 - - - -
103h LEU* 3.5 35.5 - - + +
106h TYR* 5.0 6.3 - - - -
107h TYR* 4.6 3.4 - - + -
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Residues in contact with VAL 83 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79h PHE* 2.9 42.7 + - + +
80h GLY* 3.3 8.3 - - - +
82h LYS* 1.3 77.1 - - - +
84h ALA* 1.3 62.0 + - - +
86h ALA* 3.3 8.2 + - - +
87h LEU* 3.0 20.3 + - + +
96h LEU* 4.5 2.7 - - + +
99h MET* 6.5 0.2 - - - -
100h ILE* 4.3 27.6 - - + -
103h LEU* 3.7 18.6 - - + +
122h VAL* 4.6 8.5 - - + -
125h ILE* 3.9 27.1 - - + -
126h THR* 4.5 5.2 - - + -
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Residues in contact with ALA 84 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51h LYS 5.7 0.7 - - - +
52h PHE* 3.6 20.0 - - + -
55h VAL* 4.2 20.2 - - + -
80h GLY 3.0 11.3 + - - +
81h LEU* 3.2 8.7 + - - +
83h VAL* 1.3 74.1 - - - +
85h ARG* 1.3 65.9 + - - +
87h LEU* 3.1 12.2 + - + +
88h ASN* 3.0 26.3 + - - +
125h ILE* 4.4 11.2 - - + +
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Residues in contact with ARG 85 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 A 3.8 35.7 + - - -
1447 T 2.9 33.7 + - - +
1988 T 3.0 35.7 + - - +
1998 A 3.4 29.7 + - - +
52h PHE* 3.5 11.3 - - - -
81h LEU 2.9 14.4 + - - +
82h LYS* 3.3 20.3 - - - +
84h ALA* 1.3 75.4 - - - +
86h ALA* 1.3 64.6 + - - +
88h ASN* 3.0 6.6 + - - +
89h ARG* 3.0 44.3 + - - +
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Residues in contact with ALA 86 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 A 5.6 2.2 - - - -
82h LYS 3.1 9.3 + - - +
83h VAL* 3.6 9.9 - - - +
85h ARG* 1.3 77.4 - - - +
87h LEU* 1.3 59.1 + - - +
89h ARG* 4.5 3.1 - - - +
90h ILE* 2.7 47.4 + - + +
96h LEU* 3.8 16.8 - - + -
99h MET* 3.8 27.4 - - + -
100h ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83h VAL* 3.0 13.2 + - + +
84h ALA* 3.1 13.2 + - + +
86h ALA* 1.3 76.4 - - - +
88h ASN* 1.3 64.7 + - - +
91h GLY* 2.7 30.5 + - - +
92h SER* 3.6 28.7 - - - +
96h LEU* 3.6 24.5 - - + +
125h ILE* 4.5 25.4 - - + +
126h THR* 6.0 2.7 - - + -
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Residues in contact with ASN 88 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998 A 5.4 1.5 + - - +
48h ASN* 4.9 5.2 + - - +
51h LYS* 3.8 31.8 + - - +
52h PHE* 3.4 33.7 - - - -
84h ALA 3.0 11.7 + - - +
85h ARG* 3.5 7.4 - - - +
87h LEU* 1.3 85.9 - - - +
89h ARG* 1.3 65.8 + - + +
90h ILE 4.8 0.3 - - - -
91h GLY* 4.5 1.4 + - - -
7i SER* 4.6 13.7 - - - +
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Residues in contact with ARG 89 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1417 A 4.6 10.1 + - - -
1427 T 3.6 29.6 + - - +
1437 A 3.3 31.8 + - - +
1998 A 4.1 16.7 + - - +
2008 T 4.3 16.2 + - - -
85h ARG* 3.0 46.3 + - + +
86h ALA* 4.3 2.2 - - - +
88h ASN* 1.3 80.2 - - + +
90h ILE* 1.3 61.6 + - + +
7i SER* 4.1 33.4 - - - +
60j SER* 4.5 5.9 + - - -
73j ARG* 4.6 1.9 + - - -
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Residues in contact with ILE 90 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427 T 5.6 0.4 - - - +
1437 A 4.5 11.0 - - - +
86h ALA* 2.7 28.2 + - + +
88h ASN 4.8 0.7 - - - -
89h ARG* 1.3 78.4 - - - +
91h GLY* 1.3 68.1 + - - +
95h ALA* 3.6 26.2 - - + +
96h LEU* 4.0 4.9 - - + +
99h MET* 3.8 39.3 - - + -
60j SER* 4.9 1.9 + - - -
61j ALA* 5.8 0.5 - - - -
64j THR* 2.6 37.5 + - + +
69j THR* 4.4 10.8 - - + -
73j ARG* 3.7 19.1 + - - +
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Residues in contact with GLY 91 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86h ALA 3.6 0.2 + - - -
87h LEU* 2.7 31.9 + - - -
88h ASN 4.5 0.9 - - - -
90h ILE* 1.3 90.4 - - - +
92h SER* 1.3 66.2 + - - +
96h LEU* 3.4 9.8 - - - +
64j THR* 3.6 1.4 - - - +
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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
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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