Contacts of the helix formed by residues 70 - 91 (chain d) 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 d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1787 T 3.5 25.5 + - - +
1797 A 4.4 2.8 + - - -
111a PHE* 3.5 19.6 - - - -
90b ILE* 5.6 0.6 - - - +
99b MET* 5.3 0.2 - - - +
69d THR* 1.3 76.1 - - - +
71d PRO* 1.3 65.9 - - - +
73d ARG* 2.9 35.4 + - - +
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Residues in contact with PRO 71 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1787 T 3.6 23.8 - - + +
1797 A 3.9 33.0 - - - +
71a PRO* 3.6 19.1 - - + +
74a ALA* 4.8 2.5 - - + -
75a ILE* 3.5 37.2 - - + +
107a TYR* 6.5 0.9 - - + -
111a PHE* 4.6 7.2 - - + -
69d THR 4.4 0.4 - - - +
70d GLY* 1.3 81.8 - - - +
72d ASN* 1.3 66.1 + - - +
73d ARG 3.1 0.2 - - - -
74d ALA* 3.1 4.7 + - - +
75d ILE* 3.0 24.6 + - - +
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Residues in contact with ASN 72 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72a ASN* 3.1 24.8 - - - +
75a ILE* 3.5 11.4 - - - +
111a PHE* 3.3 25.5 + - - +
112a ASN* 4.8 8.5 + - - +
68d ILE* 3.5 15.5 - - + -
69d THR* 3.3 14.6 + - - +
70d GLY 3.0 0.6 - - - -
71d PRO* 1.3 75.6 - - - +
73d ARG* 1.3 65.1 + - - +
75d ILE* 3.3 18.0 + - + +
76d TYR* 3.0 26.5 - - + -
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Residues in contact with ARG 73 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1787 T 3.0 36.0 + - - +
89b ARG 4.6 0.6 + - - -
90b ILE* 3.7 27.8 + - - +
60d SER* 2.7 46.8 + - - +
63d LEU* 3.5 15.7 - - + +
64d THR* 2.9 31.1 + - - +
68d ILE* 2.8 57.2 + - + +
69d THR* 3.8 8.1 - - - +
70d GLY 2.9 16.0 + - - +
72d ASN* 1.3 77.0 - - - +
74d ALA* 1.3 58.2 + - - +
76d TYR* 3.0 5.0 + - - -
77d GLN* 2.8 30.3 + - - +
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Residues in contact with ALA 74 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777 A 4.1 17.1 - - + +
1787 T 3.0 40.8 + - + +
1718 A 4.7 5.2 - - + -
1728 T 4.4 6.1 - - - +
71a PRO* 4.8 3.8 - - + -
70d GLY 3.6 1.0 + - - -
71d PRO 3.1 8.4 + - - +
73d ARG* 1.3 77.2 - - - +
75d ILE* 1.3 64.6 + - - +
77d GLN* 3.6 10.1 - - - +
78d GLY* 2.9 20.8 + - - -
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Residues in contact with ILE 75 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71a PRO* 3.6 26.4 - - + +
72a ASN* 3.5 35.9 - - - +
71d PRO 3.0 14.4 + - - +
72d ASN* 3.4 22.2 - - - +
73d ARG 3.2 0.2 - - - -
74d ALA* 1.3 77.3 - - - +
76d TYR* 1.3 66.8 + - + +
78d GLY* 3.4 0.5 + - - -
79d PHE* 3.1 21.3 + - - +
107d TYR* 3.5 31.2 - - + -
111d PHE* 4.6 11.4 - - + +
112d ASN 5.9 0.7 - - - +
113d ALA* 4.1 19.3 - - + -
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Residues in contact with TYR 76 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59d VAL* 4.4 2.9 - - - +
63d LEU* 3.6 28.7 - - + -
68d ILE* 4.0 18.4 - - + +
72d ASN* 3.0 28.0 - - + -
73d ARG 3.0 5.0 + - - +
75d ILE* 1.3 81.5 - - + +
77d GLN* 1.3 60.2 + - - +
79d PHE* 3.3 5.9 + - - +
80d GLY* 2.8 27.2 + - - -
112d ASN 5.0 0.2 + - - -
113d ALA* 3.9 8.8 - - + -
114d ASN* 2.9 38.5 + - - +
117d VAL* 3.7 31.5 - - + +
118d LEU* 3.7 30.3 - - + -
121d VAL* 4.2 11.9 - - + +
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Residues in contact with GLN 77 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1777 A 3.4 34.1 + - + +
1787 T 3.1 21.5 + - - +
55d VAL* 5.4 0.7 - - - +
56d ASN* 3.4 23.9 + - - +
59d VAL* 3.3 21.0 - - - +
60d SER* 3.5 26.3 - - - +
63d LEU* 4.0 2.3 - - + +
73d ARG 2.8 21.9 + - - +
74d ALA* 3.2 9.8 + - - +
76d TYR* 1.3 78.5 - - - +
78d GLY* 1.3 57.4 + - - +
80d GLY* 3.3 1.1 + - - +
81d LEU* 2.9 41.2 + - + +
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Residues in contact with GLY 78 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1777 A 5.4 1.0 + - - -
1728 T 5.1 2.9 - - - -
1738 A 4.1 24.6 - - - +
74d ALA 2.9 16.0 + - - -
75d ILE 3.8 2.0 - - - -
77d GLN* 1.3 77.7 - - - +
79d PHE* 1.3 61.0 + - - +
81d LEU* 3.4 5.3 + - - +
82d LYS* 3.0 25.1 + - - +
107d TYR* 3.5 14.4 + - - -
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Residues in contact with PHE 79 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75d ILE 3.1 14.1 + - - +
76d TYR 3.5 7.9 - - - +
77d GLN 3.3 0.2 - - - -
78d GLY* 1.3 75.3 - - - +
80d GLY* 1.3 65.2 + - - +
82d LYS* 3.1 5.8 + - - +
83d VAL* 2.9 32.9 + - + +
100d ILE* 5.1 1.8 - - + -
103d LEU* 3.7 23.8 - - + -
104d LYS* 3.8 23.6 - - + -
107d TYR* 3.5 33.3 + + + -
118d LEU* 3.3 52.5 - - + -
121d VAL* 3.8 16.8 - - + -
122d VAL* 3.7 24.2 - - + -
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Residues in contact with GLY 80 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55d VAL* 4.5 5.4 - - - -
59d VAL* 5.0 2.0 - - - -
76d TYR 2.8 16.2 + - - -
77d GLN* 3.8 0.9 - - - -
79d PHE* 1.3 75.3 - - - +
81d LEU* 1.3 63.6 + - - +
83d VAL* 3.1 2.6 + - - -
84d ALA* 3.0 19.6 + - - +
121d VAL* 3.5 26.2 - - - -
125d ILE* 3.1 18.3 - - - +
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Residues in contact with LEU 81 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1767 T 5.5 2.0 - - - +
1777 A 5.6 3.1 - - - +
1738 A 4.1 18.6 - - + +
1748 T 3.4 37.8 - - - +
52d PHE* 3.5 43.2 - - + +
55d VAL* 4.5 6.5 - - + -
56d ASN* 3.4 31.6 - - - +
77d GLN* 2.9 29.3 + - + +
78d GLY* 3.8 4.9 - - - +
80d GLY* 1.3 76.2 - - - +
82d LYS* 1.3 58.4 + - - +
84d ALA* 3.2 3.3 + - - -
85d ARG 2.9 23.2 + - - -
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Residues in contact with LYS 82 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1687 T 3.2 14.3 + - - -
1738 A 3.7 25.7 + - - +
1748 T 3.3 26.3 + - - +
106c TYR* 2.8 33.5 + - - -
78d GLY 3.0 18.1 + - - +
79d PHE* 3.5 4.9 - - - +
81d LEU* 1.3 73.6 - - - +
83d VAL* 1.3 66.0 + - - +
85d ARG* 3.3 10.8 + - - +
86d ALA* 3.1 22.2 + - - +
99d MET* 5.9 3.1 - - - -
103d LEU* 3.5 35.6 - - + +
106d TYR* 5.0 6.1 - - + -
107d TYR* 4.6 3.8 - - + -
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Residues in contact with VAL 83 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79d PHE* 2.9 43.2 + - + +
80d GLY* 3.3 8.3 - - - +
82d LYS* 1.3 77.0 - - - +
84d ALA* 1.3 62.1 + - - +
86d ALA* 3.3 7.7 + - - +
87d LEU* 3.0 20.1 + - + +
96d LEU* 4.5 2.9 - - + +
100d ILE* 4.3 27.4 - - + -
103d LEU* 3.7 19.7 - - + +
122d VAL* 4.6 8.7 - - + -
125d ILE* 3.9 26.9 - - + -
126d THR* 4.5 5.6 - - + -
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Residues in contact with ALA 84 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51d LYS 5.7 0.2 - - - +
52d PHE* 3.6 20.2 - - + -
55d VAL* 4.2 20.0 - - + -
80d GLY 3.0 11.4 + - - +
81d LEU* 3.5 8.7 - - - +
83d VAL* 1.3 74.1 - - - +
85d ARG* 1.3 66.7 + - - +
87d LEU* 3.1 12.2 + - + +
88d ASN* 3.0 25.3 + - - +
125d ILE* 4.4 10.3 - - + -
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Residues in contact with ARG 85 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677 A 3.8 35.1 + - - -
1687 T 2.9 33.1 + - - +
1748 T 3.0 35.9 + - - +
1758 A 3.4 29.9 + - - +
52d PHE* 3.5 11.3 - - - -
81d LEU 2.9 14.6 + - - +
82d LYS* 3.3 19.7 - - - +
83d VAL 3.2 0.2 - - - -
84d ALA* 1.3 75.2 - - - +
86d ALA* 1.3 63.5 + - - +
88d ASN* 3.0 6.1 + - - +
89d ARG* 3.0 45.4 + - - +
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Residues in contact with ALA 86 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677 A 5.6 2.5 - - - -
82d LYS 3.1 9.3 + - - +
83d VAL* 3.6 9.9 - - - +
85d ARG* 1.3 77.8 - - - +
87d LEU* 1.3 58.7 + - - +
89d ARG* 4.5 3.4 - - - +
90d ILE* 2.7 46.8 + - + +
96d LEU* 3.8 15.5 - - + -
99d MET* 3.8 28.9 - - + -
100d ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83d VAL* 3.0 12.9 + - + +
84d ALA* 3.2 12.6 - - + +
86d ALA* 1.3 77.1 - - - +
88d ASN* 1.3 64.5 + - - +
91d GLY* 2.7 31.4 + - - +
92d SER* 3.6 29.6 - - - +
96d LEU* 3.6 23.5 - - + +
125d ILE* 4.5 25.4 - - + +
126d THR* 6.0 2.9 - - + -
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Residues in contact with ASN 88 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1758 A 5.4 1.3 + - - +
48d ASN* 4.9 5.4 + - - +
51d LYS* 3.8 31.0 + - - +
52d PHE* 3.4 34.4 - - - -
84d ALA* 3.0 12.7 + - - +
85d ARG* 3.0 7.8 + - - +
87d LEU* 1.3 86.0 - - - +
89d ARG* 1.3 64.6 + - + +
90d ILE 4.8 0.3 - - - -
91d GLY 4.5 1.2 + - - -
7e SER* 4.6 12.9 - - - +
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Residues in contact with ARG 89 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1657 A 4.6 10.3 + - - -
1667 T 3.6 28.7 + - - +
1677 A 3.3 32.2 + - - +
1758 A 4.1 17.3 + - - +
1768 T 4.3 15.4 + - - -
85d ARG* 3.0 45.8 + - - +
86d ALA* 4.3 2.2 - - - +
88d ASN* 1.3 80.7 - - + +
90d ILE* 1.3 61.8 + - + +
7e SER* 4.1 33.4 - - - +
60f SER* 4.5 6.4 + - - -
73f ARG* 4.6 1.7 + - - -
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Residues in contact with ILE 90 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667 T 5.6 0.2 - - - +
1677 A 4.5 10.8 - - - +
86d ALA* 2.7 29.3 + - + +
88d ASN 4.8 1.1 - - - -
89d ARG* 1.3 78.0 - - - +
91d GLY* 1.3 68.2 + - - +
95d ALA* 3.6 25.8 - - + +
96d LEU* 4.0 4.9 - - + +
99d MET* 3.8 38.4 - - + -
60f SER* 4.9 1.7 + - - -
61f ALA* 5.8 0.7 - - - -
64f THR* 2.6 36.8 + - + +
69f THR* 4.4 11.0 - - + -
70f GLY 5.6 0.2 - - - +
73f ARG* 3.7 18.4 + - - +
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Residues in contact with GLY 91 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86d ALA 3.6 0.8 + - - -
87d LEU* 2.7 30.8 + - - -
88d ASN 4.5 1.1 - - - -
90d ILE* 1.3 89.2 - - - +
92d SER* 1.3 67.9 + - - +
96d LEU* 3.4 9.4 - - - +
64f THR* 3.6 1.3 - - - +
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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
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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