Contacts of the helix formed by residues 72 - 93 (chain C) in PDB entry 7A62
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 ASP 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN* 3.8 7.8 - - - +
70C LEU 3.7 0.6 + - - -
71C THR* 1.3 88.4 + - - +
73C HIS* 1.3 65.7 + - - +
74C LYS* 3.4 6.3 + - - +
75C SER* 2.8 42.7 + - - -
76C GLN* 3.0 26.7 + - - +
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Residues in contact with HIS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS* 4.3 30.4 + + + -
25C LEU* 4.3 15.1 - - + +
72C ASP* 1.3 74.1 - - - +
74C LYS* 1.3 61.4 + - + +
76C GLN* 3.0 14.9 + - - +
77C ARG* 2.9 67.9 + - + +
118C LEU* 4.1 18.3 - - + +
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Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 4.4 22.3 - - + +
26C PRO* 2.7 25.9 + - - +
27C ASN* 2.6 38.2 + - - +
29C GLN* 4.0 25.7 + - + +
72C ASP* 3.3 7.6 + - - +
73C HIS* 1.3 82.6 - - + +
75C SER* 1.3 62.2 + - - +
77C ARG* 3.3 6.8 + - - +
78C LEU* 3.0 24.4 + - - +
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Residues in contact with SER 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLN* 2.9 30.7 + - - +
32C LEU* 3.8 8.2 - - - +
33C PRO* 5.0 4.7 - - - +
70C LEU* 3.9 15.1 - - - +
71C THR* 4.2 11.8 + - - -
72C ASP* 2.8 40.5 + - - -
74C LYS* 1.3 74.2 - - - +
76C GLN* 1.3 60.7 + - - +
78C LEU* 3.6 0.4 + - - -
79C ALA* 3.1 22.3 + - - +
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE 5.9 0.2 + - - -
70C LEU* 4.2 22.9 + - + +
71C THR 5.9 0.4 - - - -
72C ASP* 3.0 18.1 + - - +
73C HIS* 3.0 15.7 + - - +
75C SER* 1.3 75.5 - - - +
77C ARG* 1.3 54.7 + - - +
79C ALA* 3.2 4.4 + - - +
80C ARG* 2.7 35.9 + - - +
114C LEU* 3.8 29.8 - - + +
117C ALA* 4.8 12.1 - - - +
118C LEU* 3.9 24.1 - - + +
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Residues in contact with ARG 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE 5.5 1.4 + - - -
25C LEU* 3.8 40.0 - - + +
73C HIS* 2.9 53.7 + - + +
74C LYS 3.3 4.7 + - - +
76C GLN* 1.3 76.6 - - - +
78C LEU* 1.3 62.3 + - - +
80C ARG* 3.3 7.7 + - - +
81C LEU* 3.0 22.7 + - - +
118C LEU* 4.3 13.9 - - + -
120C LEU* 5.6 5.6 - - - +
127C ALA* 3.0 40.0 + - - +
128C ASP* 4.7 10.1 + - - +
131C LEU* 4.2 7.9 - - - +
132C ALA* 3.9 17.0 - - + +
300C PRO* 5.0 12.5 - - - +
303C HIS* 6.1 1.8 - - - -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLN* 3.4 31.6 - - + +
30C GLU 3.5 23.8 - - - +
31C ASN 3.6 20.6 - - - +
32C LEU* 3.9 14.1 - - + +
40C MET* 4.8 1.3 - - + -
74C LYS 3.0 16.9 + - - +
75C SER 3.9 3.6 - - - +
77C ARG* 1.3 76.6 - - - +
79C ALA* 1.3 57.5 + - - +
81C LEU* 3.1 9.8 + - + +
82C VAL* 2.7 35.3 + - + +
132C ALA* 5.5 2.4 - - - +
151C LEU* 4.2 9.2 - - + -
152C PHE* 4.0 29.8 - - + -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.3 11.4 - - + +
39C TRP* 4.6 8.7 - - + -
70C LEU* 3.6 21.5 - - + -
75C SER 3.1 18.3 + - - +
76C GLN 3.2 4.2 + - - +
78C LEU* 1.3 76.5 - - - +
80C ARG* 1.3 58.8 + - - +
82C VAL* 4.2 7.4 - - - -
83C LEU* 2.9 34.5 + - - +
114C LEU* 3.6 16.8 - - + -
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Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C GLN 2.7 19.0 + - - +
77C ARG* 3.6 7.4 - - - +
79C ALA* 1.3 72.5 - - - +
81C LEU* 1.3 57.1 + - - +
84C GLY* 2.9 26.9 + - - -
111C TYR* 4.1 12.8 + - + -
114C LEU* 3.6 12.0 - - + +
115C SER* 2.9 28.8 + - - +
118C LEU* 3.6 27.6 - - + -
120C LEU* 3.4 30.3 - - - +
121C PRO 2.8 21.8 + - - -
122C PRO* 4.2 1.6 - - - +
123C ILE 2.6 29.9 + - - -
125C VAL* 3.9 11.1 - - - +
128C ASP* 2.7 37.9 + - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG 3.0 13.2 + - - +
78C LEU* 3.1 11.4 + - + +
80C ARG* 1.3 77.9 - - - +
82C VAL* 1.3 62.8 + - - +
84C GLY* 3.3 1.0 + - - -
85C CYS* 2.9 43.6 + - - -
124C LEU* 4.2 1.7 - - + +
128C ASP* 3.2 41.0 + - + +
129C CYS* 3.7 10.3 - - - +
132C ALA* 3.9 11.0 - - + +
133C ASN* 3.7 37.2 - - + +
151C LEU* 4.4 3.4 - - + -
152C PHE* 3.7 22.9 - - + -
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.6 3.8 - - + -
39C TRP* 3.9 34.1 - - + +
40C MET* 4.0 17.3 - - + +
43C ALA* 3.8 19.1 - - + +
78C LEU* 2.7 29.5 + - + +
79C ALA* 3.8 7.9 - - - +
81C LEU* 1.3 73.0 - - - +
83C LEU* 1.3 60.6 + - + +
85C CYS* 3.4 2.5 + - - +
86C ILE* 3.1 31.3 + - + +
152C PHE* 3.7 28.7 - - + -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TRP* 3.7 50.5 - - + -
67C ILE* 5.6 0.2 - - + -
79C ALA 2.9 20.3 + - - +
82C VAL* 1.3 74.2 - - + +
84C GLY* 1.3 61.2 + - - +
86C ILE* 3.4 7.1 + - + +
87C THR* 2.8 34.6 + - - +
107C ILE* 3.8 28.3 - - + +
110C PRO 4.3 1.6 - - - -
111C TYR* 3.6 46.9 - - + +
114C LEU* 4.1 11.9 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ARG 2.9 16.9 + - - -
81C LEU 3.7 0.7 - - - -
83C LEU* 1.3 78.3 - - - +
85C CYS* 1.3 59.8 + - - +
87C THR* 3.3 2.0 + - - -
88C MET* 3.0 29.6 + - - +
111C TYR* 3.4 25.2 - - - -
124C LEU* 4.1 17.9 - - - -
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Residues in contact with CYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 4.9 5.6 - - + -
46C LEU* 3.9 18.5 - - + +
81C LEU* 2.9 38.0 + - - +
82C VAL* 3.8 4.7 - - - +
84C GLY* 1.3 73.1 - - - +
86C ILE* 1.3 66.6 + - - +
88C MET 3.5 0.2 + - - -
89C ALA* 3.1 24.1 + - - +
124C LEU* 4.1 8.5 - - - +
129C CYS* 5.7 1.6 - - - -
133C ASN* 5.9 0.9 - - - -
152C PHE* 4.2 22.9 - - + -
153C SER 5.9 0.2 - - - -
154C PHE* 3.8 25.9 - - + -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C TRP* 3.6 32.3 - - + +
42C ILE* 3.9 22.7 - - + -
43C ALA* 4.1 9.6 - - + +
46C LEU* 4.8 3.1 - - + -
55C LEU* 4.8 0.9 - - + +
59C VAL* 3.7 29.6 - - + -
62C LEU* 5.4 0.2 - - + -
82C VAL* 3.1 26.8 + - + +
83C LEU* 3.8 6.5 - - + +
85C CYS* 1.3 75.2 - - - +
87C THR* 1.3 57.6 + - - +
89C ALA* 3.4 5.6 + - - +
90C TYR* 2.9 27.3 + - + +
103C LEU* 6.4 0.2 - - + -
107C ILE* 4.2 26.5 - - + -
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU 2.8 23.3 + - - -
84C GLY* 3.5 4.9 - - - -
85C CYS 3.2 0.2 - - - -
86C ILE* 1.3 73.9 - - - +
88C MET* 1.3 68.8 + - - +
90C TYR* 3.0 2.4 + - - +
91C VAL* 2.9 26.4 + - + +
103C LEU* 3.6 35.7 - - + +
107C ILE* 3.9 6.2 - - - +
111C TYR* 3.5 26.4 - - + -
122C PRO 5.3 0.7 - - - +
123C ILE* 5.8 0.9 - - - -
237C TRP* 4.2 25.1 - - + -
247C LEU* 4.6 1.3 - - + -
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Residues in contact with MET 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY 3.0 16.9 + - - +
85C CYS 4.0 3.1 - - - +
87C THR* 1.3 77.2 - - - +
89C ALA* 1.3 62.3 + - - +
91C VAL* 4.7 1.3 - - - -
92C TRP* 3.0 33.9 + - + +
123C ILE* 3.8 26.7 - - + -
124C LEU* 3.8 25.8 - - + +
154C PHE* 4.0 10.3 - - + -
233C TYR* 3.3 32.2 - - + +
234C LEU* 4.0 11.0 - - - +
235C SER 3.2 26.5 - - - +
237C TRP* 3.7 21.8 - - + -
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.8 22.4 - - + -
50C ILE* 4.0 12.6 - - + -
55C LEU* 3.4 21.3 - - + +
85C CYS 3.1 18.5 + - - +
86C ILE 3.7 2.9 - - - +
88C MET* 1.3 77.6 - - - +
90C TYR* 1.3 57.4 + - - +
93C GLY* 2.7 32.2 + - - +
154C PHE* 4.6 3.0 - - + -
233C TYR* 4.4 10.5 - - - -
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 3.5 8.2 - - + +
56C ARG* 3.0 51.8 + - + +
59C VAL* 3.8 26.5 - - + -
60C GLU* 2.6 39.0 + - + +
86C ILE 2.9 17.9 + - - +
87C THR 3.0 3.8 + - - +
89C ALA* 1.3 76.3 - - - +
91C VAL* 1.3 67.2 + - + +
100C ARG* 3.6 30.1 - - + +
102C VAL 3.4 24.0 + - - -
103C LEU* 4.1 13.9 - - + -
104C PRO* 3.5 22.7 - - + +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG* 3.0 14.2 + - - -
87C THR* 2.9 21.9 + - + +
88C MET 4.0 2.5 - - - +
90C TYR* 1.3 79.8 - - + +
92C TRP* 1.3 85.0 + - + +
99C VAL* 3.1 18.0 - - - +
100C ARG 3.2 19.3 + - - +
103C LEU* 4.9 5.8 - - + -
237C TRP* 4.0 19.7 - - + -
243C LEU* 4.2 11.9 - - + -
247C LEU* 4.0 32.8 - - + -
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Residues in contact with TRP 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG* 3.6 2.2 - - - -
88C MET* 3.0 26.3 + - - +
91C VAL* 1.3 83.9 - - + +
93C GLY* 1.3 64.7 + - - +
94C LYS 3.1 0.7 + - - -
95C GLY* 3.0 16.2 + - - -
96C HIS 4.5 1.4 + - - -
97C GLY 5.2 0.5 + - - -
98C ASP 3.7 9.0 + - - +
99C VAL* 3.7 21.9 - - + +
232C ILE* 3.4 34.5 + - + -
233C TYR* 3.9 26.7 + - + -
235C SER* 2.9 36.1 + - - -
236C GLY 3.5 10.8 - - - -
237C TRP* 3.9 14.9 - + - -
240C ASN* 3.6 17.7 - - - -
242C GLN* 4.2 16.2 - - - -
243C LEU* 3.4 33.2 - - + -
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Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 3.6 15.2 - - - +
55C LEU* 5.4 2.2 - - - -
56C ARG* 3.2 28.8 - - - +
89C ALA 2.7 23.1 + - - +
92C TRP* 1.3 71.1 - - - +
94C LYS* 1.3 52.7 + - - -
233C TYR* 2.8 29.6 + - - -
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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
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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