Contacts of the helix formed by residues 78 - 98 (chain A) in PDB entry 3QJQ
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 ILE 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY 3.4 1.8 + - - +
74A VAL* 3.3 25.3 + - + +
77A ALA* 1.3 84.0 - - - +
79A VAL* 1.3 62.0 + - + +
81A THR* 3.4 4.3 + - - -
82A GLN* 3.2 27.0 - - - +
133A TYR* 3.7 45.1 - - + +
135A PHE* 4.7 8.1 - - + -
149A ALA* 6.1 5.2 - - + -
152A PHE* 3.5 20.0 - - + -
153A VAL* 4.9 11.7 - - + -
228A PHE* 6.4 0.2 - - + -
235A ILE* 5.0 13.5 - - + -
239A TRP* 5.2 1.6 - - + +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 3.7 15.9 - - + -
74A VAL* 3.1 19.6 + - + +
75A LEU* 3.1 13.6 + - + +
78A ILE* 1.3 79.3 - - + +
80A PHE* 1.3 69.9 + - - +
83A LEU* 3.1 48.4 + - + +
117A LEU* 3.6 34.1 - - + -
152A PHE* 3.4 25.4 - - + -
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 3.6 34.2 - - - +
29A PHE* 3.7 26.2 - + - -
31A ALA* 4.1 1.2 - - - +
32A LEU* 4.0 32.8 - - + +
75A LEU 2.7 17.7 + - - +
76A ASN* 3.6 15.9 - - - +
79A VAL* 1.3 73.3 - - - +
81A THR* 1.3 74.7 + - + +
83A LEU* 3.8 1.9 - - - +
84A PHE* 2.9 31.9 + + + +
393A VAL* 4.8 4.9 - - + -
394A THR* 3.8 28.5 - - + -
397A ALA* 3.6 27.6 - - + -
800A HEM 4.3 2.5 - - + -
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASN 3.8 16.1 + - - +
77A ALA* 2.5 28.8 + - - +
78A ILE 3.4 2.6 + - - -
80A PHE* 1.3 84.9 - - + +
82A GLN* 1.3 59.6 + - - -
84A PHE* 2.6 30.4 + - - +
85A ALA* 2.7 14.7 + - - -
238A PHE* 5.0 0.4 - - - -
239A TRP* 3.2 41.1 + - + -
389A VAL* 4.4 11.2 - - + -
393A VAL* 4.7 7.2 - - + -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.2 18.2 + - - +
81A THR* 1.3 78.8 + - - +
83A LEU* 1.3 57.3 + - - +
85A ALA* 3.5 0.5 - - - +
86A GLN* 2.8 63.2 + - - +
113A ALA* 4.9 2.2 - - - +
152A PHE* 3.1 55.0 + - + +
153A VAL* 3.6 17.2 - - - +
156A THR* 3.7 25.2 - - + +
193A TRP* 5.7 1.1 - - + -
238A PHE* 3.8 21.5 - - + -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.4 45.4 - - + +
27A LEU* 3.5 28.5 - - + -
28A GLY* 3.6 19.1 - - - +
79A VAL* 3.1 41.1 + - + +
82A GLN* 1.3 75.5 - - - +
84A PHE* 1.3 60.7 + - - +
86A GLN* 3.7 16.2 - - - +
87A ALA* 3.2 16.5 + - - +
110A TRP* 5.5 0.2 - - + -
113A ALA* 3.9 21.8 - - + -
152A PHE* 3.9 7.2 - - + -
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.9 25.4 - - + -
28A GLY* 5.3 1.1 - - - -
29A PHE* 5.1 0.9 - + - -
80A PHE* 2.9 25.4 + + + +
81A THR* 2.6 17.3 + - - +
83A LEU* 1.3 70.0 - - - +
85A ALA* 1.3 64.8 + - - +
87A ALA* 3.1 5.1 + - - +
88A ILE* 3.0 54.3 + - + +
239A TRP 5.4 1.8 - - - -
242A PRO* 4.4 13.9 - - + -
243A ALA* 4.6 9.2 - - - -
246A ILE* 3.9 13.5 - - + -
393A VAL* 4.6 15.7 - - + -
396A THR* 4.7 0.7 - - + -
397A ALA* 3.5 49.8 - - + -
400A SER* 5.4 2.7 - - - -
404A LEU* 5.6 2.0 - - + -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR 2.7 15.2 + - - +
82A GLN 3.5 7.4 - - - +
84A PHE* 1.3 70.8 - - - +
86A GLN* 1.3 67.0 + - - +
87A ALA 3.0 0.5 + - - -
89A MET* 2.8 30.7 + - - +
189A PHE* 4.2 4.5 - - + -
190A TRP* 4.8 1.3 - - + -
238A PHE* 3.8 32.1 - - + +
239A TRP* 5.7 0.4 - - - -
242A PRO* 3.6 30.1 - - + -
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.7 30.7 - - + -
82A GLN* 2.8 48.0 + - - +
83A LEU* 3.7 12.9 - - - +
85A ALA* 1.3 73.8 - - + +
87A ALA* 1.3 64.6 + - - +
90A VAL* 3.3 24.9 + - - +
109A SER* 4.8 0.8 - - - -
113A ALA* 5.4 0.2 - - - +
155A SER* 3.1 26.9 + - - -
156A THR* 3.7 16.1 - - + +
159A SER* 3.0 30.4 + - - +
190A TRP* 4.2 12.5 - - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 4.3 14.9 + - + +
24A PHE* 4.3 13.4 - - + +
25A LEU* 4.2 26.7 - - + -
83A LEU 3.2 13.7 + - - +
84A PHE 3.1 9.8 + - - +
85A ALA 3.0 1.0 + - - -
86A GLN* 1.3 77.3 - - - +
88A ILE* 1.3 59.3 + - + +
90A VAL* 4.2 0.2 - - - +
91A TYR* 2.8 41.1 + - - +
404A LEU* 5.7 0.7 - - + -
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PHE* 3.0 48.0 + - + +
87A ALA* 1.3 80.3 - - + +
89A MET* 1.3 67.0 + - - +
90A VAL 3.1 0.3 + - - -
91A TYR* 5.0 0.9 - - + -
92A LEU* 2.9 62.9 + - + +
93A PRO* 3.5 0.2 - - - +
242A PRO* 3.7 25.8 - - + +
245A ALA* 4.6 1.1 - - + -
246A ILE* 3.7 19.5 - - + -
400A SER* 6.2 0.2 - - - -
403A TRP* 5.0 0.7 - - + -
404A LEU* 3.9 25.8 - - + -
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA 2.8 19.9 + - - +
86A GLN 4.1 0.2 - - - -
88A ILE* 1.3 81.0 - - - +
90A VAL* 1.3 58.3 + - - -
92A LEU* 5.9 0.7 - - - -
93A PRO* 3.9 14.3 - - - +
163A VAL* 3.5 6.2 - - - +
182A VAL* 6.4 1.1 - - - -
185A MET* 5.0 1.1 - - + -
186A ALA* 4.1 15.2 - - + +
189A PHE* 3.4 42.8 - - + -
190A TRP* 3.0 35.7 + - + +
241A LEU 3.8 8.5 - - - +
242A PRO* 3.7 23.6 - - + -
245A ALA* 3.7 25.4 - - + -
269A PHE* 4.3 11.7 - - + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN 3.3 20.3 + - - +
87A ALA 4.2 0.2 - - - +
88A ILE 3.2 0.4 - - - -
89A MET* 1.3 80.1 - - - +
91A TYR* 1.3 69.2 + - - +
92A LEU 3.3 1.5 + - - -
93A PRO* 3.6 2.9 - - - +
94A ALA* 3.1 23.4 + - + +
101A PRO* 4.6 8.5 - - + -
106A MET* 4.3 29.8 - - + -
159A SER* 4.1 20.2 - - - +
162A ILE* 4.1 22.9 - - + -
163A VAL* 3.7 17.7 - - + -
166A LEU* 4.7 2.1 - - + +
190A TRP* 4.4 4.5 - - + -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.7 18.2 - - + -
18A LYS* 3.3 37.0 - - + +
21A THR* 3.3 33.2 - - + +
87A ALA 2.8 19.4 + - - +
88A ILE* 5.0 1.3 - - + -
90A VAL* 1.3 82.1 - - - +
92A LEU* 1.3 66.1 + - + +
94A ALA* 3.4 4.9 + - + +
95A ARG* 3.0 54.4 + - + +
404A LEU* 3.9 18.8 - - + -
407A ASN* 2.8 29.0 + - - -
408A LEU* 3.7 8.1 - - + -
506A LEU* 3.8 13.7 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 2.9 44.0 + - + +
89A MET* 5.9 0.7 - - - -
91A TYR* 1.3 83.8 - - + +
93A PRO* 1.3 72.2 - - + +
95A ARG* 3.0 13.5 + - - +
96A GLU* 3.1 10.2 + - - +
182A VAL* 3.7 18.4 - - + -
245A ALA* 4.8 7.2 - - + -
246A ILE* 4.4 7.2 - - + -
249A THR* 4.6 5.4 - - - +
250A ILE* 3.7 27.6 - - + -
403A TRP* 4.5 10.8 - - + -
404A LEU* 5.1 0.9 - - + -
506A LEU* 3.6 26.2 - - + -
508A PHE* 3.9 10.4 - - + -
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Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE 3.5 9.0 - - - +
89A MET* 3.9 10.8 - - - +
90A VAL 3.6 9.4 - - - +
92A LEU* 1.3 92.2 - - + +
94A ALA* 1.3 61.1 + - - +
96A GLU* 3.0 13.4 + - + +
97A LEU* 3.0 20.5 + - - +
163A VAL* 5.0 5.2 - - + -
166A LEU* 4.5 9.0 - - + -
182A VAL* 3.8 15.7 - - + +
183A THR* 4.2 20.6 - - + +
186A ALA* 3.2 35.2 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 4.5 4.9 - - + +
90A VAL* 3.1 17.7 + - + +
91A TYR* 3.7 9.2 - - + +
93A PRO* 1.3 78.3 - - - +
95A ARG* 1.3 59.8 + - - +
97A LEU* 5.0 1.3 - - - -
98A ASN* 2.9 22.7 + - - -
99A MET 3.1 27.0 + - - +
101A PRO* 3.8 20.9 - - + -
166A LEU* 3.7 15.1 - - + +
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Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.9 30.7 - - - -
17A GLU* 3.3 24.4 + - - -
18A LYS* 5.2 1.8 - - - +
91A TYR* 3.0 53.0 + - + +
92A LEU 3.0 9.3 + - - +
94A ALA* 1.3 80.5 + - - +
96A GLU* 1.3 66.3 + - - +
98A ASN* 2.7 43.7 + - - +
99A MET 4.4 0.4 + - - -
505A PRO* 5.5 12.5 - - + +
506A LEU* 3.5 26.5 - - + -
508A PHE* 4.2 7.8 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 3.1 9.8 + - - +
93A PRO 3.0 7.7 + - - +
95A ARG* 1.3 78.7 - - - +
97A LEU* 1.3 63.2 + - + +
98A ASN* 3.4 3.1 + - - +
180A PRO* 3.3 22.9 - - + +
181A LEU* 3.5 9.0 + - - +
182A VAL* 3.2 32.9 + - + +
183A THR* 2.7 35.3 + - - -
508A PHE* 4.1 17.6 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO 3.0 13.6 + - - +
94A ALA 4.4 0.2 - - - +
96A GLU* 1.3 77.4 - - + +
98A ASN* 1.3 70.0 + - - +
99A MET* 3.1 26.0 + - + +
166A LEU* 4.4 23.8 - - + +
170A TRP* 3.9 34.5 - - + +
180A PRO* 3.8 26.7 - - + -
183A THR* 3.3 42.0 - - + +
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Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 5.4 1.0 - - - -
94A ALA 2.9 11.3 + - - -
95A ARG* 2.7 41.9 + - - +
96A GLU 3.2 5.5 - - - +
97A LEU* 1.3 80.8 - - - +
99A MET* 1.3 59.3 + - - +
100A ARG 4.4 0.2 + - - -
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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