Contacts of the helix formed by residues 83 - 105 (chain B) in PDB entry 2QQ6
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 4.8 0.4 - - - -
82A ALA* 2.8 18.4 - - - -
39B SER* 5.5 0.2 - - - -
82B ALA* 1.3 77.3 - - - +
84B ALA* 1.3 67.6 + - - -
86B ILE* 3.0 12.3 + - - +
87B THR* 3.0 12.1 + - - -
269B TYR* 3.3 34.7 - - - -
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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
----------------------------------------------------------
48A ILE* 5.2 3.8 - - + -
79A GLY* 4.6 4.4 - - - -
82A ALA* 3.8 6.3 - - - +
84A ALA* 4.2 19.0 - - + +
85A VAL* 4.6 14.1 - - + -
39B SER* 4.7 11.2 - - - +
40B ALA* 5.9 2.7 - - + -
45B ILE* 5.6 6.0 - - + +
48B ILE* 4.0 20.1 - - + +
82B ALA 3.9 0.8 + - - -
83B GLY* 1.3 68.3 - - - -
85B VAL* 1.3 56.6 + - - +
87B THR* 2.8 29.3 + - - -
88B ALA* 2.9 11.6 + - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.6 7.6 - - + -
84A ALA* 4.6 12.8 - - + +
48B ILE* 4.0 30.2 - - + +
75B ASN* 3.8 32.5 - - - +
78B THR 3.7 14.1 - - - +
79B GLY* 3.5 23.1 - - - +
80B GLY* 4.2 10.3 - - - -
82B ALA 4.8 0.2 + - - -
83B GLY 3.5 0.6 - - - -
84B ALA* 1.3 74.5 - - - +
86B ILE* 1.3 57.8 + - + +
88B ALA* 3.5 2.1 + - - +
89B LEU* 3.1 33.7 + - + +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.8 17.3 - - - +
72B ARG* 4.1 13.5 - - + -
80B GLY* 3.3 22.0 - - - +
81B GLN 4.4 1.1 - - - +
82B ALA* 3.5 27.6 - - - -
83B GLY 3.0 9.2 + - - +
85B VAL* 1.3 76.5 - - - +
87B THR* 1.3 62.7 + - - +
89B LEU* 3.5 9.2 + - + +
90B SER* 2.8 27.2 + - - -
269B TYR* 3.7 9.4 - - + -
270B THR* 4.2 9.0 - - + -
292B LYS 3.3 5.4 - - - +
293B CYS 2.7 35.9 - - - +
294B GLY* 3.8 3.6 - - - +
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B CYS* 3.7 6.8 - - + -
37B TYR* 3.5 32.1 - - + +
39B SER* 4.2 16.6 + - - -
45B ILE* 5.2 3.6 - - + -
83B GLY 3.0 11.4 + - - -
84B ALA 2.8 12.7 + - - -
86B ILE* 1.3 71.6 - - - +
88B ALA* 1.3 63.1 + - - +
90B SER* 3.1 16.2 - - - -
91B GLY 3.5 3.3 + - - -
269B TYR* 3.8 2.8 + - - -
291B ALA 3.1 18.3 - - - +
292B LYS* 3.2 29.9 + - - +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B CYS* 3.6 14.0 - - - -
45B ILE* 4.1 9.8 - - + +
48B ILE* 3.6 29.8 - - + -
49B VAL* 3.8 18.3 - - + +
84B ALA 2.9 9.7 + - - +
85B VAL 3.5 9.0 - - - +
87B THR* 1.3 73.4 - - - +
89B LEU* 1.3 67.7 + - - +
90B SER 3.0 1.1 - - - -
91B GLY* 2.8 15.4 + - - -
92B ILE* 3.3 10.9 + - + +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 6.0 0.7 - - + -
52B MSE 4.0 16.8 - - + -
68B TYR* 3.6 31.9 - - + -
71B MSE 3.3 41.5 - - + +
72B ARG* 3.8 30.3 - - + +
75B ASN* 4.5 6.5 - - - +
85B VAL* 3.1 22.4 + - + +
86B ILE* 3.9 10.5 - - + +
88B ALA* 1.3 78.6 - - + +
90B SER* 1.3 53.2 + - - +
92B ILE* 3.1 8.5 + - + +
93B GLU* 2.7 37.5 + - - +
294B GLY 4.7 0.9 - - - -
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE 2.8 21.2 + - - -
87B THR 3.1 13.7 - - - -
88B ALA 2.9 0.4 + - - -
89B LEU* 1.3 75.7 - - - +
91B GLY* 1.3 52.5 + - - +
93B GLU* 3.4 2.8 + - - +
94B THR* 2.7 32.4 + - - -
290B VAL 3.6 7.9 - - - +
291B ALA* 3.5 22.2 - - - -
292B LYS 3.6 6.1 - - - -
294B GLY* 2.9 36.4 + - - -
295B GLY* 4.0 2.8 - - - -
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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
----------------------------------------------------------
23B VAL* 4.3 8.1 - - - -
34B GLY* 3.9 5.0 - - - -
35B GLU 4.2 16.2 - - - -
36B CYS* 3.7 17.4 - - - +
87B THR 3.5 2.4 + - - -
88B ALA 2.8 10.3 + - - -
90B SER* 1.3 76.2 - - - +
92B ILE* 1.3 64.4 + - - -
94B THR* 3.0 17.8 + - - -
95B ALA* 3.1 11.1 + - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.7 2.7 - - + -
23B VAL* 4.1 13.1 - - + +
25B VAL* 4.7 10.1 - - + -
49B VAL* 3.8 36.8 - - + +
52B MSE 4.0 26.7 - - + -
56B LEU* 4.4 13.5 - - + -
71B MSE 4.1 21.5 - - + -
88B ALA* 3.3 7.8 + - + +
89B LEU* 3.1 16.1 + - + +
91B GLY* 1.3 75.0 - - - +
93B GLU* 1.3 62.0 + - - +
95B ALA* 3.3 2.6 + - - +
96B LEU* 3.2 37.9 + - + +
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.1 10.0 - - + +
65B GLU* 6.1 0.5 - - - -
68B TYR* 4.7 21.6 - - + +
71B MSE 5.2 3.3 - - + +
89B LEU 2.7 21.1 + - - +
90B SER 3.5 6.1 - - - +
91B GLY 3.1 0.2 - - - -
92B ILE* 1.3 73.2 - - - +
94B THR* 1.3 63.1 + - - +
96B LEU* 3.2 12.0 + - + +
97B TRP* 2.9 46.4 + - + +
294B GLY 4.1 10.3 - - - +
295B GLY* 3.3 6.6 - - - -
296B LEU* 2.8 32.1 + - - +
297B ALA* 3.1 32.6 + - - +
298B GLU 4.1 1.0 + - - -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 3.9 4.5 - - - +
34B GLY* 3.7 18.6 - - - -
35B GLU 4.6 6.4 + - - +
90B SER 2.7 16.6 + - - -
91B GLY* 3.3 8.3 - - - -
93B GLU* 1.3 78.7 + - - +
95B ALA* 1.3 64.3 + - - +
97B TRP* 3.2 4.0 + - - +
98B ASP* 2.8 23.4 + - - +
290B VAL* 5.3 2.6 + - - +
291B ALA* 5.7 2.1 - - - +
295B GLY* 5.2 0.2 - - - -
296B LEU* 3.6 31.1 - - + +
322B VAL* 5.5 2.5 - - + +
323B GLY* 5.9 1.3 - - - -
326B ALA* 3.8 20.4 - - + -
375B LEU* 5.0 6.3 - - + +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 4.1 8.1 - - + +
25B VAL* 3.9 20.6 - - + -
32B GLY* 3.5 20.5 - - - +
33B LEU 3.7 13.7 - - - +
34B GLY* 3.9 7.1 - - - +
91B GLY 3.1 8.4 + - - +
92B ILE 3.4 10.8 - - - +
94B THR* 1.3 77.7 - - - +
96B LEU* 1.3 51.3 + - - +
98B ASP* 2.7 7.3 + - - +
99B LEU* 2.6 34.0 + - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.3 11.9 - - + -
25B VAL* 4.0 26.0 - - + -
56B LEU* 3.9 21.5 - - + -
61B PRO* 3.8 26.9 - - + +
64B VAL* 3.9 15.0 - - + +
67B LEU* 4.2 15.9 - - + -
71B MSE 4.3 10.3 - - + -
92B ILE* 3.3 23.6 - - + +
93B GLU* 3.2 8.6 + - + +
95B ALA* 1.3 75.0 - - - +
97B TRP* 1.3 57.1 + - - +
99B LEU* 3.6 5.5 - - + +
100B ALA* 2.8 33.8 + - - +
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Residues in contact with TRP 97 (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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62B ARG 5.5 2.0 - - - -
64B VAL* 3.1 38.4 - - + +
65B GLU* 5.1 7.9 - - - -
93B GLU* 2.9 49.0 + - - +
94B THR* 3.5 8.7 - - - +
96B LEU* 1.3 77.1 - - - +
98B ASP* 1.3 59.9 + - - +
100B ALA* 4.2 4.0 - - + -
101B GLY 3.5 10.7 + - - -
108B VAL* 3.0 24.5 - - + +
111B LEU* 3.6 45.4 - - + +
112B LEU* 3.5 26.2 - - + +
296B LEU* 4.1 23.3 - - + -
297B ALA* 3.7 18.3 - - + +
375B LEU* 5.9 0.2 - - + -
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY* 3.3 4.7 - - - -
33B LEU* 2.6 34.6 + - - +
94B THR 2.8 11.5 + - - +
95B ALA 2.7 12.8 + - - +
97B TRP* 1.3 77.1 - - - +
99B LEU* 1.3 63.4 + - - -
101B GLY* 3.0 11.6 + - - -
102B LYS* 3.0 23.8 + - - +
108B VAL* 4.5 0.7 - - - -
374B GLY* 2.8 33.1 - - - +
375B LEU* 3.3 23.8 - - + +
377B LEU* 6.1 0.2 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 5.3 0.4 - - + -
25B VAL* 3.9 30.5 - - + +
27B ALA* 4.0 16.8 - - + -
30B GLU* 4.2 1.3 - - + -
31B HIS* 3.9 27.6 - - - +
32B GLY* 3.5 13.4 - - - -
61B PRO* 3.5 34.1 - - + -
95B ALA 2.6 18.8 + - - +
96B LEU* 3.6 6.3 - - + +
98B ASP* 1.3 71.3 - - - +
100B ALA* 1.3 64.3 + - - +
102B LYS* 3.0 7.1 + - - +
103B LEU* 2.9 45.4 + - + +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PRO 3.5 17.9 - - - +
62B ARG* 4.2 11.4 - - - +
64B VAL* 5.6 1.1 - - + -
96B LEU 2.8 22.2 + - - +
97B TRP* 4.2 10.8 - - + +
99B LEU* 1.3 74.5 - - - +
101B GLY* 1.3 56.1 + - - +
103B LEU* 3.2 8.8 + - - +
104B GLN* 2.8 46.1 + - - +
111B LEU* 4.3 9.2 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP 3.5 6.3 + - - -
98B ASP 3.0 7.9 + - - -
100B ALA* 1.3 78.6 - - - +
102B LYS* 1.3 54.2 + - - +
104B GLN* 4.6 1.1 - - - -
105B GLY* 2.7 28.1 + - - -
106B VAL 2.9 26.7 + - - -
108B VAL* 5.3 0.4 - - - -
111B LEU* 3.7 14.3 - - - +
373B PRO* 3.4 1.4 - - - +
374B GLY* 3.7 11.7 - - - -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 2.9 32.9 + - - +
31B HIS* 2.7 53.9 + - - +
98B ASP* 3.0 34.2 + - - +
99B LEU* 3.0 7.9 + - - +
101B GLY* 1.3 76.7 - - - +
103B LEU* 1.3 65.3 + - - +
105B GLY* 3.4 8.3 + - - -
373B PRO* 4.2 15.5 - - + +
374B GLY* 4.3 7.6 - - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO* 3.7 36.3 - - + -
27B ALA* 4.8 2.5 - - + -
30B GLU* 3.9 26.5 - - + +
61B PRO* 4.0 19.7 - - + -
62B ARG* 4.7 7.6 - - + -
99B LEU* 2.9 40.1 + - + +
100B ALA* 3.6 7.2 - - - +
102B LYS* 1.3 75.9 - - - +
104B GLN* 1.3 66.3 + - - +
105B GLY* 2.9 5.7 + - - -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.0 49.0 - - - +
100B ALA* 2.8 31.6 + - - +
101B GLY* 4.4 2.0 - - - +
103B LEU* 1.3 74.1 - - - +
105B GLY* 1.3 63.7 + - - +
106B VAL* 3.5 17.6 - - + +
111B LEU* 4.8 17.6 - - + +
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 2.7 13.5 + - - -
102B LYS 3.7 7.2 - - - -
103B LEU 2.9 4.0 - - - -
104B GLN* 1.3 76.2 - - - +
106B VAL* 1.3 66.6 + - - +
373B PRO* 3.5 19.4 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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