Contacts of the helix formed by residues 83 - 105 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 1.3 83.0 - - - +
84A ALA* 1.3 66.7 + - - +
85A VAL 3.3 1.1 - - - -
86A ILE* 2.8 5.6 + - - +
87A THR* 2.8 25.4 + - - -
269A TYR* 3.3 31.0 - - - -
79B GLY* 4.5 2.9 - - - -
82B ALA 3.1 7.7 + - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 4.9 11.0 - - - +
40A ALA* 5.8 3.4 - - + -
45A ILE* 5.6 5.8 - - + +
48A ILE* 3.9 19.7 - - + -
82A ALA* 4.7 1.0 - - - +
83A GLY* 1.3 71.2 - - - +
85A VAL* 1.3 59.7 + - - +
86A ILE 2.9 0.3 + - - -
87A THR* 2.9 8.4 + - - -
88A ALA* 2.8 31.7 + - - +
48B ILE* 5.3 3.6 - - + -
79B GLY* 4.5 8.1 + - - -
82B ALA 4.8 0.6 + - - -
84B ALA* 4.2 17.2 - - + +
85B VAL* 4.6 14.1 - - + +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 4.1 23.7 - - + +
75A ASN* 3.7 35.0 - - + +
78A THR 3.5 17.0 - - - +
79A GLY* 2.9 30.1 - - - +
80A GLY* 3.9 5.8 - - - -
82A ALA* 4.9 0.6 - - - +
83A GLY 3.3 1.2 - - - +
84A ALA* 1.3 79.8 - - - +
86A ILE* 1.3 58.1 + - + +
88A ALA* 3.7 2.8 - - - +
89A LEU* 3.1 28.2 + - + +
40B ALA* 4.5 10.3 - - + -
84B ALA* 4.6 12.5 - - + +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 4.4 7.6 - - - +
72A ARG* 5.7 1.1 - - + -
80A GLY 3.3 26.0 - - - +
81A GLN 3.2 14.4 - - - +
82A ALA 3.2 24.2 - - - +
83A GLY 2.8 8.4 + - - +
85A VAL* 1.3 79.4 - - + +
87A THR* 1.3 54.4 + - - +
88A ALA 3.1 1.3 - - - -
89A LEU* 3.0 12.7 + - + +
90A SER* 2.7 31.7 + - - -
269A TYR* 4.2 7.0 - - + -
270A THR* 3.6 18.2 - - + -
292A LYS 4.0 2.7 - - - +
293A CYS 3.1 34.1 - - - +
294A GLY* 3.9 4.9 - - - +
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A CYS* 3.6 8.3 - - + -
37A TYR* 3.6 32.5 - - + +
39A SER* 4.3 13.0 + - - -
45A ILE* 4.7 4.9 - - + -
83A GLY 2.8 20.4 + - - -
84A ALA* 3.6 9.3 - - - -
86A ILE* 1.3 72.9 - - - +
88A ALA* 1.3 63.3 + - - +
90A SER* 3.0 18.8 + - - -
91A GLY 3.4 4.7 + - - -
269A TYR* 3.7 4.3 + - - -
291A ALA 3.4 18.1 - - - +
292A LYS* 3.2 27.0 + - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A CYS* 3.9 1.7 - - - -
45A ILE* 3.9 18.8 - - + +
48A ILE* 3.4 37.2 - - + -
49A VAL* 3.6 19.2 - - + +
84A ALA 2.8 12.0 + - - +
85A VAL 3.7 2.2 - - - +
87A THR* 1.3 80.6 - - - +
89A LEU* 1.3 60.7 + - + +
91A GLY 3.6 5.2 + - - -
92A ILE* 3.4 21.0 + - - +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 6.2 1.3 - - + -
52A MSE 4.0 13.9 - - + -
68A TYR* 4.0 25.1 - - + +
71A MSE 3.6 42.3 - - + +
72A ARG* 3.9 33.0 - - + +
75A ASN* 4.7 4.5 - - - +
80A GLY* 6.0 0.4 - - - +
85A VAL* 3.1 24.0 + - + +
86A ILE* 3.0 16.5 + - + +
88A ALA* 1.3 79.3 - - + +
90A SER* 1.3 65.1 + - - +
92A ILE* 3.3 6.7 + - + +
93A GLU* 3.0 26.3 + - - +
294A GLY 5.1 0.9 - - - -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU 4.5 0.9 - - - -
86A ILE 2.7 12.3 + - - -
87A THR 3.0 10.7 + - - -
89A LEU* 1.3 78.1 - - - +
91A GLY* 1.3 60.0 + - - +
93A GLU* 3.5 3.1 + - - +
94A THR* 2.8 28.5 + - - -
290A VAL 3.5 7.0 - - - -
291A ALA* 3.4 23.8 - - - -
292A LYS 3.3 8.5 - - - -
294A GLY* 2.6 30.0 + - - -
295A GLY* 3.7 12.3 - - - +
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.2 6.2 - - - +
34A GLY* 3.3 13.4 - - - -
35A GLU 3.3 26.4 + - - -
36A CYS* 3.6 12.7 - - - -
87A THR 3.4 6.9 + - - -
88A ALA 3.6 0.8 + - - -
89A LEU 3.3 0.6 - - - -
90A SER* 1.3 75.9 - - - +
92A ILE* 1.3 65.0 + - - +
94A THR* 3.3 2.7 + - - -
95A ALA* 3.1 18.2 + - - +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 5.7 0.7 - - + -
23A VAL* 4.1 8.3 - - + +
25A VAL* 4.7 7.4 - - + -
49A VAL* 3.7 32.5 - - + +
52A MSE 3.9 26.5 - - + -
56A LEU* 3.7 21.8 - - + -
71A MSE 3.5 25.8 - - + -
88A ALA* 3.4 17.7 - - + +
89A LEU* 3.3 10.7 + - + +
91A GLY* 1.3 71.9 - - - +
93A GLU* 1.3 67.5 + - - +
95A ALA* 2.8 19.7 + - - +
96A LEU* 2.9 19.2 + - + +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.0 12.1 - - + +
68A TYR* 4.4 21.7 - - + -
71A MSE 4.4 2.0 - - + +
89A LEU 3.0 15.2 + - - +
90A SER 3.7 3.4 - - - +
92A ILE* 1.3 78.8 - - - +
94A THR* 1.3 64.0 + - - +
96A LEU* 3.3 12.8 + - + +
97A TRP* 2.7 62.4 + - + +
294A GLY 3.1 19.6 - - - +
295A GLY* 3.3 7.5 - - - -
296A LEU* 2.9 16.0 + - - +
297A ALA* 3.1 26.6 + - - +
298A GLU 3.7 0.3 + - - -
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.9 12.1 - - - +
34A GLY* 4.0 7.9 - - - -
35A GLU 4.6 5.9 + - - +
90A SER 2.8 18.0 + - - -
91A GLY* 3.5 8.9 - - - -
92A ILE 3.1 0.6 - - - -
93A GLU* 1.3 80.2 + - - +
95A ALA* 1.3 53.3 + - - +
97A TRP* 3.0 8.8 + - - +
98A ASP* 2.8 32.9 + - - +
290A VAL* 5.3 1.9 + - - +
291A ALA* 5.6 2.3 - - - -
295A GLY* 4.7 1.7 - - - -
296A LEU* 3.8 15.7 - - + +
322A VAL* 5.7 1.8 - - + -
323A GLY* 6.0 0.7 - - - -
326A ALA* 3.8 28.3 - - + +
375A LEU* 4.4 10.0 - - + +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL 3.8 18.2 - - - +
25A VAL* 3.4 26.5 - - + -
32A GLY* 3.5 10.9 - - - +
33A LEU 3.6 13.4 + - - -
91A GLY 3.1 9.1 + - - +
92A ILE* 2.8 10.0 + - - +
94A THR* 1.3 78.8 - - - +
96A LEU* 1.3 51.1 + - - +
98A ASP* 3.0 4.2 + - - +
99A LEU* 2.7 37.0 + - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.7 9.9 - - + -
25A VAL* 3.9 27.4 - - + -
56A LEU* 4.5 8.1 - - + -
61A PRO* 4.3 6.7 - - + +
64A VAL* 4.1 18.8 - - + +
67A LEU* 3.7 42.4 - - + -
68A TYR 5.4 0.2 - - - +
71A MSE 4.4 14.4 - - + -
92A ILE* 2.9 19.5 + - + +
93A GLU* 3.5 15.0 - - + +
95A ALA* 1.3 75.3 - - - +
97A TRP* 1.3 57.5 + - - +
99A LEU* 3.7 9.6 - - + +
100A ALA* 2.8 33.2 + - - +
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Residues in contact with TRP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG 5.7 0.9 - - - -
64A VAL* 3.3 36.8 - - + +
65A GLU* 4.8 12.3 - - + -
93A GLU* 2.7 51.8 + - - -
94A THR 3.3 8.1 - - - +
96A LEU* 1.3 76.9 - - - +
98A ASP* 1.3 62.3 + - - +
100A ALA* 3.9 1.8 - - - +
101A GLY* 3.0 21.1 + - - -
108A VAL* 3.9 16.2 - - + +
111A LEU* 3.7 54.6 - - + +
112A LEU* 4.1 16.6 - - + -
296A LEU* 3.9 25.5 - - + +
297A ALA* 3.7 21.2 - - + +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 5.7 0.2 + - - -
32A GLY* 3.3 4.6 - - - -
33A LEU* 2.5 36.8 + - - +
94A THR 2.8 12.7 + - - +
95A ALA 3.2 8.3 - - - +
97A TRP* 1.3 76.4 - - - +
99A LEU* 1.3 62.2 + - - +
101A GLY* 3.4 1.0 + - - -
102A LYS* 3.1 36.6 + - - +
108A VAL* 4.4 6.0 - - - +
374A GLY 2.8 24.6 - - - +
375A LEU* 3.3 25.5 - - + +
377A LEU* 5.5 2.2 + - - +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 5.0 0.2 - - + -
25A VAL* 3.7 28.9 - - + +
26A TRP 4.7 0.2 - - - -
27A ALA* 3.9 8.5 - - + -
30A GLU* 3.8 12.1 - - + -
31A HIS* 3.5 35.9 - - - +
32A GLY* 3.7 8.0 - - - -
61A PRO* 3.5 28.9 - - + -
95A ALA 2.7 19.5 + - - +
96A LEU* 3.7 6.1 - - + +
98A ASP* 1.3 70.9 - - - +
100A ALA* 1.3 60.5 + - - +
102A LYS* 3.3 3.1 + - - +
103A LEU* 2.8 56.9 + - + +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.9 18.8 - - - +
62A ARG* 4.0 9.6 - - - +
64A VAL* 4.6 6.3 - - + -
96A LEU 2.8 21.0 + - - +
97A TRP* 3.9 5.6 - - + +
99A LEU* 1.3 74.3 - - - +
101A GLY* 1.3 62.8 + - - +
103A LEU* 3.8 8.0 - - - +
104A GLN* 2.9 44.0 + - - +
111A LEU* 4.1 9.4 - - + -
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP 3.0 13.2 + - - -
98A ASP 3.8 2.7 - - - -
100A ALA* 1.3 78.6 - - - +
102A LYS* 1.3 51.2 + - - +
104A GLN* 3.6 0.8 - - - -
105A GLY 2.7 13.2 + - - -
106A VAL* 2.6 46.9 + - - -
108A VAL 5.1 0.2 - - - -
111A LEU* 3.7 15.2 - - - +
374A GLY* 3.8 7.1 + - - -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.9 24.1 + - - +
31A HIS* 2.6 54.6 + - - -
98A ASP* 3.1 35.5 + - - +
99A LEU* 3.8 3.1 - - - +
101A GLY* 1.3 72.8 - - - +
103A LEU* 1.3 66.7 + - - +
105A GLY* 3.0 12.6 + - - -
373A PRO* 3.8 30.6 - - + +
374A GLY* 4.1 3.8 - - - +
377A LEU 5.7 5.2 + - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.1 27.4 - - + -
27A ALA* 4.1 12.1 - - + +
30A GLU* 4.2 24.0 - - + +
61A PRO* 4.2 13.5 - - + -
62A ARG* 5.2 6.3 - - + -
99A LEU* 2.8 53.0 + - + +
100A ALA* 3.8 5.8 - - - +
102A LYS* 1.3 76.3 - - - +
104A GLN* 1.3 63.5 + - + +
105A GLY 3.5 0.2 + - - -
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Residues in contact with GLN 104 (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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62A ARG* 3.2 47.6 + - + +
100A ALA* 2.9 32.5 + - - +
101A GLY* 4.4 1.3 - - - +
103A LEU* 1.3 76.0 - - - +
105A GLY* 1.3 65.4 + - - +
106A VAL* 3.5 14.2 - - + +
111A LEU* 4.2 17.7 - - + +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY 2.7 9.1 + - - -
102A LYS 3.0 13.1 + - - -
103A LEU 3.2 0.6 + - - -
104A GLN* 1.3 80.7 - - - +
106A VAL* 1.3 65.1 + - - +
373A PRO* 3.8 14.6 - - - -
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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
------------------------------------------------------------
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