Contacts of the helix formed by residues 55 - 77 (chain A) in PDB entry 2QJ3
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 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU 4.6 0.7 - - - +
52A GLU* 3.8 18.3 - - - +
53A ILE 2.8 4.4 + - - -
54A THR* 1.3 74.6 - - - +
56A THR* 1.3 58.4 + - - +
57A ALA* 3.6 16.4 + - - +
58A VAL* 2.7 46.5 + - - +
59A ALA* 2.8 12.0 + - - +
190A ALA* 6.4 0.9 - - - -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.1 34.8 + - - +
55A ASP* 1.3 73.2 + - - +
57A ALA* 1.3 61.2 + - - +
59A ALA* 4.0 1.8 - - - -
60A GLN* 3.1 61.1 + - - +
117A GLY* 3.8 9.4 - - - +
120A MET* 4.9 3.1 - - + -
121A ALA* 5.4 7.1 - - - +
124A CYS* 5.5 1.2 - - - -
190A ALA* 4.3 15.2 + - - +
193A PHE* 3.6 26.6 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.1 25.5 - - + +
55A ASP* 2.8 16.1 + - - +
56A THR* 1.3 77.3 - - - +
58A VAL* 1.3 58.6 + - + +
61A PRO* 3.6 10.5 - - - +
114A ALA 4.6 3.8 - - - +
117A GLY* 3.8 14.9 + - - +
118A ALA* 4.1 20.6 - - + +
121A ALA* 4.8 7.3 - - + +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.6 10.5 - - + -
41A LEU* 6.0 0.3 - - - +
44A LEU* 3.9 37.0 - - + -
52A GLU 3.5 21.3 - - - +
53A ILE* 4.0 10.8 - - - -
55A ASP* 2.7 28.1 + - - +
57A ALA* 1.3 74.9 - - + +
59A ALA* 1.3 66.6 + - - +
60A GLN 3.3 1.7 + - - -
61A PRO* 3.4 6.6 - - - +
62A LEU* 3.2 30.2 + - + +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.7 21.8 - - - +
12A GLN* 4.4 16.1 - - - +
53A ILE* 3.2 24.4 + - - +
54A THR* 5.0 0.2 - - - -
55A ASP 2.8 16.2 + - - +
56A THR* 3.9 3.1 - - - +
58A VAL* 1.3 74.3 - - - +
60A GLN* 1.3 58.1 + - - +
62A LEU* 3.2 5.3 + - - +
63A ILE* 2.9 37.9 + - + +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.9 5.7 - - - +
56A THR* 3.1 41.3 + - + +
59A ALA* 1.3 77.9 - - - +
61A PRO* 1.4 75.0 - - + +
62A LEU 3.2 0.5 + - - -
63A ILE* 3.3 5.6 + - - +
64A VAL* 3.3 23.0 + - - +
92A VAL* 3.4 31.1 - - + +
113A ALA* 3.5 10.8 - - - +
116A ARG* 3.2 31.1 + - - +
117A GLY* 3.4 15.0 - - - -
120A MET* 3.3 25.7 - - - -
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Residues in contact with PRO 61 (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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37A ALA* 5.1 0.9 - - + -
39A LEU* 4.2 9.0 - - + -
41A LEU* 4.8 11.4 - - + -
57A ALA 3.6 19.5 - - - +
58A VAL* 3.4 12.3 - - - +
60A GLN* 1.4 93.8 - - + +
62A LEU* 1.3 49.0 + - - +
64A VAL* 3.1 4.0 + - - +
65A ALA* 2.7 35.9 + - - +
110A VAL* 3.9 29.6 - - + +
113A ALA* 3.6 21.1 - - + +
114A ALA* 3.9 14.1 - - + +
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Residues in contact with LEU 62 (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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12A GLN* 5.6 0.4 - - + -
16A MET* 3.3 27.0 - - + +
17A LEU* 3.8 28.4 - - + +
41A LEU* 4.2 24.2 - - + +
44A LEU* 3.5 27.8 - - + +
45A GLY* 4.4 0.2 - - - -
53A ILE* 3.8 32.1 - - + -
58A VAL* 3.2 23.8 + - + +
59A ALA 3.2 3.8 + - - +
60A GLN 3.1 1.0 - - - -
61A PRO* 1.3 79.1 - - - +
63A ILE* 1.3 62.4 + - + +
65A ALA* 3.4 6.1 + - + +
66A ALA* 3.2 17.5 + - - +
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Residues in contact with ILE 63 (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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7A PRO* 3.6 27.1 - - + +
8A GLY 3.2 25.4 - - - +
9A GLN* 3.7 18.2 - - + -
12A GLN* 3.7 30.3 - - + +
16A MET* 3.8 5.6 - - - -
59A ALA 2.9 22.5 + - - +
60A GLN* 3.3 5.6 + - - +
62A LEU* 1.3 75.1 - - - +
64A VAL* 1.3 68.2 + - + +
66A ALA* 3.2 5.7 + - - +
67A THR* 3.0 25.7 + - - +
92A VAL* 5.4 4.7 - - + -
93A GLY* 5.4 1.1 - - - +
269A PRO 3.7 1.0 - - - +
270A PRO* 4.0 25.1 - - + -
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Residues in contact with VAL 64 (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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60A GLN 3.3 13.9 + - - +
61A PRO 3.1 7.1 + - - +
63A ILE* 1.3 75.8 - - + +
65A ALA* 1.3 66.5 + - - +
67A THR* 3.2 1.8 + - - -
68A LEU* 3.0 44.7 + - + +
92A VAL* 4.0 17.0 - - + +
93A GLY* 5.3 0.2 - - - -
95A ILE* 4.2 18.4 - - + -
96A ALA* 3.9 26.7 - - + +
110A VAL* 4.4 15.3 - - + +
113A ALA* 3.8 17.0 - - + -
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Residues in contact with ALA 65 (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 LEU* 5.0 5.8 - - + -
30A ILE* 5.1 4.7 - - + -
33A TRP* 3.9 18.9 - - + -
41A LEU* 3.9 25.8 - - + -
61A PRO 2.7 19.1 + - - +
62A LEU* 3.4 12.1 - - + +
64A VAL* 1.3 75.7 - - - +
66A ALA* 1.3 61.8 + - - +
69A LEU* 3.1 30.5 + - - +
110A VAL* 4.5 5.6 - - + +
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Residues in contact with ALA 66 (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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16A MET* 3.7 29.2 - - + +
17A LEU* 3.8 20.6 - - + +
20A TRP* 5.0 4.0 + - + -
62A LEU 3.2 2.4 + - - +
63A ILE 3.6 7.2 - - - +
65A ALA* 1.3 77.8 - - - +
67A THR* 1.3 64.0 + - - +
69A LEU* 3.7 4.5 + - - +
70A ALA* 3.2 22.9 + - - +
269A PRO* 3.4 23.7 - - + +
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Residues in contact with THR 67 (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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6A ALA* 4.1 7.4 - - + -
7A PRO* 3.3 16.1 + - - +
63A ILE* 3.0 13.2 + - - +
64A VAL 3.2 6.9 + - - -
66A ALA* 1.3 75.4 - - - +
68A LEU* 1.3 58.8 + - - +
70A ALA* 3.2 4.9 + - - +
71A HIS* 2.9 26.2 + - - +
96A ALA* 3.8 24.9 - - + +
100A ILE* 4.0 11.0 - - + -
268A PHE* 3.5 32.6 - - + +
269A PRO 3.0 17.2 + - - -
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Residues in contact with LEU 68 (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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33A TRP* 4.2 11.4 - - + -
64A VAL* 3.0 37.9 + - + +
65A ALA 4.1 1.8 - - - +
67A THR* 1.3 73.2 - - - +
69A LEU* 1.3 54.8 + - - +
70A ALA 3.0 1.8 - - - -
71A HIS* 3.8 7.3 - - + +
72A GLN* 2.7 41.6 + - - +
96A ALA* 3.5 28.3 - - + +
99A ALA* 3.7 23.3 - - + -
100A ILE* 3.9 13.9 - - + +
106A ALA* 3.8 31.9 - - + +
109A ALA* 4.2 1.6 - - + -
110A VAL* 4.5 5.2 - - + -
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Residues in contact with LEU 69 (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 LEU* 4.0 17.3 - - + -
20A TRP* 4.2 26.6 - - + -
21A LEU* 5.0 2.0 - - + -
26A ALA* 4.1 33.4 - - + +
29A GLN* 4.7 2.9 - - + -
30A ILE* 3.6 29.6 - - + -
33A TRP* 4.0 21.2 - - + -
65A ALA 3.1 20.0 + - - +
66A ALA 4.0 4.0 - - - +
68A LEU* 1.3 77.1 - - - +
70A ALA* 1.3 59.8 + - - +
72A GLN* 3.6 16.2 - - - +
73A GLU* 3.4 20.6 + - - +
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Residues in contact with ALA 70 (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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20A TRP* 3.7 23.1 - - + -
66A ALA 3.2 11.8 + - - +
67A THR 3.2 9.3 + - - +
68A LEU 3.0 0.4 - - - -
69A LEU* 1.3 77.8 - - - +
71A HIS* 1.3 65.3 + - - +
73A GLU* 3.4 2.1 + - - +
74A LEU* 3.2 19.6 + - - +
268A PHE* 3.7 9.5 - - + -
269A PRO* 3.4 26.7 - - + -
290A VAL* 4.7 1.6 - - + -
296A LEU* 3.7 9.4 - - - +
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Residues in contact with HIS 71 (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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4A LEU* 4.6 6.4 - - + +
67A THR 2.9 15.3 + - - +
68A LEU* 3.8 10.3 - - + +
70A ALA* 1.3 72.3 - - - +
72A GLN* 1.3 65.4 - - - +
74A LEU* 2.9 7.2 + - - +
75A ALA* 2.8 45.5 + - + +
80A LEU* 5.2 6.5 - - + -
99A ALA 5.4 0.6 + - - -
100A ILE* 3.5 54.8 + - + +
268A PHE* 3.7 26.7 - - + -
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Residues in contact with GLN 72 (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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25A GLY 6.0 0.2 - - - -
26A ALA* 5.9 0.3 - - - -
29A GLN* 3.2 43.3 + - - +
33A TRP* 3.9 16.4 - - - -
68A LEU* 2.7 23.5 + - - +
69A LEU* 3.6 17.7 - - - +
70A ALA 3.3 0.2 - - - -
71A HIS* 1.3 78.9 - - + +
73A GLU* 1.3 56.9 + - - +
75A ALA* 3.7 4.8 + - - +
76A ARG* 3.1 26.9 + - - +
106A ALA* 4.2 12.1 - - - +
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Residues in contact with GLU 73 (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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20A TRP* 4.2 11.9 - - + -
23A LEU* 4.5 17.3 - - + +
69A LEU 3.4 11.1 + - - +
70A ALA 3.8 7.4 - - - +
71A HIS 3.1 0.4 - - - -
72A GLN* 1.3 77.7 - - - +
74A LEU* 1.3 59.2 + - - +
76A ARG* 3.4 40.2 + - - -
77A ARG* 2.9 62.6 + - - +
296A LEU* 3.9 11.9 - - + -
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Residues in contact with LEU 74 (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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4A LEU* 4.4 7.9 - - + -
70A ALA 3.2 13.1 + - - +
71A HIS* 2.9 11.3 + - - +
73A GLU* 1.3 73.6 - - - +
75A ALA* 1.3 67.5 + - - +
77A ARG* 3.3 10.9 + - - +
78A CYS 3.4 6.6 + - - -
79A VAL* 3.6 36.9 + - + -
80A LEU* 4.3 30.1 + - + -
266A VAL* 4.6 5.8 - - + -
268A PHE* 3.8 29.2 - - + -
296A LEU* 3.9 27.5 - - + +
299A LEU* 4.4 8.5 - - + -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 2.8 35.8 + - + +
72A GLN* 3.8 6.5 - - - +
74A LEU* 1.3 73.5 - - - +
76A ARG* 1.3 53.9 + - - +
78A CYS* 2.7 32.4 + - - +
80A LEU* 5.8 5.2 - - - -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 5.2 12.5 - - - +
72A GLN 3.1 17.2 + - - +
73A GLU* 3.4 37.5 + - - +
75A ALA* 1.3 78.5 - - - +
77A ARG* 1.3 73.5 + - - +
78A CYS* 3.4 3.5 + - - +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.5 3.0 - - - +
73A GLU* 2.9 46.4 + - - +
74A LEU* 3.7 7.2 - - + +
75A ALA 3.0 0.6 + - - -
76A ARG* 1.3 85.0 - - - +
78A CYS* 1.3 71.2 + - - +
79A VAL* 3.2 17.2 + - + +
293A PRO* 3.4 29.2 + - - +
296A LEU* 3.3 36.7 + - - +
297A ASP* 2.7 34.9 + - - +
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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