Contacts of the helix formed by residues 55 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU 4.0 0.2 + - - -
52B GLU* 3.4 18.0 + - - +
53B ILE 2.9 3.7 + - - +
54B THR* 1.3 76.2 - - - +
56B THR* 1.3 57.0 + - - +
57B ALA* 3.0 20.0 + - - +
58B VAL* 2.9 21.4 + - + +
59B ALA* 2.7 33.2 + - - +
121B ALA* 5.1 5.0 - - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.2 30.1 + - - +
54B THR 3.9 2.3 + - - -
55B ASP* 1.3 75.7 + - - +
57B ALA* 1.3 62.1 + - - +
58B VAL 3.0 1.4 + - - -
59B ALA 4.3 0.7 - - - +
60B GLN* 2.9 58.7 + - - +
117B GLY* 3.6 9.5 - - - +
120B MET* 4.7 3.8 - - + -
121B ALA* 5.3 8.0 - - - -
190B ALA* 3.8 16.3 + - - +
193B PHE* 3.6 25.9 - - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.7 12.0 - - + +
55B ASP* 3.0 16.5 + - - +
56B THR* 1.3 78.4 - - - +
58B VAL* 1.3 59.0 + - + +
61B PRO* 3.3 21.0 - - - +
114B ALA 4.6 4.0 - - - +
117B GLY 3.5 21.4 + - - +
118B ALA* 3.9 16.6 - - + +
121B ALA* 4.8 6.2 - - + +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.7 17.5 - - + -
41B LEU* 5.2 1.4 - - + +
44B LEU* 3.6 36.3 - - + -
52B GLU* 3.8 15.3 - - + +
53B ILE* 4.1 15.0 - - + +
55B ASP* 2.9 31.5 + - + +
57B ALA* 1.3 78.7 - - + +
59B ALA* 1.3 66.4 + - - +
60B GLN 3.3 1.6 - - - -
61B PRO* 3.2 14.7 - - - +
62B LEU* 3.3 17.3 - - + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.9 28.3 - - + +
12B GLN* 4.0 17.9 - - - +
53B ILE* 3.3 23.2 + - - +
54B THR* 5.0 0.2 - - - -
55B ASP 2.7 14.7 + - - +
56B THR 4.2 0.7 - - - +
58B VAL* 1.3 72.8 - - - +
60B GLN* 1.3 63.5 + - - +
62B LEU* 3.7 4.8 - - - +
63B ILE* 3.0 33.2 + - + +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.5 20.7 - - - +
56B THR* 2.9 35.0 + - - +
59B ALA* 1.3 77.4 - - - +
61B PRO* 1.4 68.4 - - + +
62B LEU 3.4 0.2 + - - -
63B ILE* 4.1 1.3 - - - +
64B VAL* 3.4 23.7 + - - +
92B VAL* 3.4 27.6 - - + +
113B ALA* 3.4 16.6 - - - +
116B ARG* 3.3 29.9 + - - +
117B GLY* 3.2 17.0 - - - -
120B MET* 3.2 21.7 - - - -
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 5.8 0.7 - - + -
39B LEU* 3.8 16.8 - - + -
41B LEU* 4.5 10.3 - - + -
57B ALA 3.3 21.8 - - - +
58B VAL 3.2 13.5 - - - +
60B GLN* 1.4 96.5 - - + +
62B LEU* 1.3 55.2 + - - +
64B VAL* 3.6 2.6 + - - +
65B ALA* 3.0 27.9 + - - +
110B VAL* 3.7 17.6 - - + +
113B ALA* 3.7 19.0 - - + +
114B ALA* 3.7 22.7 - - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 4.8 1.3 - - + -
16B MET* 3.5 32.6 - - + +
17B LEU* 4.0 14.3 - - + +
41B LEU* 4.0 23.6 - - + +
44B LEU* 4.0 14.1 - - + +
45B GLY* 3.8 26.7 - - - +
53B ILE* 3.3 35.0 - - + -
58B VAL* 3.3 19.8 + - + +
59B ALA 3.7 2.5 - - - +
60B GLN 3.2 0.4 - - - -
61B PRO* 1.3 76.9 - - - +
63B ILE* 1.3 59.5 + - - +
65B ALA* 3.3 5.0 + - - +
66B ALA* 3.0 24.4 + - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO 3.3 28.3 - - - +
8B GLY* 4.1 5.4 - - - +
9B GLN* 3.9 23.8 - - + +
12B GLN* 3.6 27.4 - - + +
16B MET* 3.7 10.8 - - + -
59B ALA* 3.0 29.8 + - + +
60B GLN* 4.1 4.3 - - - +
62B LEU* 1.3 73.1 - - + +
64B VAL* 1.3 70.2 + - + +
66B ALA* 3.2 4.2 + - - +
67B THR* 2.9 24.6 + - - +
92B VAL* 5.4 4.9 - - + -
93B GLY* 5.5 0.4 - - - +
270B PRO* 3.8 30.3 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN 3.4 16.9 + - - +
61B PRO 3.7 2.9 - - - +
62B LEU 3.3 0.4 - - - -
63B ILE* 1.3 77.9 - - + +
65B ALA* 1.3 54.4 + - - +
67B THR* 3.1 4.2 + - - -
68B LEU* 2.8 47.7 + - + +
92B VAL* 4.1 16.8 - - + +
93B GLY 5.3 0.4 - - - +
95B ILE* 4.3 1.6 - - + -
96B ALA* 4.0 30.7 - - + +
109B ALA* 4.3 3.6 - - + +
110B VAL* 3.8 33.9 - - + +
113B ALA* 3.7 15.5 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.7 11.7 - - + -
30B ILE* 5.3 4.3 - - + -
33B TRP* 3.9 28.2 - - + -
41B LEU* 5.3 6.7 - - + -
61B PRO 3.0 16.5 + - - +
62B LEU* 3.3 11.9 - - - +
64B VAL* 1.3 77.1 - - - +
66B ALA* 1.3 56.9 + - - +
68B LEU* 3.3 1.9 + - - +
69B LEU* 2.9 37.5 + - - +
110B VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B MET* 3.5 31.6 - - + +
17B LEU* 4.1 16.7 - - + +
20B TRP* 4.8 4.3 - - + -
62B LEU 3.0 5.6 + - - +
63B ILE 3.4 7.9 - - - +
65B ALA* 1.3 75.6 - - - +
67B THR* 1.3 62.1 + - - +
69B LEU* 3.7 3.6 + - - +
70B ALA* 3.3 16.3 + - - +
269B PRO* 3.3 34.8 - - + +
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Residues in contact with THR 67 (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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6B ALA* 3.7 15.2 - - + +
7B PRO* 3.5 13.3 + - - +
63B ILE* 2.9 12.6 + - - +
64B VAL 3.5 7.0 - - - -
66B ALA* 1.3 76.4 - - - +
68B LEU* 1.3 58.0 + - - +
70B ALA* 3.3 4.9 + - - +
71B HIS* 2.9 25.1 + - - +
96B ALA* 3.8 11.1 - - + +
100B ILE* 3.7 27.4 - - + -
268B PHE* 3.5 21.8 - - + +
269B PRO 2.8 22.2 + - - -
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Residues in contact with LEU 68 (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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33B TRP* 4.7 8.3 - - + -
64B VAL* 2.8 42.1 + - + +
65B ALA* 4.0 3.4 - - - +
67B THR* 1.3 70.9 - - - +
69B LEU* 1.3 59.2 + - - +
71B HIS* 3.2 6.5 + - + +
72B GLN* 2.9 38.6 + - + +
96B ALA* 3.5 28.9 - - + +
99B ALA* 3.7 11.0 - - + -
100B ILE* 4.1 13.7 - - + +
106B ALA* 3.9 39.3 - - + +
109B ALA* 4.1 8.3 - - + -
110B VAL* 4.1 4.7 - - + -
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Residues in contact with LEU 69 (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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17B LEU* 4.3 7.4 - - + -
20B TRP* 3.8 38.8 - - + +
23B LEU* 4.4 7.3 - - + +
26B ALA* 3.7 28.5 - - + +
29B GLN* 4.2 4.3 - - + +
30B ILE* 3.7 28.0 - - + -
33B TRP* 4.1 19.5 - - + -
65B ALA 2.9 19.5 + - - +
66B ALA 4.0 3.8 - - - +
68B LEU* 1.3 76.3 - - - +
70B ALA* 1.3 62.3 + - - +
72B GLN* 3.6 18.0 + - - +
73B GLU* 3.3 20.8 + - - +
76B ARG* 5.2 1.2 + - - -
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Residues in contact with ALA 70 (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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20B TRP* 3.7 27.1 - - + -
66B ALA 3.3 12.2 + - - +
67B THR 3.5 8.1 - - - +
68B LEU 3.2 0.4 - - - -
69B LEU* 1.3 78.0 - - - +
71B HIS* 1.3 64.7 + - - +
73B GLU* 3.3 4.7 + - - +
74B LEU* 3.1 21.7 + - - +
268B PHE* 3.6 11.4 - - + -
269B PRO* 3.6 23.6 - - + -
290B VAL* 4.7 1.1 - - + -
296B LEU* 4.2 4.5 - - + +
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Residues in contact with HIS 71 (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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4B LEU* 4.4 7.2 - - + -
67B THR 2.9 16.3 + - - +
68B LEU* 3.2 10.3 + - + +
70B ALA* 1.3 77.7 - - - +
72B GLN* 1.3 61.9 + - + +
74B LEU* 3.2 17.9 + - + +
75B ALA* 2.9 37.5 + - + +
99B ALA 5.3 0.7 - - - -
100B ILE* 3.5 60.8 + - + +
268B PHE* 3.8 16.9 - - + -
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Residues in contact with GLN 72 (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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29B GLN* 2.7 42.9 + - - -
33B TRP* 4.8 2.2 - - - -
68B LEU* 2.9 24.7 + - + +
69B LEU* 3.8 12.6 - - - +
70B ALA 3.3 0.2 - - - -
71B HIS* 1.3 81.0 - - + +
73B GLU* 1.3 57.3 + - - +
75B ALA* 3.4 7.5 + - - +
76B ARG* 3.0 51.1 + - - +
106B ALA* 3.8 21.8 - - - +
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Residues in contact with GLU 73 (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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20B TRP* 4.8 3.1 - - + -
23B LEU* 3.6 30.3 - - + +
24B PRO* 4.9 1.6 - - - +
69B LEU 3.3 12.0 + - - +
70B ALA* 3.5 10.8 - - - +
71B HIS 3.2 0.2 - - - -
72B GLN* 1.3 77.4 - - - +
74B LEU* 1.3 63.1 + - - +
76B ARG* 2.5 41.4 + - - +
77B ARG* 3.2 52.7 + - - +
293B PRO* 5.0 2.0 - - + -
296B LEU* 3.7 18.8 - - + -
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Residues in contact with LEU 74 (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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4B LEU* 4.3 18.6 - - + -
70B ALA 3.1 13.1 + - - +
71B HIS* 3.2 19.9 + - + +
73B GLU* 1.3 76.9 - - - +
75B ALA* 1.3 63.1 + - - +
77B ARG* 3.4 6.4 + - - +
78B CYS 3.4 14.7 + - - -
79B VAL* 3.8 27.1 + - + -
80B LEU* 5.1 12.4 + - + +
266B VAL* 5.3 2.5 - - + -
268B PHE* 3.7 26.0 - - + -
296B LEU* 3.8 18.3 - - + +
299B LEU* 3.8 29.6 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 2.9 29.0 + - + +
72B GLN* 3.7 7.9 - - - +
73B GLU 3.3 0.2 - - - -
74B LEU* 1.3 76.4 - - - +
76B ARG* 1.3 64.4 + - - +
78B CYS* 3.1 17.6 + - - +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.3 9.5 - - - +
24B PRO* 4.4 24.9 + - - +
29B GLN* 5.3 2.2 - - - +
69B LEU 5.2 0.8 + - - -
72B GLN* 3.0 49.6 + - - +
73B GLU* 2.5 40.1 + - - +
74B LEU 3.4 0.2 - - - -
75B ALA* 1.3 76.9 - - - +
77B ARG* 1.3 61.0 + - + +
78B CYS* 3.3 10.6 + - - -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 6.2 0.2 - - - +
73B GLU* 3.2 41.1 + - - +
74B LEU* 3.9 7.0 - - - +
75B ALA 3.3 0.8 - - - -
76B ARG* 1.3 75.4 - - + +
78B CYS* 1.3 69.3 + - - +
79B VAL* 3.3 16.5 + - + +
293B PRO* 3.8 22.8 + - - +
294B ALA* 5.3 0.4 - - - +
296B LEU* 3.7 31.8 + - - +
297B ASP* 2.8 31.3 + - - +
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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