Contacts of the helix formed by residues 46 - 74 (chain B) in PDB entry 2J3R
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 SER 46 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.1 10.3 - - - +
45B TYR* 1.3 80.6 - - - +
47B VAL* 1.3 67.1 + - - +
48B SER* 3.1 19.5 + - - -
49B GLU* 3.1 18.1 + - - +
50B LEU 3.0 17.0 + - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 1.3 71.3 + - - +
48B SER* 1.3 67.7 + - - +
50B LEU* 3.0 17.7 + - + +
51B GLN* 3.0 44.9 + - + +
136B THR* 6.4 1.6 - - - -
138B ASN* 5.0 5.2 - - - +
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.1 12.8 + - - -
47B VAL* 1.3 80.2 - - - +
49B GLU* 1.3 60.9 + - - +
51B GLN* 3.6 11.2 + - - +
52B ALA* 3.2 19.4 + - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG 5.3 0.3 - - - +
44B VAL* 3.4 24.0 - - + +
45B TYR* 3.4 38.6 + - - +
46B SER* 3.1 15.7 + - - +
48B SER* 1.3 77.4 - - - +
50B LEU* 1.3 65.9 + - - +
52B ALA* 3.2 8.0 + - + +
53B ARG* 3.0 21.1 + - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.7 22.0 - - + +
40B CYS* 3.2 32.1 - - + -
41B GLN* 3.8 30.1 - - + +
44B VAL* 3.8 12.1 - - + +
46B SER 3.0 12.8 + - - +
47B VAL* 3.3 21.5 - - + +
49B GLU* 1.3 76.4 - - - +
51B GLN* 1.3 57.4 + - - +
53B ARG* 3.2 5.0 + - - +
54B LEU* 3.0 34.9 + - + +
138B ASN* 4.0 17.7 - - - +
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.0 32.5 + - + +
48B SER* 3.8 8.6 - - - +
50B LEU* 1.3 74.9 - - - +
52B ALA* 1.3 57.5 + - - +
54B LEU* 3.3 5.1 + - - -
55B ALA* 2.8 30.9 + - - +
136B THR* 5.7 0.3 - - - -
137B LEU* 3.6 33.9 + - - +
138B ASN* 3.8 16.3 - - - +
141B ALA* 3.4 19.7 - - + +
162B VAL* 4.1 20.2 + - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER 3.2 11.3 + - - +
49B GLU* 3.2 13.1 + - + +
50B LEU 3.2 0.4 - - - -
51B GLN* 1.3 78.6 - - - +
53B ARG* 1.3 59.2 + - + +
55B ALA* 3.4 8.0 + - - +
56B ASP* 2.9 34.0 + - - +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 4.2 8.8 + - - +
33A ASP* 3.7 23.4 + - - -
39B TYR* 4.5 6.3 - - - -
40B CYS* 4.0 27.7 - - + -
43B ARG* 3.2 51.8 + - - +
44B VAL* 3.8 20.3 - - + +
49B GLU 3.0 12.7 + - - +
50B LEU 3.2 8.9 + - - +
52B ALA* 1.3 75.8 - - + +
54B LEU* 1.3 64.9 + - - +
56B ASP* 3.0 23.2 + - - +
57B MET* 3.0 19.7 + - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 4.2 19.3 - - + -
36B MET* 4.5 3.6 - - + +
37B VAL* 4.3 16.2 - - + +
40B CYS* 4.0 17.3 - - - -
50B LEU* 3.0 29.5 + - + +
51B GLN* 3.6 8.3 - - - +
53B ARG* 1.3 74.4 - - - +
55B ALA* 1.3 64.6 + - - +
57B MET* 3.1 14.5 + - - +
58B GLY 3.0 17.8 + - - -
138B ASN* 3.5 48.0 - - + +
142B PHE* 3.3 25.3 - - + +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN 2.8 18.2 + - - +
52B ALA* 3.6 9.0 - - - +
54B LEU* 1.3 76.0 - - - +
56B ASP* 1.3 59.0 + - - +
58B GLY 3.3 0.9 + - - -
59B GLN* 3.0 33.2 + - - +
141B ALA* 3.4 25.5 + - + +
142B PHE* 4.1 1.1 - - - +
144B GLY 5.3 0.2 - - - -
145B GLY* 3.3 14.6 - - - +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 4.2 19.5 + - - +
32A LYS* 5.7 1.0 + - - -
52B ALA* 2.9 20.3 + - - +
53B ARG* 3.0 19.5 + - + +
55B ALA* 1.3 74.9 - - - +
57B MET* 1.3 66.8 + - - +
58B GLY 3.2 0.2 + - - -
59B GLN* 3.2 16.2 + - - +
60B GLY* 3.1 18.9 + - - -
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Residues in contact with MET 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.4 24.7 - - + +
26A LEU* 3.8 31.2 - - + -
29A GLN* 3.2 39.0 - - + -
36B MET* 3.8 22.0 - - + -
39B TYR* 4.2 18.2 - - + -
40B CYS* 3.7 22.9 - - - -
53B ARG* 3.0 14.4 + - - +
54B LEU* 3.1 17.2 + - - +
56B ASP* 1.3 76.1 - - - +
58B GLY* 1.3 62.1 + - - +
60B GLY* 3.3 9.8 + - - -
61B VAL 3.8 4.0 + - - -
142B PHE* 3.9 11.9 - - + -
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU 3.0 9.9 + - - -
55B ALA 3.6 1.1 - - - -
56B ASP 3.1 0.4 - - - -
57B MET* 1.3 77.6 - - - +
59B GLN* 1.3 61.2 + - - +
61B VAL* 3.2 5.9 + - - +
62B GLY 3.1 17.2 + - - -
142B PHE* 3.5 36.0 - - - -
146B ILE* 3.5 20.3 - - - +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 3.0 25.3 + - - +
56B ASP* 3.2 16.0 + - - +
58B GLY* 1.3 75.0 - - - +
60B GLY* 1.3 62.6 - - - +
61B VAL 3.3 0.7 + - - -
62B GLY 3.5 1.1 + - - -
63B ALA* 4.5 1.9 + - - +
145B GLY* 2.9 28.0 + - - +
148B GLU* 2.9 37.5 + - + +
149B ALA* 3.3 25.9 + - + +
152B THR* 5.5 1.9 + - - +
153B HIS* 5.5 2.3 + - - -
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.8 12.8 - - - +
32A LYS* 4.8 15.7 - - - -
56B ASP 3.1 12.8 + - - -
57B MET* 3.3 5.8 + - - -
58B GLY 3.1 1.0 - - - -
59B GLN* 1.3 78.3 - - - +
61B VAL* 1.3 63.1 + - - +
63B ALA* 5.1 4.2 + - - +
64B SER* 5.5 0.9 + - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.5 39.0 - - + +
24A GLY 3.9 6.7 - - - +
25A ALA* 3.6 37.5 - - + +
28A THR* 4.4 5.6 - - - +
116A VAL* 3.9 17.7 - - + -
57B MET 3.9 6.5 - - - +
58B GLY* 3.5 13.9 - - - +
60B GLY* 1.3 79.1 - - - +
62B GLY* 1.3 66.1 + - - +
63B ALA 3.2 2.7 - - - -
64B SER* 3.2 18.7 + - - +
65B LEU* 3.3 8.0 + - - +
142B PHE* 5.1 0.4 - - + -
146B ILE* 4.6 2.5 - - + -
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Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 3.1 11.3 + - - -
59B GLN 3.5 3.4 + - - -
61B VAL* 1.3 75.9 - - - +
63B ALA* 1.3 63.0 + - - +
65B LEU* 3.1 5.1 + - - +
66B LEU 3.0 17.3 + - - -
146B ILE* 3.8 22.9 - - - -
149B ALA* 3.6 19.1 - - - -
150B ILE* 3.5 12.7 - - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN 4.5 1.9 + - - +
60B GLY 5.5 3.6 - - - +
61B VAL 3.2 0.8 - - - -
62B GLY* 1.3 76.4 - - - +
64B SER* 1.3 62.1 + - - +
66B LEU* 3.0 17.9 + - + +
67B ASP* 3.0 23.3 + - - +
78B ARG* 6.2 1.3 - - - +
149B ALA* 3.9 6.8 - - - +
153B HIS* 3.9 39.5 - - + +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 4.0 21.7 + - - -
116A VAL* 4.2 22.3 - - - +
117A GLU 4.4 8.0 + - - -
60B GLY 5.5 0.5 + - - -
61B VAL* 3.2 15.9 + - - +
63B ALA* 1.3 77.8 - - - +
65B LEU* 1.3 62.2 + - - +
67B ASP* 3.4 6.7 + - - +
68B VAL* 3.1 30.9 + - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 4.9 6.1 - - + +
21A LEU* 4.6 11.7 - - + -
115A PHE* 4.3 22.4 - - + -
61B VAL 3.3 6.8 + - - +
62B GLY* 3.1 10.4 + - - +
64B SER* 1.3 77.7 - - - +
66B LEU* 1.3 64.9 + - - +
68B VAL* 4.6 3.8 - - + +
69B LEU* 3.1 48.9 + - + +
93B VAL* 4.0 20.0 - - + +
96B ALA* 4.7 7.4 - - + -
97B LEU* 3.9 34.8 - - + -
146B ILE* 4.1 12.3 - - + -
150B ILE* 4.1 4.0 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 3.0 13.2 + - - +
63B ALA* 3.0 11.2 + - - +
65B LEU* 1.3 77.5 - - - +
67B ASP* 1.3 58.6 + - - +
69B LEU* 4.1 0.5 - - - +
70B VAL* 2.9 49.1 + - + +
78B ARG* 3.6 37.9 - - + +
85B ILE* 5.6 1.3 - - + -
88B PHE* 3.7 22.7 - - + -
150B ILE* 4.0 24.6 - - + +
153B HIS* 4.2 10.5 - - + +
154B SER* 3.4 27.6 - - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 3.0 21.0 + - - +
64B SER* 4.0 6.5 - - - +
66B LEU* 1.3 74.4 - - - +
68B VAL* 1.3 65.4 + - + +
70B VAL* 4.5 3.4 - - - -
71B MET* 3.1 35.3 + - + +
78B ARG* 2.7 32.4 + - - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 5.0 0.7 - - - +
115A PHE* 3.5 44.2 - - + +
64B SER 3.1 19.0 + - - +
65B LEU* 4.2 5.6 - - + +
67B ASP* 1.3 77.3 - - + +
69B LEU* 1.3 60.6 + - + +
71B MET* 4.5 2.7 - - - +
72B ARG* 3.0 62.4 + - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 5.7 0.2 - - - +
65B LEU* 3.1 35.8 + - + +
68B VAL* 1.3 73.9 - - + +
70B VAL* 1.3 59.3 + - - +
72B ARG* 3.5 27.1 - - - +
73B GLU* 2.7 55.0 + - - +
74B LYS* 3.5 1.4 + - - +
88B PHE* 3.5 18.6 - - + -
92B ASN 3.7 7.6 - - - +
93B VAL* 3.7 42.8 - - + +
96B ALA* 3.8 17.5 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 2.9 43.4 + - + +
67B ASP* 3.9 5.4 - - - +
69B LEU* 1.3 77.2 - - - +
71B MET* 1.3 63.8 + - + +
74B LYS* 2.8 30.9 + - + -
76B GLY* 3.0 41.0 + - - +
77B LYS 3.6 15.0 - - - +
78B ARG* 4.2 21.1 - - + +
88B PHE* 4.1 8.7 - - + -
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 3.1 22.4 + - + +
68B VAL* 4.5 2.5 - - - +
70B VAL* 1.3 80.4 - - + +
72B ARG* 1.3 60.2 + - - +
75B ASN* 4.7 4.5 + - - -
76B GLY* 3.1 43.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.2 35.6 + - - +
115A PHE* 5.2 0.8 - - - -
21B LYS* 6.6 0.7 - - - +
68B VAL* 3.0 44.1 + - + +
69B LEU* 3.5 21.5 - - - +
71B MET* 1.3 80.0 - - + +
73B GLU* 1.3 80.9 + - + +
74B LYS 3.8 0.2 - - - -
75B ASN 5.1 0.7 - - - -
96B ALA* 4.8 6.1 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 2.7 47.2 + - - +
72B ARG* 1.3 101.5 + - - +
74B LYS* 1.3 68.6 + - + +
75B ASN* 3.7 5.7 - - - +
92B ASN* 3.3 34.4 - - - +
96B ALA* 5.5 1.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 3.5 0.9 + - - +
70B VAL* 2.8 17.7 + - + +
73B GLU* 1.3 86.3 - - - +
75B ASN* 1.3 61.5 + - - +
76B GLY 2.8 15.7 + - - -
77B LYS* 2.9 31.6 + - - +
79B GLU* 3.7 23.7 + - + +
84B ASN 5.9 0.4 + - - -
88B PHE* 4.0 25.8 - - + -
92B ASN* 4.0 26.4 - - - +
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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