Contacts of the helix formed by residues 60 - 84 (chain B) in PDB entry 2OTM
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 THR 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.4 3.6 - - - +
56B GLY* 5.1 1.8 - - - +
59B TYR* 1.3 76.0 - - - +
61B VAL* 1.3 65.2 + - - +
62B SER* 3.3 14.9 + - - -
63B GLU* 3.1 32.2 + - - +
64B GLY 2.9 19.6 + - - -
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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
----------------------------------------------------------
55B LEU* 4.2 8.5 - - + -
56B GLY* 6.5 0.2 - - - -
60B THR* 1.3 74.8 - - - +
62B SER* 1.3 57.9 + - - +
64B GLY* 3.1 1.7 + - - -
65B TYR* 2.9 27.8 + - + +
105B CYS* 4.3 15.3 - - - -
107B GLU* 3.7 32.3 - - + +
110B LYS* 3.8 30.3 - - + -
111B ALA* 4.2 6.4 - - + +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.3 11.2 + - - -
61B VAL* 1.3 77.1 - - - +
63B GLU* 1.3 61.8 + - - +
65B TYR* 3.3 10.9 - - - +
66B ALA* 3.1 25.5 + - - +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.8 12.2 - - + -
58B ASP 4.2 2.1 - - - +
59B TYR* 3.4 29.1 - - + -
60B THR* 3.1 40.5 + - - +
62B SER* 1.3 77.4 + - - +
64B GLY* 1.3 58.8 + - - +
66B ALA* 3.2 8.7 + - - +
67B ALA* 2.8 28.6 + - - +
144B LEU* 4.9 1.3 - - - -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 20.6 - - - +
60B THR 2.9 11.9 + - - -
61B VAL 3.1 3.6 + - - -
63B GLU* 1.3 74.6 - - - +
65B TYR* 1.3 55.8 + - - +
67B ALA* 3.1 1.7 + - - +
68B CYS* 2.9 34.8 + - - -
99B LEU* 5.2 1.6 - - - -
111B ALA* 3.7 10.1 - - - -
144B LEU* 4.0 14.3 - - - +
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 2.9 14.2 + - + +
62B SER* 3.3 14.8 - - - +
63B GLU 3.3 0.2 - - - -
64B GLY* 1.3 76.7 - - - +
66B ALA* 1.3 61.6 + - + +
68B CYS 3.3 0.2 + - - -
69B ARG* 3.0 44.9 + - - +
110B LYS 3.4 13.5 - - - +
111B ALA* 3.4 14.9 - - - +
113B ASP* 3.6 5.4 - - + -
114B GLY* 3.3 34.3 - - - -
117B ASP* 2.6 40.3 + - - +
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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
----------------------------------------------------------
51B TYR* 3.5 19.0 + - - +
62B SER 3.1 10.7 + - - +
63B GLU* 3.4 11.0 - - - +
65B TYR* 1.3 83.2 - - + +
67B ALA* 1.3 57.8 + - - +
69B ARG* 3.3 10.6 + - - +
70B LEU* 2.9 29.3 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 3.5 8.0 - - - +
51B TYR* 3.6 36.1 - - + -
63B GLU 2.8 14.0 + - - +
64B GLY 3.1 8.3 + - - +
66B ALA* 1.3 76.8 - - - +
68B CYS* 1.3 58.1 + - - +
70B LEU 3.2 1.0 + - - -
71B ALA* 2.9 26.5 + - - +
144B LEU* 3.8 15.7 - - + -
145B CYS* 3.7 13.2 - - - -
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Residues in contact with CYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 2.9 16.8 + - - +
67B ALA* 1.3 73.1 - - - +
69B ARG* 1.3 58.7 + - - +
71B ALA* 3.9 2.8 - - - +
72B THR* 2.7 37.6 + - - -
99B LEU* 3.9 25.4 - - - -
111B ALA 3.4 26.0 - - - +
112B LEU* 4.0 14.6 - - + -
115B ALA* 3.8 17.9 - - + +
145B CYS* 4.1 18.8 - - - -
147B VAL* 4.2 3.8 - - + +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 4.7 4.2 + - - +
14B LEU* 3.6 32.8 - - + +
65B TYR* 3.0 39.4 + - - +
66B ALA* 3.5 9.9 - - - +
68B CYS* 1.3 77.6 - - - +
70B LEU* 1.3 56.2 + - - +
72B THR* 3.2 2.2 + - - -
73B LEU* 2.9 25.7 + - + +
114B GLY* 3.5 19.6 + - - +
117B ASP* 5.3 1.0 - - - +
118B LEU* 3.5 33.6 - - + +
121B GLU* 3.0 33.9 + - - -
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Residues in contact with LEU 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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17B PRO* 5.7 0.9 - - + -
43B PRO* 3.7 28.7 - - + +
44B TYR 3.5 23.1 - - - +
45B LEU* 4.0 15.3 - - + -
50B LEU* 3.7 27.8 - - + -
51B TYR* 4.1 5.4 - - + +
66B ALA 2.9 16.7 + - - +
67B ALA* 3.7 4.0 - - - +
69B ARG* 1.3 75.0 - - - +
71B ALA* 1.3 65.7 + - - +
73B LEU* 3.2 24.4 + - + +
74B ASN* 3.0 30.4 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 3.7 25.2 - - - +
42B PHE 3.5 20.0 - - - -
43B PRO* 3.8 2.6 - - - +
67B ALA 2.9 16.9 + - - +
68B CYS 3.9 0.9 - - - +
70B LEU* 1.3 74.4 - - - +
72B THR* 1.3 58.3 + - - +
74B ASN* 3.3 5.0 + - - +
75B ALA* 2.9 25.8 + - - +
145B CYS* 4.0 8.7 - - - -
147B VAL* 3.7 20.6 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B CYS 2.7 23.5 + - - -
69B ARG 3.6 4.5 - - - -
70B LEU 3.2 0.2 - - - -
71B ALA* 1.3 73.0 - - - +
73B LEU* 1.3 61.0 + - - +
75B ALA* 3.1 6.3 + - - +
76B ILE* 2.8 31.8 + - + +
115B ALA* 2.9 30.6 - - + +
118B LEU* 3.9 15.7 - - + -
119B LEU* 3.8 30.1 - - + -
147B VAL* 3.7 8.8 - - - +
149B LEU* 4.5 8.5 - - + -
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Residues in contact with LEU 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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9B LEU* 3.6 31.0 - - + -
14B LEU* 4.2 30.7 - - + -
15B GLU 3.6 20.6 - - - +
16B LEU* 3.6 18.4 - - + +
17B PRO* 3.9 12.7 - - + +
45B LEU* 6.4 0.9 - - + -
69B ARG* 2.9 13.3 + - + +
70B LEU* 3.2 26.0 + - + +
72B THR* 1.3 76.3 - - - +
74B ASN* 1.3 57.2 + - - +
76B ILE* 3.3 3.5 + - + -
77B ALA* 3.0 23.7 + - - +
118B LEU* 3.7 10.6 - - + +
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 3.5 25.8 - - - +
18B GLU 4.2 7.6 - - - +
19B VAL* 5.4 2.8 - - - +
20B ALA* 5.1 4.0 + - - +
41B GLN* 3.4 15.9 - - + +
42B PHE 3.2 22.1 + - - +
44B TYR* 3.0 43.7 + - - +
70B LEU* 3.0 26.5 + - - +
71B ALA 3.3 8.7 - - - +
73B LEU* 1.3 75.9 - - - +
75B ALA* 1.3 62.7 + - - +
77B ALA* 3.1 5.7 + - - +
78B GLN* 3.0 17.2 + - - +
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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
----------------------------------------------------------
38B THR* 4.5 1.9 - - - +
41B GLN* 3.6 27.3 + - + -
71B ALA 2.9 16.9 + - - +
72B THR* 3.1 11.4 + - - +
74B ASN* 1.3 72.4 - - - +
76B ILE* 1.3 57.9 + - - +
78B GLN* 3.1 4.9 + - - +
79B LEU* 3.0 30.7 + - - +
147B VAL* 4.3 4.7 - - + -
149B LEU* 3.5 31.2 - - + -
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Residues in contact with ILE 76 (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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9B LEU* 4.4 7.9 - - + -
16B LEU* 3.9 12.8 - - + -
72B THR* 2.8 32.5 + - + +
73B LEU* 3.6 7.0 - - - +
75B ALA* 1.3 69.8 - - - +
77B ALA* 1.3 60.4 + - - +
79B LEU* 3.1 8.4 + - + +
80B LYS* 2.9 28.1 + - - +
86B LEU* 3.6 26.4 - - + +
118B LEU* 3.9 26.5 - - + +
119B LEU* 4.5 3.8 - - + -
122B ILE* 4.5 11.9 - - + -
123B PHE* 4.0 30.1 - - + -
149B LEU* 4.5 7.4 - - + -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.7 18.5 - - + +
17B PRO* 3.3 36.1 - - + +
19B VAL* 3.7 14.0 - - + +
73B LEU 3.0 12.7 + - - +
74B ASN 3.1 9.8 + - - +
76B ILE* 1.3 76.4 - - - +
78B GLN* 1.3 61.7 + - - +
80B LYS* 3.3 3.4 + - - +
81B GLN* 3.0 22.9 + - - +
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Residues in contact with GLN 78 (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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19B VAL* 2.9 26.3 - - + +
20B ALA 4.6 1.2 - - - +
28B PRO* 3.2 31.7 - - - +
29B TYR* 3.4 18.1 - - + -
38B THR* 4.0 11.9 - - + -
41B GLN* 3.5 27.5 + - - +
74B ASN 3.0 11.0 + - - +
75B ALA 3.1 9.6 + - - +
77B ALA* 1.3 77.8 - - - +
79B LEU* 1.3 62.4 + - - +
81B GLN* 3.1 32.4 + - - +
82B ALA* 3.1 19.9 + - - +
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Residues in contact with LEU 79 (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 TYR* 6.1 0.4 - - + -
36B LEU* 3.9 29.3 - - + +
38B THR* 3.8 23.1 - - + -
75B ALA 3.0 14.8 + - - +
76B ILE* 3.1 10.5 + - - +
78B GLN* 1.3 75.8 - - - +
80B LYS* 1.3 58.2 + - - +
82B ALA* 3.1 6.8 + - - +
83B CYS* 2.9 32.2 + - - -
86B LEU* 4.0 10.1 - - + -
89B ILE* 4.0 11.9 - - + -
92B ILE* 3.6 31.0 - - + -
123B PHE* 4.7 4.7 - - + -
149B LEU* 3.8 22.9 - - + +
151B ALA* 4.5 7.4 - - + -
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Residues in contact with LYS 80 (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 GLU* 2.8 36.8 + - + +
16B LEU* 3.7 25.1 - - + -
76B ILE 2.9 16.4 + - - +
77B ALA 3.6 4.9 - - - +
78B GLN 3.3 0.4 - - - -
79B LEU* 1.3 78.7 - - - +
81B GLN* 1.3 57.5 + - - +
83B CYS* 4.5 2.7 - - - -
84B GLY* 2.8 55.6 + - - +
85B GLU* 4.3 7.3 + - - +
86B LEU* 3.6 16.7 - - + +
157B GOL 4.3 7.6 - - - -
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.9 25.5 - - + +
28B PRO* 5.0 4.9 - - - +
29B TYR* 4.1 13.6 + - + -
77B ALA 3.0 12.5 + - - +
78B GLN* 3.1 30.1 - - - +
80B LYS* 1.3 79.1 - - - +
82B ALA* 1.3 61.7 + - - +
84B GLY* 4.3 2.4 + - - -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 3.5 48.3 + - + -
31B ILE* 5.6 4.1 - - + +
36B LEU* 4.0 18.6 - - + -
78B GLN 3.1 10.3 + - - +
79B LEU* 3.5 8.7 - - + +
81B GLN* 1.3 79.5 - - - +
83B CYS* 1.3 59.1 + - - +
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.0 2.9 - - + -
79B LEU 2.9 27.4 + - - +
80B LYS* 4.5 0.4 - - - -
82B ALA* 1.3 79.2 - - + +
84B GLY* 1.3 57.9 + - - +
85B GLU 2.9 32.7 + - - +
86B LEU* 4.2 2.9 - - - -
88B ARG* 3.0 28.7 + - + -
89B ILE* 4.1 26.9 - - - -
153B LEU* 4.3 20.0 - - + -
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LYS* 2.8 54.8 + - - +
81B GLN 4.3 2.1 + - - -
82B ALA 3.7 1.2 - - - -
83B CYS* 1.3 69.4 - - - +
85B GLU* 1.3 59.0 + - - +
86B LEU 4.1 0.2 - - - -
88B ARG* 3.9 6.3 - - - -
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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