Contacts of the helix formed by residues 60 - 84 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.4 4.1 - - - +
56A GLY* 5.3 1.8 - - - -
59A TYR* 1.3 76.5 - - - +
61A VAL* 1.3 66.0 + - - +
62A SER* 3.3 11.0 + - - -
63A GLU* 3.0 34.1 + - - +
64A GLY 2.9 19.4 + - - -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.3 9.0 - - + -
60A THR* 1.3 73.4 - - - +
62A SER* 1.3 58.5 + - - +
64A GLY* 3.1 1.7 + - - -
65A TYR* 2.9 27.7 + - + +
105A CYS* 4.4 14.6 - - - -
107A GLU* 3.7 30.5 - - + +
110A LYS* 3.7 37.7 - - + +
111A ALA* 4.2 5.2 - - + +
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.3 10.8 + - - -
61A VAL* 1.3 79.3 - - - +
63A GLU* 1.3 61.6 + - - +
65A TYR* 3.4 10.4 - - - +
66A ALA* 3.0 25.8 + - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.6 12.7 - - + +
58A ASP 4.1 2.9 - - - +
59A TYR* 3.3 30.2 - - + -
60A THR* 3.0 42.0 + - - +
62A SER* 1.3 78.8 + - - +
64A GLY* 1.3 59.8 + - - +
66A ALA* 3.2 8.5 + - - +
67A ALA* 2.8 28.4 + - - +
144A LEU* 4.7 1.3 - - - -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.7 21.0 - - - +
60A THR 2.9 11.3 + - - -
61A VAL 3.1 4.0 + - - -
63A GLU* 1.3 77.0 - - - +
65A TYR* 1.3 55.4 + - - +
67A ALA* 3.2 1.9 + - - +
68A CYS* 2.9 35.0 + - - -
99A LEU* 5.1 1.1 - - - -
111A ALA* 3.7 10.3 - - - -
144A LEU* 3.9 13.4 - - - +
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 2.9 12.9 + - + +
62A SER* 3.4 14.8 - - - +
64A GLY* 1.3 74.6 - - - +
66A ALA* 1.3 61.2 + - + +
68A CYS 3.3 1.0 + - - -
69A ARG* 2.9 47.6 + - - +
110A LYS 3.5 15.3 - - - +
111A ALA* 3.4 12.8 - - - +
113A ASP* 3.6 5.2 - - + -
114A GLY* 3.4 31.6 + - - -
117A ASP* 2.6 39.2 + - - +
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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
----------------------------------------------------------
51A TYR* 3.4 21.9 + - - +
62A SER 3.0 14.4 + - - +
63A GLU* 3.5 9.0 - - - +
65A TYR* 1.3 79.7 - - + +
67A ALA* 1.3 56.6 - - - +
69A ARG* 3.4 10.6 + - - +
70A LEU* 3.0 28.9 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.5 8.6 - - + +
51A TYR* 3.5 38.3 - - + -
63A GLU 2.8 13.7 + - - +
64A GLY 3.2 7.6 + - - +
66A ALA* 1.3 76.6 - - - +
68A CYS* 1.3 56.6 + - - +
70A LEU* 3.2 1.1 + - - -
71A ALA* 2.8 27.2 + - - +
144A LEU* 3.7 15.3 - - + -
145A CYS* 3.7 14.4 - - + -
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Residues in contact with CYS 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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64A GLY 2.9 16.6 + - - +
65A TYR 3.9 0.2 - - - +
67A ALA* 1.3 73.3 - - - +
69A ARG* 1.3 57.6 + - - +
71A ALA* 3.9 2.6 - - - +
72A THR* 2.7 38.7 + - - -
99A LEU* 3.9 22.2 - - - -
111A ALA 3.4 30.1 - - - +
112A LEU* 3.9 15.3 - - + -
115A ALA* 3.8 17.2 - - + +
145A CYS* 4.0 16.8 - - - -
147A VAL* 4.2 3.4 - - + +
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Residues in contact with ARG 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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12A ALA* 4.8 3.4 + - - +
14A LEU* 3.7 30.6 - - + +
65A TYR* 2.9 39.6 + - - +
66A ALA* 3.4 8.7 - - - +
68A CYS* 1.3 76.7 - - - +
70A LEU* 1.3 58.5 + - - +
72A THR* 3.3 2.3 + - - -
73A LEU* 2.9 25.1 + - + +
114A GLY* 3.5 19.8 + - - +
117A ASP* 5.3 0.6 - - - +
118A LEU* 3.5 31.0 - - + +
121A GLU* 3.0 38.2 + - - -
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Residues in contact with LEU 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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17A PRO* 5.5 1.6 - - + -
43A PRO* 3.6 29.8 - - + +
44A TYR 3.4 22.9 - - - +
45A LEU* 4.1 16.2 - - + -
50A LEU* 3.8 26.7 - - + -
51A TYR* 4.2 6.3 - - + -
66A ALA 3.0 17.6 + - - +
67A ALA* 3.7 4.5 - - - +
69A ARG* 1.3 72.8 - - - +
71A ALA* 1.3 65.9 + - - +
73A LEU* 3.2 23.5 + - + +
74A ASN* 3.0 30.9 + - - +
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Residues in contact with ALA 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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41A GLN* 3.6 25.5 - - - +
42A PHE 3.5 20.4 - - - -
43A PRO* 3.8 2.3 - - - +
67A ALA 2.8 16.9 + - - +
68A CYS 3.9 0.4 - - - +
70A LEU* 1.3 75.7 - - - +
72A THR* 1.3 57.3 + - - +
74A ASN* 3.2 5.5 + - - +
75A ALA* 2.9 25.6 + - - +
145A CYS* 4.0 9.2 - - - -
147A VAL* 3.7 20.4 - - + -
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Residues in contact with THR 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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68A CYS 2.7 22.8 + - - -
69A ARG 3.6 4.3 - - - -
71A ALA* 1.3 74.2 - - - +
73A LEU* 1.3 59.9 + - - +
75A ALA* 3.1 5.8 + - - +
76A ILE* 2.8 30.4 + - + +
115A ALA* 2.9 31.5 - - + +
118A LEU* 4.0 15.0 - - + -
119A LEU* 3.8 29.8 - - + -
147A VAL* 3.7 9.2 - - - +
149A LEU* 4.5 9.6 - - + -
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Residues in contact with LEU 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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9A LEU* 3.7 30.1 - - + -
14A LEU* 4.1 32.1 - - + -
15A GLU 3.7 18.2 - - - +
16A LEU* 3.8 13.1 - - + +
17A PRO* 3.8 15.7 - - + +
45A LEU* 6.3 1.3 - - + -
69A ARG* 2.9 14.6 + - + +
70A LEU* 3.5 24.5 - - + +
72A THR* 1.3 75.8 - - - +
74A ASN* 1.3 63.1 + - - +
76A ILE* 3.4 5.6 + - + +
77A ALA* 3.0 22.7 + - - +
118A LEU* 3.7 11.1 - - + +
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Residues in contact with ASN 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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17A PRO* 3.6 23.5 - - - +
18A GLU 4.1 8.5 - - - +
19A VAL* 5.1 2.8 - - - +
20A ALA* 5.0 3.8 + - - +
41A GLN* 3.6 15.7 - - + +
42A PHE 3.3 20.8 + - - +
44A TYR* 2.9 44.8 + - + +
70A LEU* 3.0 26.5 + - - +
71A ALA 3.3 9.4 - - - +
73A LEU* 1.3 77.2 - - - +
75A ALA* 1.3 62.7 + - - +
77A ALA* 3.1 6.5 + - - +
78A GLN* 3.0 17.3 + - - +
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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
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38A THR* 4.7 3.1 - - + +
41A GLN* 3.6 29.6 + - + -
71A ALA 2.9 11.5 + - - +
72A THR* 3.1 9.4 + - - +
74A ASN* 1.3 74.7 - - - +
76A ILE* 1.3 57.9 + - - +
78A GLN* 3.0 6.1 + - - +
79A LEU* 3.0 28.8 + - - +
147A VAL* 4.4 3.6 - - + -
149A LEU* 3.4 33.0 - - + -
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Residues in contact with ILE 76 (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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9A LEU* 4.4 5.4 - - + -
16A LEU* 3.8 15.5 - - + -
72A THR* 2.8 27.7 + - + +
73A LEU* 3.7 8.5 - - + +
74A ASN 3.3 0.2 - - - -
75A ALA* 1.3 71.9 - - - +
77A ALA* 1.3 60.7 + - - +
79A LEU* 3.1 9.4 + - + +
80A LYS* 2.8 28.4 + - - +
86A LEU* 3.8 26.5 - - + -
118A LEU* 3.9 27.8 - - + -
119A LEU* 4.5 4.0 - - + -
122A ILE* 4.5 11.4 - - + -
123A PHE* 3.9 30.1 - - + -
149A LEU* 4.5 7.6 - - + -
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Residues in contact with ALA 77 (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 LEU* 4.0 16.1 - - + +
17A PRO* 3.3 35.9 - - + +
19A VAL* 3.6 18.0 - - + +
73A LEU 3.0 13.3 + - - +
74A ASN* 3.1 11.2 + - - +
76A ILE* 1.3 76.3 - - - +
78A GLN* 1.3 62.4 + - - +
80A LYS* 3.4 2.8 + - - +
81A GLN* 3.1 18.5 + - - +
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Residues in contact with GLN 78 (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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19A VAL* 2.8 31.0 - - + +
20A ALA 4.9 0.2 - - - +
28A PRO* 3.2 29.8 - - - +
29A TYR* 3.3 31.7 - - + -
36A LEU* 6.2 0.2 - - + -
38A THR* 4.4 10.1 - - + -
41A GLN* 4.0 18.7 + - - +
74A ASN 3.0 10.0 + - - +
75A ALA* 3.0 11.4 + - - +
77A ALA* 1.3 77.1 - - - +
79A LEU* 1.3 63.4 + - - +
81A GLN* 3.1 26.8 + - - +
82A ALA* 3.1 14.4 + - - +
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Residues in contact with LEU 79 (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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36A LEU* 3.4 33.6 - - + +
38A THR* 4.1 12.6 - - + -
75A ALA 3.0 16.0 + - - +
76A ILE* 3.4 11.7 - - + +
78A GLN* 1.3 75.2 - - - +
80A LYS* 1.3 59.1 + - - +
82A ALA* 3.3 4.9 + - - +
83A CYS* 2.9 35.5 + - - +
86A LEU* 4.1 8.7 - - + -
89A ILE* 4.1 11.9 - - + -
92A ILE* 3.5 31.6 - - + -
123A PHE* 4.7 5.6 - - + -
149A LEU* 3.9 22.4 - - + +
151A ALA* 4.4 9.9 - - + -
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Residues in contact with LYS 80 (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 GLU* 2.6 42.0 + - + +
16A LEU* 4.1 20.6 - - + -
76A ILE 2.8 15.7 + - - +
77A ALA 3.7 4.7 - - - +
78A GLN 3.3 0.2 - - - -
79A LEU* 1.3 75.5 - - - +
81A GLN* 1.3 57.8 + - - +
83A CYS* 4.2 2.0 - - - -
84A GLY* 2.8 52.2 + - - +
85A GLU* 4.0 9.1 + - - -
86A LEU* 3.7 21.5 - - + +
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.9 24.7 - - + +
28A PRO* 5.3 2.8 - - - +
29A TYR* 4.4 7.6 + - + +
77A ALA 3.1 13.4 + - - +
78A GLN* 3.1 31.4 + - - +
80A LYS* 1.3 80.2 - - - +
82A ALA* 1.3 61.2 + - - +
84A GLY* 4.2 2.6 + - - -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.4 39.6 + - + -
31A ILE* 5.8 0.9 - - + -
36A LEU* 3.6 25.6 - - + -
78A GLN* 3.1 10.8 + - - +
79A LEU* 3.3 6.5 + - - +
81A GLN* 1.3 77.9 - - - +
83A CYS* 1.3 60.8 + - - +
84A GLY 3.7 0.4 + - - -
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Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 5.9 0.7 - - + -
79A LEU 2.9 22.5 + - - +
80A LYS* 4.2 0.9 - - - -
82A ALA* 1.3 78.4 - - + +
84A GLY* 1.3 58.6 + - - +
85A GLU 2.9 34.5 + - - +
86A LEU* 3.8 6.1 - - - -
88A ARG* 3.1 26.9 + - + -
89A ILE* 3.8 30.5 - - + -
153A LEU* 4.9 14.1 - - + -
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Residues in contact with GLY 84 (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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80A LYS* 2.8 47.6 + - - -
81A GLN 4.2 2.8 + - - -
82A ALA 3.7 1.2 - - - -
83A CYS* 1.3 68.7 - - - +
85A GLU* 1.3 64.5 + - - +
86A LEU 4.2 0.2 - - - -
88A ARG* 4.2 6.1 - - - -
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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