Contacts of the helix formed by residues 88 - 111 (chain B) in PDB entry 2C8U
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 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 4.2 6.4 + - - -
86B GLY 4.2 0.5 - - - -
87B GLY* 1.3 83.2 + - - +
89B GLU* 1.3 59.4 + - - +
90B GLU* 2.8 36.6 + - - +
91B GLU* 2.9 22.8 + - + +
92B TYR* 2.8 27.5 + - - +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.3 24.7 - - + +
80A LYS* 3.8 36.0 - - + +
81A LYS* 3.2 41.7 - - + +
88B THR* 1.3 72.8 - - - +
90B GLU* 1.3 57.0 + - + +
92B TYR* 3.4 3.7 + - - +
93B TYR 2.9 23.7 + - - -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 5.8 5.4 - - - +
77A TYR* 4.1 12.2 - - + +
88B THR* 2.8 32.2 + - - +
89B GLU* 1.3 72.3 - - + +
91B GLU* 1.3 68.1 + - - +
93B TYR* 3.5 4.8 + - - +
94B ASN* 2.9 32.7 + - - +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY* 3.8 6.1 - - - -
87B GLY* 2.9 28.8 + - - +
88B THR* 2.9 24.0 + - - +
90B GLU* 1.3 79.9 - - - +
92B TYR* 1.3 60.4 + - - +
94B ASN* 3.2 6.0 + - - +
95B VAL* 2.8 35.2 + - - +
147B THR* 4.6 6.3 + - - +
152B VAL* 3.6 22.6 - - + +
153B GLY* 4.1 18.9 - - - -
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.5 48.8 - - + +
77A TYR* 4.1 6.5 - - - -
80A LYS* 3.5 39.7 - - + +
85A MET* 3.5 21.1 - - + +
92A TYR* 4.1 14.8 - + - -
80B LYS* 6.4 1.3 - - + -
85B MET* 3.5 48.8 + - + +
86B GLY 5.4 0.2 - - - -
88B THR 2.8 12.6 + - - +
89B GLU 3.4 9.0 - - - +
90B GLU 3.3 0.2 - - - -
91B GLU* 1.3 76.0 - - - +
93B TYR* 1.3 64.6 + - - +
95B VAL* 3.1 4.4 + - - +
96B GLU* 3.1 30.3 + - + +
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Residues in contact with TYR 93 (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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66A LYS* 5.0 7.4 - - - -
67A TRP 4.7 3.5 + - - -
68A MET* 3.5 35.3 - - + -
69A VAL* 2.7 44.8 + - - +
73A ALA* 3.7 24.5 - - + -
74A ILE* 4.0 6.7 - - + -
77A TYR* 3.6 28.3 - - + -
89B GLU 2.9 7.5 + - - -
90B GLU* 3.6 7.2 - - - +
91B GLU 3.3 0.2 - - - -
92B TYR* 1.3 79.0 - - - +
94B ASN* 1.3 81.7 + - - +
96B GLU* 3.3 5.4 + - - +
97B LYS* 2.8 46.2 + - + +
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Residues in contact with ASN 94 (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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90B GLU* 2.9 25.1 + - - +
91B GLU* 3.2 9.8 + - - +
93B TYR* 1.3 85.2 - - - +
95B VAL* 1.3 65.6 + - - +
97B LYS* 3.3 30.5 - - - +
98B LEU* 3.2 22.0 + - - +
151B ALA 5.5 0.4 - - - +
152B VAL* 3.6 24.2 - - + +
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Residues in contact with VAL 95 (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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84B MET 4.5 0.2 - - - +
85B MET* 4.0 35.9 - - + +
86B GLY 4.0 1.3 - - - +
91B GLU 2.8 19.5 + - - +
92B TYR 3.1 6.9 + - - +
94B ASN* 1.3 78.4 - - - +
96B GLU* 1.3 57.7 + - - +
98B LEU 3.3 0.2 + - - -
99B ILE* 3.0 45.2 + - + +
152B VAL* 3.8 18.4 - - + -
157B THR* 3.8 26.7 - - + +
159B ALA* 3.7 19.4 - - - +
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Residues in contact with GLU 96 (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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73A ALA* 3.6 25.7 + - + +
76A ARG* 3.4 31.0 + - + -
96A GLU* 3.9 1.2 - - - +
76B ARG* 2.7 49.6 + - - -
85B MET* 3.5 15.1 - - + +
92B TYR* 3.1 31.5 + - + +
93B TYR* 3.6 8.1 - - - +
95B VAL* 1.3 73.7 - - - +
97B LYS* 1.3 59.2 + - - +
99B ILE* 3.8 4.6 - - - +
100B GLY* 2.9 26.5 + - - -
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Residues in contact with LYS 97 (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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69A VAL* 3.6 18.5 - - + +
70A GLU* 3.5 7.0 - - + +
73A ALA* 3.5 9.6 - - - +
93B TYR* 2.8 49.2 + - + +
94B ASN* 3.3 28.9 - - - +
95B VAL 3.3 0.2 - - - -
96B GLU* 1.3 74.6 - - - +
98B LEU* 1.3 59.4 - - - +
100B GLY 3.2 1.6 + - - -
101B GLN* 3.0 45.9 + - - +
142B SER* 2.8 43.0 + - - +
145B ALA* 5.4 4.8 - - - +
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Residues in contact with LEU 98 (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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94B ASN 3.2 14.7 + - - +
97B LYS* 1.3 78.8 - - - +
99B ILE* 1.3 66.1 + - - +
101B GLN* 3.3 22.2 + - - +
102B ALA* 2.9 25.3 + - - +
139B ILE* 4.1 26.9 - - + +
142B SER* 3.7 23.6 - - - -
143B LEU* 4.1 7.4 - - + -
151B ALA* 3.5 43.1 - - + +
152B VAL* 4.9 0.2 - - + -
159B ALA* 3.9 17.9 - - + +
163B LEU* 5.1 7.0 - - + -
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Residues in contact with ILE 99 (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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72B LEU* 4.7 5.6 - - + -
76B ARG* 3.5 26.2 - - - +
85B MET* 4.7 0.7 - - + -
95B VAL* 3.0 33.6 + - + +
96B GLU* 3.8 17.9 - - - +
98B LEU* 1.3 76.5 - - - +
100B GLY* 1.3 58.4 + - - +
102B ALA* 3.3 1.4 + - - +
103B GLU* 2.9 45.1 + - + +
158B LEU* 3.7 31.9 - - + -
159B ALA* 4.0 15.5 - - - +
162B VAL* 4.2 21.7 - - + +
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Residues in contact with GLY 100 (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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70A GLU* 3.6 19.0 - - - +
73A ALA* 6.1 0.2 - - - -
96B GLU 2.9 15.2 + - - -
97B LYS 3.5 4.7 - - - -
99B ILE* 1.3 78.1 - - - +
101B GLN* 1.3 55.9 + - - +
103B GLU* 3.5 12.8 + - - +
104B ASP* 3.0 33.3 + - - +
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Residues in contact with GLN 101 (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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52A ARG* 4.4 4.8 - - - +
69A VAL* 4.1 13.9 - - - +
70A GLU* 3.8 16.6 - - + +
97B LYS* 3.0 34.9 + - - +
98B LEU* 3.3 12.5 + - - +
100B GLY* 1.3 74.6 - - - +
102B ALA* 1.3 63.2 + - - +
104B ASP* 3.4 8.6 + - - +
105B LEU* 3.2 20.1 + - - +
135B LEU* 4.5 5.5 - - + +
138B ILE* 3.4 28.8 - - + +
139B ILE* 4.0 17.8 - - + +
142B SER* 2.6 36.4 + - - -
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Residues in contact with ALA 102 (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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98B LEU 2.9 17.4 + - - +
101B GLN* 1.3 73.2 - - - +
103B GLU* 1.3 55.8 + - - +
105B LEU* 3.1 10.2 + - - +
106B GLU* 2.7 33.3 + - - +
139B ILE* 4.3 5.5 - - + +
159B ALA 5.8 0.2 - - - +
162B VAL* 3.6 26.9 - - + +
163B LEU* 4.5 17.3 - - + -
166B VAL* 3.5 19.2 - - + +
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Residues in contact with GLU 103 (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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1208A BME 3.4 32.1 + - - -
72B LEU* 3.4 31.9 - - + +
76B ARG* 4.3 0.2 + - - -
99B ILE* 2.9 30.3 + - + +
100B GLY* 3.6 10.6 - - - +
102B ALA* 1.3 74.1 - - - +
104B ASP* 1.3 60.7 + - - +
106B GLU* 3.5 11.1 - - + +
107B HIS* 2.9 29.5 + - - +
162B VAL* 5.0 3.8 - - + +
166B VAL* 4.9 0.6 - - - +
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Residues in contact with ASP 104 (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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52A ARG* 2.6 38.4 + - - +
70A GLU* 3.0 13.1 - - - +
1207A SO4 5.0 2.0 - - - -
100B GLY 3.0 16.6 + - - +
101B GLN* 3.4 10.3 - - - +
103B GLU* 1.3 75.8 - - - +
105B LEU* 1.3 63.0 + - - +
107B HIS* 3.4 15.2 + - - +
108B GLU* 3.4 12.3 + - - +
135B LEU* 3.5 22.7 - - + +
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Residues in contact with LEU 105 (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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101B GLN 3.2 9.0 + - - +
102B ALA* 3.1 11.5 + - - +
104B ASP* 1.3 77.8 - - - +
106B GLU* 1.3 64.2 + - - +
108B GLU* 3.0 16.3 + - + +
109B TYR* 3.2 10.4 + - - +
132B VAL* 3.9 35.7 - - + +
135B LEU* 3.5 15.2 - - + +
136B LEU* 3.8 27.1 - - + -
139B ILE* 3.9 16.2 - - + -
166B VAL* 3.5 19.1 - - + -
167B ILE* 4.3 6.1 - - + -
170B VAL* 3.8 24.2 - - + -
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Residues in contact with GLU 106 (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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15B GLY 5.5 1.7 - - - +
16B ARG* 5.6 1.4 - - - +
102B ALA 2.7 19.7 + - - +
103B GLU* 3.5 12.8 - - + +
105B LEU* 1.3 72.7 - - - +
107B HIS* 1.3 56.7 + - - +
109B TYR* 3.2 11.6 + - - +
110B TYR* 2.9 66.6 + - + +
165B ALA* 5.9 0.5 - - - +
166B VAL* 3.6 22.0 - - + +
169B HIS* 2.7 41.7 + - - +
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Residues in contact with HIS 107 (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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107A HIS* 3.5 37.1 + + - -
110A TYR* 6.0 6.3 - + + -
103B GLU 2.9 17.1 + - - +
104B ASP* 3.5 8.5 - - - +
105B LEU 3.2 0.2 - - - -
106B GLU* 1.3 73.1 - - - +
108B GLU* 1.3 84.0 + - - +
110B TYR* 3.4 25.0 + - + +
111B LYS* 3.5 23.8 + - + +
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Residues in contact with GLU 108 (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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104B ASP 3.4 12.1 + - - +
105B LEU 3.0 10.0 + - - +
107B HIS* 1.3 89.6 - - - +
109B TYR* 1.3 66.6 + - - +
111B LYS* 2.8 52.7 + - - +
112B THR 4.0 0.2 + - - -
127B ILE* 3.4 25.4 - - + +
131B LYS* 3.3 46.1 - - + +
132B VAL* 4.0 20.4 - - + -
135B LEU* 4.2 8.3 - - + +
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Residues in contact with TYR 109 (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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12B ASN* 5.7 0.7 + - - -
14B ARG* 5.1 4.7 + - - +
105B LEU 3.2 7.7 + - - +
106B GLU* 3.2 25.2 + - - +
108B GLU* 1.3 76.6 - - - +
110B TYR* 1.3 72.9 + + - +
112B THR* 2.7 27.9 + - - -
113B LEU* 3.4 40.4 + - + +
120B LYS* 5.9 0.7 - - - -
127B ILE* 4.1 9.8 - - - +
132B VAL* 5.6 0.6 - - - +
166B VAL* 5.9 0.7 - - + -
169B HIS* 3.4 62.9 + + + -
170B VAL* 5.4 4.9 - - + +
172B ASP* 4.5 9.0 + - + +
173B LEU* 4.0 24.7 - - + -
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Residues in contact with TYR 110 (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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107A HIS* 6.0 6.3 - + + -
16B ARG* 3.6 30.6 - - + +
106B GLU* 2.9 56.0 + - + +
107B HIS* 3.5 20.6 - - + +
108B GLU 3.1 0.4 - - - -
109B TYR* 1.3 87.3 - + - +
111B LYS* 1.3 55.8 + - - +
112B THR 3.1 0.2 - - - -
113B LEU* 3.0 45.5 + - + +
169B HIS* 5.6 0.2 - + - -
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Residues in contact with LYS 111 (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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107B HIS* 3.6 26.7 - - + +
108B GLU* 2.8 51.5 + - - +
110B TYR* 1.3 75.6 - - - +
112B THR* 1.3 59.1 + - - +
113B LEU 3.3 0.2 - - - -
115B LYS* 3.5 22.7 - - - +
123B ILE* 3.6 23.5 - - + +
127B ILE* 4.0 10.5 - - + +
131B LYS* 3.6 13.9 - - - +
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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