Contacts of the helix formed by residues 92 - 117 (chain B) in PDB entry 2AXT
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 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.5 5.6 - - - -
73B GLY 3.4 15.9 - - - -
75B TRP* 3.0 38.7 + - - -
88B PRO* 3.7 15.0 - - - -
90B PHE 2.5 7.5 + - - -
91B TRP* 1.3 73.2 - - - +
93B PHE* 1.3 65.4 + - - +
94B GLU* 3.1 13.8 + - - -
95B GLY 2.9 8.8 + - - -
96B VAL* 2.9 22.2 + - - +
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 4.9 0.5 - - - +
42B LEU* 3.6 25.2 - - + +
55B MET* 5.2 0.7 - - + -
63B LEU* 3.6 33.0 - - + -
66B MET* 3.7 30.4 - - + +
67B ALA* 5.2 1.1 - - - -
71B VAL* 3.3 33.1 - - + +
72B THR* 3.8 7.9 - - - -
73B GLY 3.1 35.9 + - - -
74B SER* 4.4 0.7 - - - -
78B TRP* 3.8 32.5 - + - -
80B ILE* 4.3 13.5 - - + -
92B SER* 1.3 74.6 - - - +
94B GLU* 1.3 64.6 + - - +
96B VAL* 3.5 3.9 + - - +
97B ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 5.1 2.7 - - + +
42B LEU* 3.6 29.9 - - + +
74B SER* 2.7 24.2 + - - -
75B TRP* 2.6 62.0 + - + +
76B SER* 4.8 2.7 + - - -
78B TRP* 5.1 0.2 - - - -
92B SER* 3.0 9.1 + - - -
93B PHE* 1.3 76.9 - - - +
95B GLY* 1.3 59.3 + - - +
97B ALA* 3.4 4.3 + - - +
98B LEU* 2.9 29.2 + - - +
5568a LMT 4.4 29.5 - - + +
5489c UNK 5.8 3.8 - - + -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 3.9 5.3 - - - -
90B PHE* 3.5 42.8 - - - -
91B TRP* 4.3 0.7 - - - -
92B SER* 2.9 11.9 + - - -
94B GLU* 1.3 77.7 - - - +
96B VAL* 1.3 60.3 + - - +
98B LEU* 3.0 3.8 + - - +
99B ALA* 2.8 28.1 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 3.8 18.4 - - - -
71B VAL* 3.7 32.5 - - + -
91B TRP* 4.3 12.0 - - + -
92B SER 2.9 23.9 + - - +
93B PHE 3.8 3.8 - - - +
95B GLY* 1.3 70.4 - - - +
97B ALA* 1.3 64.6 + - - +
99B ALA* 3.4 1.6 + - - +
100B HIS* 3.0 41.7 + - + +
515B CLA 3.7 29.2 - - + -
516B CLA 3.8 15.0 - - + +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY* 3.8 14.4 - - - +
38B ALA* 3.6 24.6 - - + +
39B LEU* 3.6 27.4 - - + -
42B LEU* 4.9 0.2 - - + -
93B PHE 3.1 16.0 + - - +
94B GLU 3.6 1.8 - - - +
96B VAL* 1.3 81.3 - - - +
98B LEU* 1.3 63.6 + - - +
100B HIS* 3.4 2.9 + - - +
101B ILE* 3.0 27.9 + - - +
515B CLA 5.8 0.2 - - - -
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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
----------------------------------------------------------
39B LEU* 5.4 0.6 - - - +
75B TRP* 4.4 4.0 - - + -
90B PHE* 3.5 28.9 - - + -
94B GLU 2.9 14.5 + - - +
95B GLY* 3.0 9.4 + - - +
97B ALA* 1.3 73.3 - - - +
99B ALA* 1.3 70.2 + - - +
101B ILE* 2.8 25.0 + - + +
102B VAL* 3.0 27.5 + - + +
5568a LMT 3.6 46.4 - - + -
5486c UNK 4.9 15.9 - - + -
5488c UNK 5.2 0.7 - - + -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 4.8 3.3 - - + -
91B TRP* 3.8 13.5 - - + -
95B GLY 2.8 18.4 + - - +
96B VAL 3.6 4.9 - - - +
98B LEU* 1.3 74.9 - - - +
100B HIS* 1.3 63.8 + - - +
102B VAL* 3.1 10.3 + - - +
103B LEU* 2.9 21.7 + - - +
516B CLA 3.7 42.8 - - + +
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 4.0 14.9 - - + +
34B ALA* 3.3 25.7 - - + +
35B GLY* 3.8 15.9 - - - +
96B VAL* 3.0 36.3 + - + +
97B ALA 3.6 7.9 - - - +
98B LEU 2.9 1.4 + - - -
99B ALA* 1.3 78.4 - - - +
101B ILE* 1.3 62.9 + - - +
103B LEU* 3.1 8.5 + - + +
104B SER* 2.9 25.6 + - - -
515B CLA 2.5 60.2 + + + -
516B CLA 3.5 20.1 - - + +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY* 4.2 9.2 - - - +
35B GLY* 4.3 1.3 - - - -
36B SER* 4.1 28.3 - - - +
39B LEU* 4.6 16.6 - - + -
97B ALA 3.0 17.3 + - - +
98B LEU* 2.8 20.0 + - + +
100B HIS* 1.3 72.3 - - - +
102B VAL* 1.3 59.9 + - + +
104B SER* 3.0 17.7 + - - -
105B GLY 3.4 4.5 + - - -
528B BCR 3.7 52.3 - - + +
5217t LMT 5.0 9.6 - - + -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.0 34.2 + - + +
99B ALA* 3.3 7.6 - - - +
101B ILE* 1.3 76.4 - - + +
103B LEU* 1.3 57.9 + - - +
105B GLY* 2.7 21.0 + - - -
106B LEU* 3.0 21.7 + - + +
516B CLA 3.8 19.7 - - + -
528B BCR 3.3 24.6 - - + +
5486c UNK 5.7 8.5 - - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 4.7 5.8 - - + -
99B ALA 2.9 12.2 + - - +
100B HIS* 3.5 8.3 - - + +
102B VAL* 1.3 74.0 - - - +
104B SER* 1.3 60.1 + - - +
105B GLY 3.0 0.2 + - - -
106B LEU* 3.2 3.2 + - - +
107B LEU* 2.8 44.3 + - + +
515B CLA 3.8 42.0 - - + -
516B CLA 3.4 37.8 - - + +
525B CLA 4.6 11.9 - - + -
529B BCR 3.8 32.3 - - + -
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 2.9 35.5 - - - +
31B ALA* 3.6 7.4 - - - +
32B GLY* 3.4 23.0 - - - -
100B HIS 2.9 9.0 + - - -
101B ILE 3.0 15.6 + - - -
103B LEU* 1.3 77.5 - - - +
105B GLY* 1.3 59.6 + - - +
108B PHE* 3.2 14.8 + - - +
528B BCR 3.8 11.6 - - - +
213t SQD 3.2 18.4 - - - +
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE 3.4 0.8 + - - -
102B VAL 2.7 13.5 + - - -
104B SER* 1.3 80.7 + - - +
106B LEU* 1.3 62.0 + - - -
108B PHE* 3.2 6.1 + - - +
109B LEU* 3.1 25.3 + - - +
528B BCR 3.9 41.5 - - - +
213t SQD 5.1 0.2 - - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.0 18.9 + - + +
103B LEU 3.7 4.5 - - - +
105B GLY* 1.3 72.6 - - - +
107B LEU* 1.3 62.4 + - - +
109B LEU* 3.0 16.7 + - + +
110B ALA* 2.8 31.4 + - - +
516B CLA 4.1 33.0 - - + -
528B BCR 4.7 7.4 - - + +
529B BCR 3.7 57.9 - - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.2 32.3 - - + +
27B THR* 3.3 35.7 - - + +
28B ALA* 3.5 25.4 - - + +
103B LEU* 2.8 42.1 + - + +
104B SER* 4.6 0.2 - - - -
106B LEU* 1.3 75.9 - - - +
108B PHE* 1.3 57.0 + - - +
110B ALA* 3.8 3.9 - - - +
111B ALA* 2.8 30.8 + - - +
515B CLA 4.6 4.0 - - + -
525B CLA 4.7 9.6 - - + -
526B CLA 4.1 16.2 - - + -
529B BCR 4.6 4.9 - - + +
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.5 32.5 - - + -
28B ALA* 3.8 5.3 - - - +
104B SER 3.2 13.7 + - - +
105B GLY* 3.2 11.3 + - - +
106B LEU 3.1 0.6 - - - -
107B LEU* 1.3 79.5 - - - +
109B LEU* 1.3 75.2 + - + +
111B ALA* 3.0 19.8 + - - +
112B CYS* 3.3 16.8 + - - -
527B BCR 4.5 9.9 - - + -
528B BCR 4.9 0.9 - - + -
104t BCR 4.3 28.7 - - + -
213t SQD 3.8 37.2 - - + -
5015t ALA* 6.5 0.4 - - + -
5018t PHE* 3.9 37.5 - + - -
5019t PHE* 4.8 4.7 - + - -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY 3.5 14.1 - - - +
106B LEU* 3.0 15.3 + - + +
108B PHE* 1.3 85.3 - - + +
110B ALA* 1.3 58.2 + - - +
112B CYS* 2.7 27.2 + - - +
113B TRP 3.2 9.4 + - - -
528B BCR 4.0 23.8 - - + -
529B BCR 3.9 43.5 - - + +
212a SQD 5.0 9.9 - - + +
104t BCR 3.7 26.9 - - + -
5018t PHE* 4.6 1.8 - - + -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.4 11.5 - - + +
106B LEU 2.8 18.2 + - - +
107B LEU 3.8 3.8 - - - +
109B LEU* 1.3 73.9 - - - +
111B ALA* 1.3 62.1 + - - +
112B CYS 3.2 0.9 + - - -
113B TRP* 3.4 6.8 + - - +
114B HIS* 3.2 20.8 + - - +
526B CLA 3.5 44.4 - - + -
529B BCR 3.9 17.1 - - + +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.8 16.1 - - - +
24B LEU* 3.3 28.9 - - + +
25B MET* 4.1 18.8 - - + +
107B LEU 2.8 16.3 + - - +
108B PHE* 3.1 15.0 - - - +
109B LEU 3.0 0.4 - - - -
110B ALA* 1.3 78.7 - - - +
112B CYS* 1.3 58.7 + - - +
114B HIS 4.2 0.7 - - - -
115B TRP* 3.6 18.5 + - - +
527B BCR 3.9 5.5 - - + +
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.3 23.0 + - - -
109B LEU* 2.7 17.4 + - - +
111B ALA* 1.3 70.0 - - - +
113B TRP* 1.3 69.1 + - - +
114B HIS 3.1 1.1 - - - -
115B TRP* 2.6 18.8 + - - +
116B VAL* 3.0 16.0 + - - +
527B BCR 3.8 26.7 - - + -
529B BCR 3.6 23.3 - - + -
5018t PHE* 4.0 26.0 - - - -
5023t PHE* 4.6 5.4 - - + -
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU 3.2 3.0 + - - -
110B ALA* 3.8 7.9 - - - +
112B CYS* 1.3 81.6 - - - +
114B HIS* 1.3 95.7 + + - +
116B VAL* 3.3 0.5 + - - -
117B TYR* 3.0 56.6 + + + +
120B LEU* 4.0 23.3 - - + -
526B CLA 3.4 69.7 - + + +
529B BCR 4.1 31.0 - - + +
3H ARG* 5.8 3.6 - - - -
5H THR* 5.4 3.4 - - + -
212a SQD 2.8 42.7 + - - -
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY* 3.5 28.6 + - - +
20B ILE* 3.9 14.1 - - + +
21B ALA* 4.0 6.7 - - + -
24B LEU* 3.6 28.3 - - + -
110B ALA 3.2 12.2 + - - +
112B CYS 3.1 1.0 - - - -
113B TRP* 1.3 98.7 - + - +
115B TRP* 1.3 59.6 + - - +
117B TYR 3.7 11.6 + - - +
118B TRP* 3.9 1.9 - - - -
120B LEU* 4.4 8.9 - - + +
123B PHE* 5.4 3.6 - + - -
526B CLA 2.9 76.2 + + + -
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Residues in contact with TRP 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 2.6 94.9 + - + +
21B ALA* 3.6 16.2 - - + -
22B ALA 5.2 0.7 - - - -
111B ALA 3.6 12.9 + - - +
112B CYS 2.6 17.9 + - - +
114B HIS* 1.3 71.4 - - - +
116B VAL* 1.3 72.9 + - + +
118B TRP* 3.6 2.6 - - - +
524B CLA 3.6 37.7 - + + -
527B BCR 3.6 40.6 - - + -
7L ARG* 3.6 22.0 - - - -
213t SQD 4.0 31.8 + - - -
5023t PHE* 5.6 2.5 - + - -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 5.5 0.7 - - - +
112B CYS* 3.0 10.3 + - - +
113B TRP 3.9 3.8 - - - +
115B TRP* 1.3 83.3 - - + +
117B TYR* 1.3 77.5 + - + +
118B TRP* 3.0 22.4 + - - -
529B BCR 3.5 38.1 - - + -
1L MET* 3.3 38.9 - - + +
213t SQD 5.6 1.5 + - - -
5023t PHE* 5.3 7.4 - - + -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY* 5.5 0.2 - - - -
113B TRP* 3.0 61.4 + + + +
114B HIS* 3.7 12.2 + - - +
116B VAL* 1.3 87.8 - - + +
118B TRP* 1.3 59.0 + - - +
119B ASP 3.5 2.7 - - - +
120B LEU* 3.5 26.4 - - + +
123B PHE* 5.4 0.2 - - - -
529B BCR 3.6 14.0 - - + +
3H ARG* 4.3 35.2 + - - +
1L MET* 4.5 15.7 - - + -
212a SQD 3.0 31.2 + - - -
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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