Contacts of the helix formed by residues 39 - 64 (chain B) in PDB entry 2B5F
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 ARG 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 3.5 46.7 + - - +
263A VAL* 4.7 17.0 - - + +
34B LEU 5.3 0.2 + - - -
35B TRP* 3.0 80.2 - - - +
36B SER* 3.6 6.3 - - - +
37B PHE 2.4 10.3 + - - +
38B TRP* 1.3 74.7 - - - +
40B ALA* 1.3 50.4 + - - +
41B ALA 3.1 1.3 - - - -
42B ILE* 2.5 31.0 + - - +
43B ALA* 2.7 16.8 + - - +
95B ILE* 6.1 4.0 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER 4.2 4.0 + - - +
37B PHE* 2.6 21.6 + - + +
39B ARG* 1.3 72.6 - - - +
41B ALA* 1.3 57.2 + - - +
43B ALA* 3.0 20.1 + - - +
44B GLU* 3.1 16.1 + - - +
95B ILE* 3.9 11.2 - - - +
96B SER* 3.7 13.8 - - - -
118B ARG* 3.8 15.5 - - - +
122B TYR* 3.6 24.7 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.0 13.0 + - + +
38B TRP* 4.7 10.5 - - + +
39B ARG 3.1 0.2 - - - -
40B ALA* 1.3 75.7 - - - +
42B ILE* 1.3 61.2 + - + +
44B GLU* 4.1 5.6 - - - -
45B PHE* 3.5 6.9 + - - +
121B VAL* 3.2 34.8 - - + -
122B TYR* 4.4 5.5 - - + -
125B ALA* 3.0 31.9 - - + +
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TYR* 3.3 23.6 + - + +
262A TYR* 5.8 9.9 - - + +
263A VAL* 5.6 3.1 - - + -
38B TRP 3.6 15.9 - - - +
39B ARG* 2.5 22.5 + - - +
41B ALA* 1.3 75.9 - - + +
43B ALA* 1.3 62.2 + - - +
44B GLU 3.2 1.3 - - - -
45B PHE* 3.5 12.7 - - + +
46B ILE* 3.3 22.9 + - + +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 5.2 3.6 + - - +
259A TYR* 4.1 8.9 + - - -
263A VAL* 5.9 5.2 - - + -
39B ARG 2.7 9.4 + - - +
40B ALA* 3.0 11.6 + - - +
42B ILE* 1.3 78.7 - - - +
44B GLU* 1.3 60.8 + - - +
46B ILE* 4.3 2.4 - - - +
47B ALA* 3.2 22.7 + - - +
92B THR* 3.9 14.7 - - + +
95B ILE* 4.3 17.5 - - + -
96B SER* 3.7 19.7 - - - +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA 3.5 13.7 - - - +
41B ALA 4.0 5.8 - - - +
42B ILE 3.2 0.2 - - - -
43B ALA* 1.3 75.7 - - - +
45B PHE* 1.3 70.9 + - - +
47B ALA* 2.8 6.2 + - - +
48B THR* 2.8 24.5 + - - -
92B THR* 4.7 2.4 + - - -
96B SER* 2.9 24.0 + - - +
98B GLY* 4.1 2.3 + - - -
99B HIS* 3.5 18.3 + - - -
100B ILE* 3.0 28.1 + - - +
122B TYR* 4.2 24.2 - - + -
125B ALA* 4.2 10.1 - - + -
126B GLN* 3.0 23.5 + - + +
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 3.5 13.8 + - - +
42B ILE* 3.5 18.6 + - + +
44B GLU* 1.3 83.6 - - - +
46B ILE* 1.3 87.2 + - + +
47B ALA 2.8 3.6 + - - -
48B THR* 3.1 2.6 + - - -
49B LEU* 3.0 26.6 + - + +
125B ALA* 3.5 25.3 - - + +
128B LEU* 3.7 17.0 - - + -
129B GLY* 3.4 26.8 - - - -
132B CYS* 4.0 21.5 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 4.5 19.7 - - + -
177A TYR* 4.8 9.4 - - + +
259A TYR* 3.2 50.3 - - + +
42B ILE* 3.3 10.1 + - + +
43B ALA 4.3 2.0 - - - +
45B PHE* 1.3 98.0 - - + +
47B ALA* 1.3 62.9 + - - +
49B LEU* 3.4 20.3 - - + +
50B LEU* 3.4 24.1 + - + +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 5.9 2.0 - - - -
43B ALA 3.2 16.1 + - - +
44B GLU* 2.8 11.6 + - - +
45B PHE 2.8 1.6 + - - -
46B ILE* 1.3 74.2 - - - +
48B THR* 1.3 64.4 + - - +
49B LEU 2.9 5.0 + - - -
50B LEU* 3.2 3.6 + - - -
51B PHE 3.1 16.6 + - - -
88B LEU* 3.4 24.4 - - + +
92B THR* 4.1 11.9 - - + -
100B ILE* 3.7 26.9 - - + -
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU 2.8 18.4 + - - -
45B PHE 3.8 2.5 - - - -
47B ALA* 1.3 73.7 - - - +
49B LEU* 1.3 63.4 + - - +
51B PHE* 3.4 10.8 - - + +
52B LEU* 3.2 25.4 + - + +
100B ILE* 3.7 20.2 - - + +
126B GLN* 3.0 52.0 - - + +
129B GLY 4.1 1.8 - - - +
130B ALA* 3.4 17.3 - - + +
222B ASN* 6.2 0.2 - - - +
224B ALA* 4.6 5.2 - - + -
225B ARG 5.6 0.2 - - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 4.7 5.8 - - + -
45B PHE* 3.0 21.4 + - + +
46B ILE* 3.4 31.2 - - + +
47B ALA 2.9 1.4 - - - -
48B THR* 1.3 72.4 - - - +
50B LEU* 1.3 79.6 + - + +
51B PHE 2.9 8.9 + - - -
52B LEU* 3.1 4.0 + - - -
53B TYR* 2.9 23.1 + - + +
129B GLY* 3.5 19.2 + - - +
132B CYS* 4.4 14.1 - - + +
133B GLY* 3.8 17.3 - - - +
136B LEU* 5.3 10.3 - - + -
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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
----------------------------------------------------------
170A ILE* 3.1 33.2 - - + -
173A PHE* 3.4 38.1 - - + -
174A VAL* 3.5 26.0 - - + -
177A TYR* 4.8 8.3 - - + -
46B ILE* 3.4 17.7 + - + +
47B ALA 3.2 4.1 + - - +
49B LEU* 1.3 89.4 - - + +
51B PHE* 1.3 57.1 + - - +
53B TYR* 3.8 5.2 - - - -
54B ILE* 2.9 35.9 + - - +
84B MET* 3.2 9.1 - - + +
88B LEU* 4.8 5.8 - - + -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 3.1 6.3 + - - +
48B THR* 3.4 15.7 - - + +
49B LEU 2.9 0.8 + - - -
50B LEU* 1.3 76.2 - - - +
52B LEU* 1.3 69.5 + - + +
54B ILE* 4.2 0.5 - - - +
55B THR* 2.5 37.2 + - + +
81B PHE* 3.8 34.5 - + + -
84B MET* 4.0 16.6 - - + -
85B ILE* 3.2 41.3 - - + -
88B LEU* 3.5 18.1 - - + +
100B ILE* 4.4 7.2 - - + -
206B VAL* 5.7 2.0 - - + -
222B ASN* 3.9 23.1 - - + -
225B ARG* 4.0 20.2 - - + -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 3.2 12.2 + - + +
49B LEU 3.1 4.7 + - - +
51B PHE* 1.3 89.5 - - + +
53B TYR* 1.3 69.6 + - - +
55B THR* 3.5 4.5 - - - +
56B VAL* 3.2 49.0 + - + +
130B ALA* 3.6 46.7 - - + +
133B GLY* 4.1 6.2 - - - -
134B VAL* 4.0 11.4 + - + -
137B VAL* 4.6 1.6 - - - +
225B ARG* 3.7 42.8 - - + +
228B GLY* 5.4 0.7 - - - -
229B ALA* 5.1 0.7 - - + -
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Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 3.7 28.4 + - - +
170A ILE* 3.3 41.9 - - + +
171A GLY* 5.3 1.1 - - - -
209A VAL* 6.6 0.2 - - + -
212A ALA* 4.6 6.8 + - + +
213A THR* 4.7 7.5 + - - -
216A ILE* 6.0 0.7 - - - +
49B LEU* 2.9 19.4 + - + +
50B LEU* 3.9 9.0 - - + +
51B PHE 3.2 0.2 - - - -
52B LEU* 1.3 75.9 - - - +
54B ILE* 1.3 100.3 + - + +
57B ALA* 2.6 41.6 + - + +
133B GLY* 4.3 9.1 - - - +
136B LEU* 5.3 4.7 - - + -
137B VAL* 4.1 24.8 - - + +
140B PHE* 5.1 19.9 - + + -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 5.7 0.4 - - + -
171A GLY* 5.7 0.4 - - - -
174A VAL* 4.2 18.6 - - + -
208A MET* 3.8 20.6 - - + +
209A VAL* 4.2 23.8 - - + -
212A ALA* 3.6 6.4 - - + +
50B LEU 2.9 19.9 + - - +
53B TYR* 1.3 100.2 - - + +
55B THR* 1.3 67.3 + - - +
57B ALA* 3.0 5.1 - - - +
58B THR* 2.9 22.1 + - - +
80B ALA* 4.8 7.6 - - + -
84B MET* 3.5 38.4 - - + -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 2.5 30.6 + - + +
52B LEU* 3.4 8.8 + - - +
53B TYR 3.1 0.2 + - - -
54B ILE* 1.3 77.6 - - - +
56B VAL* 1.3 56.9 + - - +
58B THR* 2.5 26.3 + - - -
59B VAL* 2.7 19.7 + - - +
80B ALA* 3.6 29.8 - - - +
81B PHE* 3.4 52.8 - - + -
84B MET* 4.8 1.6 - - + -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.2 40.6 + - + +
55B THR* 1.3 82.9 + - - +
57B ALA* 1.3 58.6 + - - +
58B THR 3.0 0.9 - - - -
59B VAL* 3.5 8.7 - - + +
60B ILE* 3.2 31.6 + - + +
81B PHE* 5.2 1.6 - - + -
134B VAL* 4.8 9.2 - - + -
137B VAL* 4.1 13.8 - - + +
145B TYR* 4.3 8.7 - - + -
150B GLY 4.1 18.6 - - - +
151B GLY* 4.2 23.6 - - - +
225B ARG* 4.9 6.1 - - - +
229B ALA* 5.4 0.9 - - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ALA* 3.4 29.8 - - + +
53B TYR* 2.6 49.7 + - + +
54B ILE* 3.0 8.3 - - - +
56B VAL* 1.3 73.7 - - - +
58B THR* 1.3 57.2 + - - +
60B ILE* 4.4 1.1 - - - -
61B GLY* 4.0 11.8 + - - -
137B VAL* 4.4 11.9 - - + +
141B MET* 4.9 10.7 - - + +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A MET 4.8 0.2 + - - -
211A LEU* 2.5 45.8 + - + +
212A ALA* 2.7 8.8 + - - +
54B ILE* 2.9 6.2 + - - +
55B THR 2.5 16.2 + - - +
57B ALA* 1.3 71.3 - - - +
59B VAL* 1.3 60.1 + - + -
60B ILE 3.3 1.6 - - - -
61B GLY* 3.9 8.9 + - - +
62B HIS* 3.9 13.5 + - - +
72B VAL* 4.2 12.6 - - + +
76B GLY 4.4 0.7 - - - +
77B ILE* 3.9 20.2 - - + +
80B ALA* 4.0 20.7 - - + +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR 2.7 21.6 + - - +
56B VAL* 3.4 11.6 + - + +
58B THR* 1.3 75.8 - - - +
60B ILE* 1.3 59.8 + - + +
62B HIS* 4.1 2.8 - - - +
63B SER* 3.1 24.0 + - - +
77B ILE* 3.6 40.7 - - + +
81B PHE* 3.8 16.2 - - + -
151B GLY* 4.2 23.3 - - - +
225B ARG* 5.5 2.5 - - - +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.2 22.6 + - + +
57B ALA 5.0 0.2 - - - +
59B VAL* 1.3 79.6 - - + +
61B GLY* 1.3 57.0 + - - +
62B HIS 3.1 4.7 - - - -
63B SER* 3.5 3.5 + - - +
64B LYS* 2.9 27.7 + - + +
137B VAL* 4.7 2.2 - - + -
141B MET* 3.8 21.8 - - + -
144B PRO* 3.7 31.2 - - + +
145B TYR* 3.5 49.1 - - + +
148B PHE* 4.4 14.1 - - + +
151B GLY 4.3 12.1 - - - +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO* 3.6 33.1 - - - +
57B ALA 4.0 9.5 + - - -
58B THR* 3.9 8.4 + - - -
59B VAL 3.5 0.6 - - - -
60B ILE* 1.3 76.7 - - - +
62B HIS* 1.3 57.2 + - - +
64B LYS* 4.3 14.8 - - - -
65B GLU* 4.0 9.9 - - - +
71B SER* 4.6 5.0 - - - -
72B VAL* 4.8 5.0 - - - +
141B MET* 5.4 6.0 - - - -
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR 3.9 14.4 - - - +
59B VAL 4.1 4.5 - - - +
61B GLY* 1.3 77.2 - - - +
63B SER* 1.3 68.4 + - - +
64B LYS 3.2 0.7 - - - -
65B GLU* 2.9 26.9 - - - +
71B SER* 2.9 39.1 - - - -
72B VAL* 4.1 4.8 + - + +
73B GLY* 3.4 31.1 + - - -
74B LEU* 3.5 22.1 + - + +
77B ILE* 3.8 21.3 - - + -
69D CYS 6.0 1.6 - - - -
70D GLY* 6.1 2.8 - - - -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 3.1 17.5 + - - +
60B ILE* 3.5 7.0 + - - +
62B HIS* 1.3 80.3 - - - +
64B LYS* 1.3 53.0 + - - +
65B GLU* 2.6 21.2 + - - +
148B PHE* 3.4 50.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 4.8 6.8 + - - -
158A GLY* 5.9 2.2 - - - -
159A TYR* 2.9 40.2 + - + +
215A PRO* 6.1 0.8 - - + +
60B ILE* 2.9 22.4 + - + +
61B GLY* 4.3 7.6 - - - -
62B HIS 3.9 2.2 - - - -
63B SER* 1.3 74.1 - - - +
65B GLU* 1.3 63.0 + - - +
141B MET* 5.3 2.0 - - + -
144B PRO* 3.2 41.1 - - + -
147B GLN* 6.0 0.9 - - - +
148B PHE* 3.5 14.3 - - + -
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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