Contacts of the helix formed by residues 39 - 64 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 2.5 78.4 - - - +
36A SER* 4.2 12.8 - - - +
37A PHE 2.4 13.7 + - - -
38A TRP* 1.3 70.2 + - - +
40A ALA* 1.3 56.6 + - - +
41A ALA 3.1 1.6 - - - -
42A ILE* 2.5 32.7 + - - +
43A ALA* 2.7 12.7 + - - +
95A ILE* 6.2 2.0 - - + -
262C TYR* 3.1 47.3 + - - -
263C VAL* 4.6 24.7 - - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER 4.1 5.5 + - - +
37A PHE* 2.5 20.9 + - + +
39A ARG* 1.3 75.4 - - - +
41A ALA* 1.3 58.0 + - - +
43A ALA* 2.9 19.1 + - - +
44A GLU* 3.1 15.9 + - - +
95A ILE 4.1 7.8 + - - +
96A SER* 3.8 16.2 - - - -
118A ARG* 3.8 15.0 - - - +
122A TYR* 3.6 24.0 - - + +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.0 12.8 + - + +
38A TRP* 4.7 10.5 - - + +
40A ALA* 1.3 75.5 - - - +
42A ILE* 1.3 61.2 + - + +
44A GLU* 4.1 5.6 - - - -
45A PHE* 3.5 7.1 + - - +
121A VAL* 3.2 34.8 - - + -
122A TYR* 4.4 4.9 - - - -
125A ALA* 3.0 32.3 - - + +
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP 3.7 15.9 - - - +
39A ARG* 2.5 26.1 + - - +
41A ALA* 1.3 75.9 - - + +
43A ALA* 1.3 62.7 + - - +
44A GLU 3.2 0.9 - - - -
45A PHE* 3.7 12.1 - - + -
46A ILE* 3.3 23.8 + - + -
259C TYR* 3.7 18.9 + - + +
262C TYR 5.8 3.6 - - - +
263C VAL* 6.0 1.8 - - + -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 2.7 9.3 + - - +
40A ALA 2.9 10.5 + - - +
42A ILE* 1.3 80.8 - - - +
44A GLU* 1.3 61.5 + - - +
46A ILE* 4.1 2.3 - - - +
47A ALA* 3.2 22.6 + - - +
92A THR* 4.0 11.8 - - + +
95A ILE* 3.8 22.9 - - + -
96A SER* 3.5 19.3 - - - +
177C TYR* 5.3 4.1 + - - +
259C TYR* 4.3 9.0 + - - -
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.5 13.0 - - - +
41A ALA* 4.0 6.7 - - - +
43A ALA* 1.3 75.2 - - - +
45A PHE* 1.3 71.6 + - - +
47A ALA* 2.8 5.9 + - - +
48A THR* 2.8 24.5 + - - -
92A THR* 4.7 3.1 - - - +
96A SER* 3.3 21.8 + - - +
98A GLY* 4.1 2.9 + - - -
99A HIS* 3.5 18.6 + - - -
100A ILE* 3.0 28.7 + - - +
122A TYR* 4.2 24.9 - - + -
125A ALA* 4.2 10.1 - - + -
126A GLN* 3.0 23.3 + - + +
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA 3.5 13.3 + - - +
42A ILE* 3.6 18.6 - - + +
44A GLU* 1.3 84.3 - - - +
46A ILE* 1.3 87.0 + - + +
47A ALA 2.8 3.5 + - - -
48A THR* 3.1 2.8 + - - -
49A LEU* 3.0 26.1 + - + +
125A ALA* 3.5 25.0 - - + +
128A LEU* 3.7 16.8 - - + -
129A GLY* 3.4 26.4 - - - -
132A CYS* 4.0 21.3 - - + -
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.3 13.7 + - + +
43A ALA 4.3 1.8 - - - +
45A PHE* 1.3 97.7 - - + +
47A ALA* 1.3 63.1 + - - +
49A LEU* 3.4 21.1 - - + +
50A LEU* 3.4 25.2 + - + +
173C PHE* 4.5 20.6 - - + -
177C TYR* 4.9 9.0 - - + +
259C TYR* 3.3 44.9 - - + +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 3.2 15.9 + - - +
44A GLU* 2.8 10.5 + - - +
45A PHE 2.8 1.6 + - - -
46A ILE* 1.3 74.2 - - - +
48A THR* 1.3 63.6 + - - +
49A LEU 2.9 4.8 + - - -
50A LEU* 3.2 3.6 + - - -
51A PHE 3.1 17.0 + - - -
88A LEU* 3.4 26.6 - - + +
92A THR* 4.4 8.1 - - + -
100A ILE* 3.7 27.4 - - + -
177C TYR* 6.0 3.6 - - + +
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU 2.8 18.2 + - - -
45A PHE 3.8 2.9 - - - -
47A ALA* 1.3 73.5 - - - +
49A LEU* 1.3 64.2 + - - +
51A PHE* 3.4 10.3 - - + +
52A LEU* 3.2 24.8 + - + +
100A ILE* 3.7 21.2 - - + +
126A GLN* 3.0 51.2 - - + +
129A GLY 4.1 1.8 - - - +
130A ALA* 3.4 17.5 - - + +
222A ASN* 6.2 0.4 - - - +
224A ALA* 4.6 4.9 - - + -
225A ARG 5.6 0.4 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.0 21.9 + - + +
46A ILE* 3.4 31.2 - - + +
47A ALA 2.9 1.2 - - - -
48A THR* 1.3 73.0 - - - +
50A LEU* 1.3 79.8 + - + +
51A PHE 2.9 9.1 + - - -
52A LEU 3.1 2.8 + - - -
53A TYR* 2.9 21.8 + - + +
129A GLY* 3.5 19.2 + - - +
132A CYS* 4.4 12.1 - - + -
133A GLY* 3.7 18.9 - - - +
136A LEU* 4.3 19.5 - - + -
170C ILE* 4.7 1.3 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.5 17.3 - - + +
47A ALA 3.2 4.7 + - - +
49A LEU* 1.3 89.2 - - + +
51A PHE* 1.3 55.9 + - - +
53A TYR* 3.8 5.4 - - - -
54A ILE* 2.9 35.6 + - + +
84A MET* 3.2 10.1 - - + +
88A LEU* 4.8 7.2 - - + -
170C ILE* 3.1 33.0 - - + -
173C PHE* 3.5 32.3 - - + -
174C VAL* 3.5 30.5 - - + -
177C TYR* 5.0 7.6 - - + -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.1 6.9 + - - +
48A THR* 3.4 15.0 - - + +
49A LEU 2.9 1.0 + - - -
50A LEU* 1.3 75.9 - - - +
52A LEU* 1.3 69.9 + - + +
54A ILE* 4.2 0.5 - - - +
55A THR* 2.5 37.7 + - + +
81A PHE* 3.8 35.0 - + + -
84A MET* 4.0 16.8 - - + -
85A ILE* 3.2 41.3 - - + -
88A LEU* 3.5 18.6 - - + +
100A ILE* 4.4 7.0 - - + -
206A VAL* 5.7 1.6 - - + -
222A ASN* 3.9 23.3 - - + -
225A ARG* 4.0 20.6 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.2 12.4 + - + +
49A LEU 3.1 4.4 + - - +
51A PHE* 1.3 87.6 - - + +
53A TYR* 1.3 70.0 + - - +
55A THR* 3.5 3.8 - - - +
56A VAL* 3.2 41.8 + - + +
81A PHE* 5.7 0.4 - - + -
130A ALA* 3.6 35.7 - - + +
134A VAL* 3.3 38.7 + - + +
137A VAL* 4.5 1.6 - - - +
225A ARG* 3.7 41.3 - - + +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 2.9 21.8 + - + +
50A LEU* 3.9 9.2 - - - +
51A PHE 3.2 0.2 - - - -
52A LEU* 1.3 75.3 - - - +
54A ILE* 1.3 100.1 + - + +
57A ALA* 2.6 41.1 + - + +
133A GLY* 4.3 8.4 - - - +
136A LEU* 4.8 14.6 - - + -
137A VAL* 4.0 21.3 - - + +
140A PHE* 4.3 21.8 - + + -
141A MET* 5.9 2.0 - - + +
167C ALA* 3.8 26.5 + - - +
170C ILE* 3.4 39.5 - - + -
171C GLY* 5.8 0.9 - - - -
212C ALA* 4.6 7.7 + - + +
213C THR* 4.8 6.3 + - - -
216C ILE* 4.9 5.7 - - - +
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU 2.9 19.2 + - - +
53A TYR* 1.3 101.0 - - + +
55A THR* 1.3 65.5 + - - +
57A ALA* 3.0 4.9 + - - +
58A THR* 2.9 22.3 + - - +
80A ALA* 4.8 9.0 - - + -
84A MET* 3.5 39.9 - - + -
170C ILE* 5.7 0.4 - - + -
171C GLY* 5.9 0.9 - - - -
174C VAL* 4.4 17.5 - - + -
208C MET* 3.9 18.2 - - + +
209C VAL* 4.4 18.8 - - + -
212C ALA* 3.8 11.1 - - + +
213C THR* 5.9 0.2 - - - +
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 2.5 30.8 + - + +
52A LEU* 3.4 9.2 + - - +
53A TYR 3.1 0.4 + - - -
54A ILE* 1.3 76.1 - - - +
56A VAL* 1.3 57.9 + - - +
58A THR* 2.5 26.0 + - - +
59A VAL* 2.7 19.6 + - - +
80A ALA* 3.6 29.8 - - - +
81A PHE* 3.4 52.5 - - + -
84A MET* 4.8 1.1 - - + -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.2 39.3 + - + +
55A THR* 1.3 83.6 + - - +
57A ALA* 1.3 59.7 + - - +
58A THR 3.0 0.7 - - - -
59A VAL* 3.5 9.4 - - + +
60A ILE* 3.2 31.8 + - + +
81A PHE* 5.2 1.6 - - + -
134A VAL* 4.6 10.1 - - + -
137A VAL* 4.2 14.4 - - + +
145A TYR* 4.3 12.8 - - + -
150A GLY 4.8 0.2 - - - +
151A GLY* 4.2 34.8 - - - +
225A ARG* 4.9 7.2 - - - +
229A ALA* 5.4 0.4 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 2.6 48.2 + - + +
54A ILE* 3.0 10.3 - - - +
56A VAL* 1.3 73.4 - - - +
58A THR* 1.3 57.8 + - - +
60A ILE* 5.0 0.4 - - - -
61A GLY* 3.6 15.8 + - - -
137A VAL* 4.3 11.6 - - + +
141A MET* 4.7 13.4 - - + +
212C ALA* 3.7 26.5 - - + +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 2.9 8.0 + - - +
55A THR 2.5 15.3 + - - +
57A ALA* 1.3 72.4 - - - +
59A VAL* 1.3 60.9 + - + +
60A ILE 3.3 2.2 - - - -
61A GLY* 3.8 4.7 - - - +
62A HIS* 3.6 20.4 + - - +
72A VAL* 4.4 10.7 - - + +
76A GLY 4.4 3.4 - - - +
77A ILE* 3.9 19.7 - - + +
80A ALA* 4.0 20.9 - - + +
211C LEU* 2.7 40.3 + - + +
212C ALA* 2.9 8.1 + - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR 2.7 22.0 + - - +
56A VAL* 3.4 12.0 + - + +
58A THR* 1.3 73.1 - - + +
60A ILE* 1.3 63.7 + - + +
62A HIS* 3.9 1.2 + - - +
63A SER* 3.1 27.9 + - - +
77A ILE* 3.6 39.7 - - + +
81A PHE* 3.8 16.2 - - + -
148A PHE 6.1 0.4 - - - +
151A GLY* 4.4 19.7 - - - +
225A ARG* 5.5 3.4 - - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.2 22.2 + - + +
59A VAL* 1.3 78.3 - - + +
61A GLY* 1.3 53.0 + - - +
62A HIS 2.5 17.5 + - - -
63A SER* 3.0 2.5 + - - -
64A LYS* 2.8 31.6 + - + +
137A VAL* 4.5 4.7 - - + -
141A MET* 3.9 18.2 - - - -
144A PRO* 3.7 31.0 - - + -
145A TYR* 3.6 49.6 - - + +
148A PHE* 4.5 13.9 - - + +
151A GLY* 4.4 12.1 - - - +
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 3.6 17.8 + - - -
58A THR* 3.8 6.2 + - - -
59A VAL 3.6 0.4 - - - -
60A ILE* 1.3 77.6 - - - +
62A HIS* 1.3 55.8 + - - +
64A LYS* 4.5 10.0 - - - -
65A GLU* 5.3 3.8 - - - +
71A SER* 4.5 6.6 - - - -
72A VAL* 5.5 1.9 + - - +
141A MET* 5.0 3.7 - - - -
159C TYR* 5.7 2.2 - - - -
211C LEU 6.1 0.4 - - - -
215C PRO* 3.9 31.0 - - - +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR 3.6 14.7 + - - +
59A VAL 4.2 3.1 - - - +
60A ILE 2.5 6.5 + - - -
61A GLY* 1.3 75.1 - - - +
63A SER* 1.3 62.9 + - - +
64A LYS 2.5 17.4 + - - -
65A GLU* 3.0 21.2 + - + +
71A SER* 3.4 33.8 + - - -
72A VAL* 5.2 4.5 - - + -
73A GLY* 3.7 27.1 - - - -
74A LEU* 3.9 21.7 + - + +
77A ILE* 4.1 15.7 - - + +
69B CYS 6.0 0.4 - - - -
70B GLY* 5.1 10.5 - - - -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.1 22.2 + - - +
60A ILE* 3.0 3.9 + - - -
62A HIS* 1.3 87.2 + - - +
64A LYS* 1.3 49.5 + - - +
65A GLU* 3.1 5.5 + - - +
77A ILE* 5.7 1.6 - - - +
148A PHE* 2.7 58.5 + - - -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 2.8 20.7 + - + +
61A GLY* 4.8 7.0 - - - -
62A HIS* 2.5 8.2 + - - +
63A SER* 1.3 70.2 - - - +
65A GLU* 1.3 67.2 + - - +
66A THR* 5.5 0.9 - - - +
144A PRO* 3.0 34.3 - - + +
148A PHE* 3.5 29.6 - - + -
157C LEU 5.6 2.2 - - - -
158C GLY* 4.5 13.9 + - - -
159C TYR* 3.0 41.2 + - - +
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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