Contacts of the helix formed by residues 53 - 80 (chain A) in PDB entry 2BEW
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 PRO 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS 3.6 4.7 - - - +
52A LEU* 1.3 98.0 - - + +
54A LYS* 1.3 67.6 + - - +
55A GLU* 4.5 5.8 - - + +
56A LYS* 3.1 20.1 + - + +
57A VAL* 3.1 18.4 + - - +
328A TRP* 4.3 0.2 - - - -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO* 1.3 71.3 - - - +
55A GLU* 1.3 58.0 + - - +
57A VAL* 3.2 2.6 + - - +
58A LEU* 2.8 52.4 + - + +
327A GLY 4.6 4.0 + - - -
328A TRP* 3.6 75.6 - - + +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO* 3.2 4.2 + - + +
54A LYS* 1.3 79.8 - - - +
56A LYS* 1.3 58.7 + - - +
58A LEU* 3.5 9.3 + - - +
59A LYS* 3.0 28.3 + - + +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.0 27.6 - - + +
53A PRO* 3.1 24.8 + - + +
55A GLU* 1.3 80.3 - - - +
57A VAL* 1.3 65.9 + - - +
59A LYS* 3.2 8.1 + - + +
60A LEU* 2.9 22.8 + - + +
101A ALA* 3.3 33.4 + - + -
121A TYR* 3.6 25.5 + - - +
262A TYR* 3.7 14.3 + - - -
266A LYS* 5.2 4.2 - - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.6 35.2 - - + +
53A PRO 3.1 8.7 + - - +
54A LYS 3.9 1.1 - - - +
56A LYS* 1.3 76.2 - - - +
58A LEU* 1.3 63.4 + - - +
60A LEU* 3.2 8.4 + - + +
61A TYR* 3.1 20.4 + - - +
259A PHE* 4.2 15.9 - - + -
319A LEU* 3.8 20.8 - - + +
322A TYR* 4.1 13.0 - - + -
323A LEU* 3.6 21.5 - - + -
328A TRP* 3.9 15.5 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 2.8 52.0 + - + +
55A GLU* 3.8 7.9 - - - +
57A VAL* 1.3 73.9 - - - +
59A LYS* 1.3 56.5 + - - +
61A TYR* 3.2 4.8 + - + +
62A LYS* 2.8 44.2 + - + +
323A LEU* 3.8 25.1 - - + -
328A TRP 3.9 8.3 - - - +
329A TRP* 3.8 34.3 - - + -
333A GLN* 5.9 1.1 - - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.0 16.7 + - + +
56A LYS* 3.2 11.9 + - + +
58A LEU* 1.3 75.4 - - - +
60A LEU* 1.3 62.6 + - - +
62A LYS* 4.5 5.4 - - - +
63A SER* 2.7 39.6 + - - +
120A MET 5.0 0.6 + - - -
121A TYR* 3.2 51.0 + - + +
123A ASP* 2.9 32.2 + - - -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.2 22.2 - - + -
56A LYS* 2.9 17.2 + - + +
57A VAL* 3.2 21.1 + - + +
59A LYS* 1.3 74.7 - - - +
61A TYR* 1.3 65.7 + - - +
63A SER* 3.7 1.8 - - - -
64A MET* 3.1 28.9 + - - +
97A VAL* 3.4 43.4 - - + +
98A GLY* 4.3 3.4 - - - +
101A ALA* 3.7 17.7 - - + -
121A TYR* 4.1 6.7 - - + -
258A VAL* 4.5 13.2 - - + +
259A PHE* 4.4 13.2 - - + -
262A TYR* 5.9 1.6 - - + -
319A LEU* 4.0 9.9 - - + -
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL 3.1 10.2 + - - +
58A LEU* 3.7 7.9 - - + +
60A LEU* 1.3 81.6 - - - +
62A LYS* 1.3 69.6 + - + +
64A MET* 3.2 5.9 + - - +
65A THR* 3.0 48.4 + - + +
316A ILE* 3.8 16.8 - - + -
319A LEU* 3.7 22.9 - - + +
320A ARG* 2.9 40.9 + - + -
323A LEU* 3.6 25.8 - - + -
329A TRP* 3.7 26.2 - + - -
334A GLU* 2.5 30.2 + - - -
337A TRP* 4.5 2.7 - + - -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 2.8 32.5 + - + +
59A LYS* 4.3 4.3 - - - +
61A TYR* 1.3 80.1 - - + +
63A SER* 1.3 57.3 + - - +
65A THR* 3.4 6.1 + - - -
66A LEU* 2.8 34.1 + - - +
329A TRP* 4.0 23.7 - - + -
337A TRP* 3.5 51.2 - - + +
340A GLN* 5.3 2.6 + - - -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 2.7 29.5 + - - +
60A LEU 3.7 3.6 - - - -
62A LYS* 1.3 76.4 - - - +
64A MET* 1.3 58.3 + - - +
66A LEU* 4.6 1.3 - - - -
67A LEU* 3.0 31.5 + - - +
97A VAL* 3.9 18.2 - - - -
117A GLY* 5.7 0.2 - - - -
120A MET* 3.7 23.8 + - - +
121A TYR* 3.9 22.6 - - - -
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU 3.1 13.3 + - - +
61A TYR* 3.2 6.3 + - + +
63A SER* 1.3 76.9 - - - +
65A THR* 1.3 59.1 + - + +
67A LEU* 3.6 6.0 - - - +
68A ASN* 3.0 26.7 + - - +
93A GLU* 3.8 16.0 - - + +
94A GLY* 3.7 27.1 - - - +
97A VAL* 3.3 35.4 - - + -
258A VAL* 3.9 5.4 - - + -
315A PRO 3.8 24.5 - - - +
316A ILE* 3.8 30.8 - - + +
319A LEU* 3.4 18.6 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.0 36.0 + - + +
62A LYS* 3.4 1.7 + - - -
64A MET* 1.3 75.5 - - - +
66A LEU* 1.3 58.2 + - - +
68A ASN* 3.7 6.9 - - + +
69A THR* 2.9 33.7 + - - -
316A ILE* 3.7 29.8 - - + -
320A ARG* 4.5 3.6 - - - +
334A GLU* 5.5 1.8 - - - +
337A TRP* 2.8 32.9 + - + -
341A SER* 5.5 0.7 - - - -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 2.8 19.3 + - - +
63A SER* 4.0 3.8 - - - +
65A THR* 1.3 72.3 + - - +
67A LEU* 1.3 65.8 + - - +
69A THR* 3.3 4.8 + - - -
70A MET* 3.0 23.6 + - - +
120A MET* 3.7 27.8 - - + -
126A LEU* 4.3 19.1 - - + -
337A TRP* 4.2 16.5 - - + -
341A SER* 3.8 24.9 - - - +
344A LYS* 4.8 8.5 - - + -
345A VAL* 3.8 23.6 - - + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.0 19.4 + - - +
64A MET* 3.6 3.8 - - - +
66A LEU* 1.3 76.3 - - - +
68A ASN* 1.3 57.1 + - - +
70A MET* 3.1 20.0 + - + +
71A ASP* 2.8 32.7 + - - +
89A ASN* 3.8 38.4 - - + +
93A GLU* 4.0 17.0 - - + +
96A HIS* 3.9 5.6 - - - +
97A VAL* 6.2 0.9 - - + -
116A ALA* 3.9 18.2 - - + -
117A GLY* 3.7 26.2 - - - +
120A MET* 3.8 17.8 - - + +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET 3.0 18.0 + - - +
65A THR* 3.3 9.8 + - + +
67A LEU* 1.3 76.7 - - - +
69A THR* 1.3 59.8 + - - +
71A ASP* 3.4 7.4 + - - +
72A ARG* 2.7 67.8 + - - +
90A TYR* 3.5 18.7 - - - -
93A GLU* 3.2 22.4 + - - +
314A HIS* 5.0 5.1 + - - -
316A ILE* 4.1 11.7 - - + +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 2.9 21.0 + - - -
66A LEU* 3.5 8.5 - - - -
67A LEU 3.3 0.2 - - - -
68A ASN* 1.3 71.4 + - - +
70A MET* 1.3 64.1 + - - +
72A ARG* 3.4 10.6 + - - +
73A ILE* 3.2 31.9 + - + +
341A SER* 3.8 22.3 + - - +
342A ARG* 3.9 34.1 + - + +
345A VAL* 3.9 17.0 - - + -
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 3.0 16.8 + - - +
67A LEU* 3.6 24.0 - - + +
69A THR* 1.3 74.2 - - - +
71A ASP* 1.3 66.9 + - - +
73A ILE* 3.3 1.9 + - - +
74A LEU* 2.9 41.4 + - + +
86A TYR* 3.9 15.3 - - - +
116A ALA* 5.3 1.8 - - + -
120A MET* 4.1 4.5 - - + -
126A LEU* 4.0 14.1 - - - -
129A PHE* 3.8 51.8 - - + -
130A MET* 3.9 15.7 - - + -
150A TYR* 4.5 3.6 - - - +
345A VAL* 4.0 15.7 - - + +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 2.8 24.2 + - - +
68A ASN* 3.5 6.9 - - - +
70A MET* 1.3 78.0 - - - +
72A ARG* 1.3 58.3 + - - +
75A TYR* 2.9 32.9 + - - +
86A TYR* 2.6 35.2 + - - -
88A THR* 3.7 6.6 - - + -
89A ASN* 2.8 49.6 + - - +
90A TYR* 3.6 21.6 + - + +
93A GLU* 5.1 0.7 - - - +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 2.7 42.9 + - - +
69A THR* 3.7 6.5 - - - +
70A MET 3.3 0.2 - - - -
71A ASP* 1.3 78.5 - - - +
73A ILE* 1.3 65.7 + - + +
75A TYR* 3.8 3.4 - - - +
76A GLU* 3.1 23.7 + - - +
90A TYR* 3.5 19.2 - - + +
342A ARG* 3.7 29.7 - - - +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.2 22.8 + - + +
70A MET 3.8 2.9 - - - +
72A ARG* 1.3 77.6 - - + +
74A LEU* 1.3 60.2 + - + +
76A GLU* 3.2 7.8 + - - +
77A SER* 2.9 25.6 + - - -
342A ARG* 4.3 17.0 - - + +
345A VAL* 3.3 37.0 - - + -
346A MET* 3.7 31.9 - - + -
349A PHE* 3.8 29.6 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 2.9 48.8 + - + +
73A ILE* 1.3 70.0 - - + +
75A TYR* 1.3 66.0 + - - +
77A SER* 3.2 3.6 + - - -
78A GLN* 3.0 20.4 + - - +
83A ILE* 3.6 21.5 - - + +
86A TYR* 3.6 37.8 - - + +
129A PHE 5.4 0.4 - - - +
130A MET* 3.7 32.1 - - + -
133A CYS* 4.3 13.0 - - + -
134A TYR* 4.5 5.4 - - + -
150A TYR* 4.7 1.3 - - - +
349A PHE* 4.2 20.0 - - + -
----------------------------------------------------------
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP 2.9 20.7 + - - +
72A ARG* 3.8 5.2 - - - +
74A LEU* 1.3 76.0 - - - +
76A GLU* 1.3 67.3 + - - +
78A GLN* 3.2 4.4 + - - +
79A ARG* 3.1 57.6 + - + +
86A TYR* 3.8 10.1 - + - -
87A MET* 6.3 0.2 - - - -
88A THR* 4.0 23.1 - - + -
90A TYR* 4.7 3.6 - + - +
290A HIS* 3.4 33.7 + + + -
292A SER 4.8 2.2 - - - -
293A THR* 3.7 34.3 + - + -
295A ASP 5.2 1.2 + - - -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 3.1 12.9 + - - +
73A ILE* 3.2 9.4 + - - +
75A TYR* 1.3 80.9 - - - +
77A SER* 1.3 63.6 + - - +
79A ARG* 3.2 14.4 + - - +
80A GLN* 3.0 55.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE 2.9 14.0 + - - -
74A LEU* 3.5 13.0 - - - -
75A TYR 3.2 0.2 - - - -
76A GLU* 1.3 77.1 - - - +
78A GLN* 1.3 61.4 + - - +
80A GLN* 3.2 5.1 + - - +
81A GLY 3.2 3.8 + - - -
82A ARG* 3.0 44.3 + - - +
83A ILE* 3.8 10.5 + - - +
134A TYR* 3.0 22.3 + - - -
349A PHE* 3.7 20.0 - - - -
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 3.0 12.5 + - - +
75A TYR 3.5 8.3 - - - +
77A SER* 1.3 78.2 - - - +
79A ARG* 1.3 97.6 + - - +
81A GLY* 2.9 14.6 + - - -
83A ILE* 3.6 15.4 + - + +
84A SER 3.4 18.0 + - - -
85A PHE* 3.6 23.3 - - - +
86A TYR* 4.2 2.0 - - + -
293A THR* 3.2 31.4 + - + +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.1 52.3 + - + +
76A GLU* 3.2 19.7 + - - +
78A GLN* 1.3 107.6 + - - +
80A GLN* 1.3 60.2 + - - +
293A THR* 3.0 25.9 + - - -
----------------------------------------------------------
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.0 43.0 + - - +
77A SER* 3.7 7.4 - - - +
78A GLN 3.0 1.4 - - - -
79A ARG* 1.3 76.6 - - + +
81A GLY* 1.3 59.3 + - - +
82A ARG* 2.9 43.8 + - + +
----------------------------------------------------------
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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