Contacts of the helix formed by residues 58 - 87 (chain A) in PDB entry 2L6X
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 TRP 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.2 9.6 - - + -
55A SER* 3.3 36.8 + - - +
56A ALA 3.0 1.2 - - - -
57A LYS* 1.3 84.2 - - + +
59A LYS* 1.3 65.3 + - - +
60A THR 3.2 2.5 - - - -
61A SER* 3.6 31.2 - - - -
62A LEU* 2.9 37.2 + - + +
109A PHE* 4.5 9.9 - + - -
113A LEU* 5.3 13.2 - - + -
181A ALA* 4.8 18.0 - - + +
182A VAL* 5.6 1.6 - - + -
185A ALA* 3.5 32.8 - - + -
238A ILE* 3.5 26.7 - - + -
242A ALA* 3.4 27.3 + - + +
246A SER* 5.8 0.2 - - - -
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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
----------------------------------------------------------
51A ARG* 4.6 24.3 + - - +
54A VAL* 5.2 7.4 - - + -
55A SER 3.5 4.1 + - - +
56A ALA* 2.7 29.5 + - - +
57A LYS 3.1 1.0 - - - -
58A TRP* 1.3 79.2 - - - +
60A THR* 1.3 55.8 + - + +
62A LEU* 4.2 2.3 - - - +
63A THR* 2.6 31.0 + - - -
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Residues in contact with THR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 4.2 5.9 + - - -
59A LYS* 1.3 77.0 - - - +
61A SER* 1.3 67.1 + - - +
63A THR* 3.0 10.7 + - + -
64A VAL* 2.9 33.1 + - + +
112A ILE* 3.8 26.8 - - + +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TRP* 3.1 43.9 + - - -
60A THR* 1.3 78.4 - - - +
62A LEU* 1.3 57.8 + - - +
64A VAL* 3.3 2.4 - - - +
65A SER* 2.9 35.2 + - - -
109A PHE* 4.5 10.2 + - - -
112A ILE* 3.2 35.9 - - - +
113A LEU* 4.2 7.3 + - - -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.2 43.1 - - + -
51A ARG* 5.7 12.1 - - + -
54A VAL* 3.6 38.1 - - + -
58A TRP* 2.9 34.5 + - + +
59A LYS 4.2 2.7 - - - +
61A SER* 1.3 75.4 - - - +
63A THR* 1.3 56.9 + - - +
65A SER* 4.5 3.6 - - - -
66A GLY* 2.7 33.3 + - - +
235A GLY* 5.4 2.0 - - - +
238A ILE* 5.0 6.7 - - + -
239A TRP* 4.6 22.4 - - + -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.9 19.0 + - - +
59A LYS 2.6 20.8 + - - -
60A THR* 3.0 16.3 + - + +
62A LEU* 1.3 79.6 - - - +
64A VAL* 1.3 62.9 + - + +
67A LEU* 2.9 54.6 + - + +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 2.9 28.9 + - + +
61A SER 3.3 6.1 - - - +
63A THR* 1.3 76.1 - - + +
65A SER* 1.3 72.8 + - - +
67A LEU* 3.8 6.1 - - + +
68A VAL* 2.9 31.0 + - - +
108A GLU* 3.6 37.9 - - + +
109A PHE* 4.7 0.4 - - - +
111A LEU* 5.7 3.4 - - + -
112A ILE* 3.6 28.7 - - + -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER 2.9 22.3 + - - -
62A LEU* 4.5 5.8 - - - -
64A VAL* 1.3 80.9 - - - +
66A GLY* 1.3 57.5 + - - +
68A VAL* 3.2 6.8 - - - +
69A THR* 2.6 35.9 + - - -
105A LEU 4.9 1.6 + - - -
108A GLU* 5.2 2.5 - - - -
109A PHE* 4.4 16.9 - - - +
234A PHE* 3.0 36.8 - - - -
238A ILE* 5.0 7.2 - - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.8 26.7 - - - -
62A LEU* 2.7 26.5 + - - +
65A SER* 1.3 71.9 - - - +
67A LEU* 1.3 55.9 + - - +
69A THR* 4.5 3.6 - - - -
70A GLY* 2.7 31.2 + - - -
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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 THR* 2.9 44.2 + - + +
64A VAL* 3.8 7.9 - - + +
66A GLY* 1.3 77.0 - - - +
68A VAL* 1.3 58.1 + - - +
70A GLY* 3.9 0.2 - - - -
71A ILE* 2.9 50.4 + - + +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL 2.9 26.1 + - - +
65A SER* 3.2 13.0 - - - +
67A LEU* 1.3 74.0 - - - +
69A THR* 1.3 70.5 + - - +
71A ILE* 3.5 7.3 + - - +
72A ALA* 3.0 28.2 + - - +
101A THR* 3.7 14.4 - - + +
104A LEU* 3.6 22.4 - - + +
105A LEU* 3.3 49.4 - - + +
108A GLU* 5.0 2.5 - - + -
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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 SER 2.6 24.6 + - - -
66A GLY* 4.2 3.1 - - - -
68A VAL* 1.3 81.0 - - - +
70A GLY* 1.3 56.6 + - - +
72A ALA* 4.1 3.9 - - - +
73A PHE* 3.0 28.7 + - + +
105A LEU* 4.6 6.9 - - - +
231A LYS* 2.9 40.9 - - + +
232A ILE* 5.3 0.9 - - + -
234A PHE* 3.0 29.0 - - + -
235A GLY* 4.8 3.6 - - - +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 2.7 23.7 + - - -
67A LEU* 3.9 0.7 - - - -
69A THR* 1.3 72.6 - - - +
71A ILE* 1.3 59.6 + - - +
73A PHE* 3.9 6.7 - - - +
74A TRP* 3.1 30.0 + - - +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 2.9 40.6 + - + +
68A VAL* 4.0 6.1 - - - +
70A GLY* 1.3 72.5 - - - +
72A ALA* 1.3 62.1 + - - +
74A TRP* 4.0 6.9 - - + +
75A HIS* 3.0 32.6 + - + +
97A ASP* 5.5 2.0 - - - +
100A LEU* 6.5 0.9 - - + -
101A THR* 5.8 3.6 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.0 15.5 + - + +
69A THR* 4.6 0.4 - - - -
71A ILE* 1.3 76.2 - - - +
73A PHE* 1.3 56.9 + - - +
76A TYR* 2.8 38.5 + - - +
97A ASP* 3.8 12.0 - - - +
101A THR* 3.2 31.8 - - + +
105A LEU* 5.9 1.1 - - + -
231A LYS* 3.2 26.2 - - + -
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 5.3 0.4 - - + -
40A LEU* 3.2 43.7 - - + -
44A THR* 5.2 2.9 - - - -
69A THR* 3.0 22.4 + - + +
70A GLY* 3.9 6.1 - - - +
72A ALA* 1.3 76.9 - - - +
74A TRP* 1.3 62.0 + + + +
76A TYR* 4.1 1.3 - - - +
77A MET* 2.8 45.2 + - + +
224A ASN* 5.9 0.4 - - - -
227A ASP* 4.9 2.7 - - - -
228A PHE* 3.4 32.1 - + + -
231A LYS* 3.6 23.5 - - + +
232A ILE* 3.2 44.2 - - + -
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Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.7 17.9 - - + +
70A GLY 3.1 16.0 + - - +
71A ILE* 4.0 6.3 - - + +
73A PHE* 1.3 84.6 - + + +
75A HIS* 1.3 64.9 + - - +
77A MET* 3.6 10.2 - - - +
78A TYR* 3.0 28.2 + - + +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.0 23.1 + - + +
74A TRP* 1.3 78.3 - - - +
76A TYR* 1.3 64.4 + - - +
78A TYR* 3.1 8.2 + - - +
79A MET* 2.9 42.8 + - + +
93A PHE* 3.4 41.0 + + - +
94A ARG* 4.1 2.9 - - - -
97A ASP* 3.1 45.5 + - + +
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 2.8 22.6 + - - +
73A PHE 4.1 0.4 - - - +
75A HIS* 1.3 78.8 + - - +
77A MET* 1.3 54.6 + - - +
79A MET* 3.1 5.3 + - - +
80A ARG* 2.8 50.3 + - + +
94A ARG* 3.4 46.1 + - + +
97A ASP* 3.5 18.6 - - - +
98A TRP* 4.5 15.8 - + + -
137A PHE* 4.9 11.4 - - - -
223A TYR* 5.4 6.1 - + + -
227A ASP* 2.9 48.6 - - + +
231A LYS* 3.8 6.7 - - - -
301A RET 4.5 4.6 - - + +
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Residues in contact with MET 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 5.0 18.2 - - + -
36A VAL* 4.1 31.2 - - + -
37A THR* 5.6 4.7 - - - +
40A LEU* 4.2 21.3 - - + -
73A PHE* 2.8 36.7 + - + +
74A TRP* 3.6 13.0 - - - +
76A TYR* 1.3 75.0 - - - +
78A TYR* 1.3 72.7 + - + +
80A ARG* 3.4 5.2 + - - +
81A GLY* 3.0 23.0 + - - -
224A ASN* 4.2 13.0 - - - +
227A ASP* 4.7 1.7 + - - -
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Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.0 17.2 + - + +
75A HIS* 3.5 9.0 - - - +
77A MET* 1.3 86.7 - - + +
79A MET* 1.3 78.8 + - + +
81A GLY* 3.3 1.3 + - - -
82A VAL* 3.0 47.5 + - + +
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Residues in contact with MET 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 2.9 37.0 + - + +
76A TYR* 3.4 8.1 - - - +
78A TYR* 1.3 93.0 - - + +
80A ARG* 1.3 52.6 + - - +
82A VAL* 3.1 10.7 + - + +
83A TRP* 2.8 34.8 + - - +
89A SER* 4.4 12.7 + - - +
90A PRO* 4.2 18.6 - - + +
93A PHE* 3.4 43.3 - - + -
94A ARG* 3.9 20.9 - - - +
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 2.8 35.0 + - + +
77A MET* 3.7 0.9 - - - +
79A MET* 1.3 71.2 - - - +
81A GLY* 1.3 63.6 + - - +
83A TRP* 2.9 42.5 + - - +
84A ILE* 3.1 13.7 + - - +
94A ARG* 3.1 39.8 - - - +
219A LEU* 4.5 2.0 - - - +
220A ASN* 3.3 30.7 + - - +
223A TYR* 3.1 60.6 - - - +
224A ASN* 3.2 34.5 - - + +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 6.5 1.6 - - - -
77A MET* 3.0 15.0 + - - -
78A TYR* 3.8 2.9 - - - -
80A ARG* 1.3 79.1 - - - +
82A VAL* 1.3 56.7 + - - +
84A ILE* 3.1 12.4 - - - +
85A GLU* 2.8 30.5 + - - +
220A ASN* 4.8 0.2 - - - -
224A ASN* 4.3 3.7 + - - -
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.0 50.5 + - + +
79A MET* 3.5 9.6 - - + +
81A GLY* 1.3 72.6 - - - +
83A TRP* 1.3 67.2 + - - +
85A GLU* 3.2 31.0 + - + +
86A THR* 3.5 12.4 + - + +
88A ASP 4.8 1.3 - - - +
89A SER* 4.7 9.7 - - - -
90A PRO* 6.0 2.0 - - + -
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Residues in contact with TRP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET 2.8 8.7 + - - +
80A ARG* 2.9 35.4 + - - +
82A VAL* 1.3 75.8 - - - +
84A ILE* 1.3 61.6 + - + +
87A GLY* 2.7 57.2 + - - -
88A ASP* 5.1 4.0 - - - -
89A SER* 3.3 56.3 - - - -
91A THR* 3.4 22.7 - - + -
94A ARG* 3.4 34.3 - - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 5.3 15.0 - - + +
80A ARG 3.1 3.3 + - - +
81A GLY* 3.1 19.3 - - - +
83A TRP* 1.3 85.3 - - + +
85A GLU* 1.3 68.1 + - - +
86A THR 3.2 2.1 + - - -
87A GLY* 3.9 7.3 + - - +
216A ALA* 3.8 28.3 - - + +
217A LEU* 4.7 7.4 - - + +
220A ASN* 2.9 59.7 - - + +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 6.4 1.8 - - - -
81A GLY 2.8 21.1 + - - +
82A VAL* 3.2 25.3 - - - +
83A TRP 3.2 0.2 - - - -
84A ILE* 1.3 80.6 - - - +
86A THR* 1.3 68.5 + - + +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.5 9.8 + - + +
84A ILE 4.0 2.0 - - - -
85A GLU* 1.3 92.3 - - + +
87A GLY* 1.3 62.4 + - - +
88A ASP* 3.3 21.2 + - - +
----------------------------------------------------------
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TRP* 2.7 42.3 + - - -
84A ILE* 3.9 7.1 + - - -
85A GLU 3.9 0.4 - - - -
86A THR* 1.3 74.7 + - - +
88A ASP* 1.3 68.1 + - - +
----------------------------------------------------------
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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