Contacts of the helix formed by residues 76 - 110 (chain A) in PDB entry 6XWQ
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 1.3 74.5 - - - +
77A PRO* 1.3 64.9 - - - +
78A ALA* 3.0 11.1 + - - +
79A ARG* 3.1 14.4 + - - +
80A LEU* 2.7 32.6 + - - +
168A THR* 4.7 2.0 - - - -
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Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE 3.5 3.6 - - - +
76A SER* 1.3 89.2 - - - +
78A ALA* 1.3 54.7 + - - +
80A LEU* 3.7 12.6 - - + +
81A GLY* 2.9 24.4 + - - -
165A ILE* 5.3 8.3 - - + -
168A THR* 3.6 24.5 - - + +
169A TYR* 3.3 42.6 - - + +
172A ASN* 5.8 1.8 - - - +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 3.0 8.1 + - - +
77A PRO* 1.3 75.9 - - - +
79A ARG* 1.3 66.5 + - - +
81A GLY* 3.2 2.1 + - - -
82A ARG* 3.0 31.4 + - - +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER 5.1 6.1 + - - -
75A ILE* 3.7 18.4 - - + +
76A SER* 3.1 16.2 + - - +
78A ALA* 1.3 78.2 - - - +
80A LEU* 1.3 58.0 + - - +
82A ARG* 3.4 26.9 + - - +
83A VAL* 2.9 38.4 + - + +
298A ASP* 5.8 4.9 + - - +
300A GLY* 3.9 27.9 - - - +
301A ILE* 5.0 7.4 - - - +
420A GLU* 3.2 28.3 + - - +
422A GLU* 5.1 10.1 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 3.2 35.0 - - + +
75A ILE* 3.4 26.5 - - + +
76A SER 2.7 21.2 + - - +
77A PRO* 3.7 9.0 - - + +
79A ARG* 1.3 73.7 - - - +
81A GLY* 1.3 58.4 + - - +
83A VAL* 3.8 1.0 - - - +
84A GLY* 2.8 26.2 + - - -
161A ILE* 5.3 2.9 - - + -
165A ILE* 3.6 31.4 - - + -
168A THR* 5.4 0.9 - - + -
304A PHE* 3.7 36.8 - - + -
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO 2.9 17.5 + - - -
78A ALA* 3.2 1.3 + - - -
80A LEU* 1.3 75.0 - - - +
82A ARG* 1.3 65.0 + - - +
84A GLY* 3.2 1.6 + - - -
85A VAL* 2.9 32.8 + - - +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA* 3.0 19.7 + - - +
79A ARG* 3.4 37.7 + - - +
81A GLY* 1.3 76.0 - - - +
83A VAL* 1.3 60.1 + - + +
85A VAL* 3.9 3.6 - - - +
86A LYS* 2.9 57.3 + - + +
419A THR 5.4 0.7 - - - -
420A GLU* 4.3 18.6 + - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 5.7 2.5 - - + -
79A ARG* 2.9 27.7 + - + +
80A LEU* 4.1 4.0 - - - +
82A ARG* 1.3 80.5 - - + +
84A GLY* 1.3 58.2 + - - +
86A LYS* 3.7 6.5 - - - +
87A ILE* 2.9 28.8 + - - +
300A GLY 5.3 3.8 - - - +
301A ILE* 4.9 9.0 - - + +
304A PHE* 4.4 10.5 - - + -
305A THR* 3.6 28.3 - - + -
416A VAL* 3.7 15.9 - - + -
420A GLU* 3.4 29.4 - - + +
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU 2.8 18.9 + - - -
81A GLY* 3.2 2.4 + - - -
83A VAL* 1.3 77.6 - - - +
85A VAL* 1.3 56.0 + - - +
87A ILE* 3.2 7.7 - - - +
88A VAL* 2.9 38.9 + - - +
304A PHE* 4.1 13.7 - - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY* 2.9 19.3 + - - +
82A ARG* 4.0 3.1 - - - +
84A GLY* 1.3 74.7 - - - +
86A LYS* 1.3 60.3 + - + +
88A VAL* 4.7 3.1 - - - -
89A VAL* 3.0 50.7 + - + +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG* 2.9 45.6 + - + +
83A VAL* 3.7 4.9 - - - +
85A VAL* 1.3 79.1 - - + +
87A ILE* 1.3 57.4 + - - +
89A VAL* 5.1 2.6 - - - +
90A TYR* 3.7 15.7 + - - +
416A VAL* 3.4 31.3 + - + +
419A THR* 2.5 59.4 + - + +
420A GLU* 4.0 3.6 - - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL 2.9 20.2 + - - +
84A GLY* 3.2 13.0 - - - +
86A LYS* 1.3 78.4 - - - +
88A VAL* 1.3 71.7 + - + +
89A VAL 3.5 0.4 - - - -
90A TYR* 3.4 6.0 + - + +
91A TYR* 2.9 80.0 + - + +
304A PHE* 4.7 1.8 - - + -
305A THR* 3.8 22.9 - - + -
308A LEU* 4.5 10.3 - - + -
412A GLY 3.8 18.6 - - - +
413A THR 4.5 0.2 - - - +
416A VAL* 3.5 21.1 - - + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 2.9 23.5 + - - +
85A VAL* 4.1 3.8 - - - +
87A ILE* 1.3 81.3 - - + +
89A VAL* 1.3 67.8 + - + +
91A TYR* 3.2 6.6 + - + +
92A LEU* 3.0 44.5 + - + +
304A PHE* 6.5 0.2 - - + -
308A LEU* 4.8 12.8 - - + -
312A ILE* 5.1 8.1 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.0 34.0 + - + +
86A LYS* 5.1 3.1 - - - -
88A VAL* 1.3 77.5 - - + +
90A TYR* 1.3 57.1 + - - +
92A LEU* 3.5 5.8 + - - +
93A ALA* 2.9 35.9 + - + +
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS 3.7 15.9 + - - +
87A ILE* 3.4 10.1 + - + +
88A VAL 3.2 0.6 - - - -
89A VAL* 1.3 78.9 - - - +
91A TYR* 1.3 87.1 + + - +
93A ALA* 4.5 3.8 - - - -
94A THR* 2.9 57.7 + - + +
249A TYR* 3.7 14.9 - - - -
252A LEU* 3.5 22.0 - - + -
313A ASN* 4.6 2.2 - - - -
315A ASP* 5.0 0.4 + - - -
408A GLY* 3.1 21.0 + - - -
411A ALA* 3.7 11.4 - - + +
412A GLY* 3.3 33.0 + - - -
415A ILE* 5.1 14.8 - - + -
416A VAL* 5.5 0.9 - - + -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 2.9 53.3 + - + +
88A VAL* 3.2 6.9 + - - +
90A TYR* 1.3 91.4 - + - +
92A LEU* 1.3 61.3 + - + +
94A THR* 3.2 3.9 + - - -
95A SER* 2.4 39.2 + - - +
305A THR* 3.1 24.6 + - - -
306A LEU* 5.0 0.3 - - - +
308A LEU* 4.2 9.0 - - + -
309A GLY* 3.2 24.8 - - - -
312A ILE* 3.6 29.8 - - + +
313A ASN* 3.4 34.5 - - + +
353A ILE* 6.2 1.6 - - + -
409A ASP* 4.5 7.3 + - - -
412A GLY* 5.0 2.5 - - - -
413A THR 5.4 0.2 + - - -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.0 37.8 + - + +
89A VAL* 4.1 4.5 - - - +
91A TYR* 1.3 80.9 - - + +
93A ALA* 1.3 62.7 + - - +
95A SER* 3.3 4.8 + - - -
96A ALA* 3.0 26.5 + - - +
312A ILE* 6.0 2.5 - - + -
349A VAL* 4.6 9.6 - - + +
350A LEU* 6.3 0.4 - - + -
353A ILE* 3.7 29.8 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 2.9 23.3 + - + +
90A TYR* 3.8 5.2 - - - +
92A LEU* 1.3 77.5 - - - +
94A THR* 1.3 60.8 + - + +
96A ALA* 3.4 4.9 + - - +
97A MET* 2.9 37.2 + - + +
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 2.9 53.5 + - + +
91A TYR* 3.2 7.6 + - - -
93A ALA* 1.3 74.9 - - + +
95A SER* 1.3 61.9 + - - +
97A MET* 3.7 7.6 - - - +
98A ALA* 2.8 26.3 + - - +
244A GLN* 4.6 2.0 + - - +
248A THR* 4.5 11.0 - - + -
249A TYR* 4.9 2.0 - - + -
252A LEU* 4.1 13.5 - - + -
313A ASN* 4.0 3.1 + - - -
315A ASP* 3.2 28.3 + - - +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 2.4 30.2 + - - +
92A LEU* 3.7 4.8 - - - -
93A ALA 3.3 0.2 - - - -
94A THR* 1.3 77.4 + - - +
96A ALA* 1.3 57.1 + - - +
98A ALA* 3.2 4.3 + - - +
99A VAL* 3.0 34.9 + - - +
312A ILE 5.1 2.1 + - - -
313A ASN* 4.5 5.0 + - - -
314A MET 4.7 12.1 + - - -
315A ASP* 3.3 12.9 + - - -
318A ALA* 4.3 6.0 - - - +
349A VAL* 4.1 23.0 - - - +
352A SER* 5.3 2.0 - - - -
353A ILE* 5.2 4.3 - - - +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 3.0 16.9 + - - +
93A ALA* 3.8 4.9 - - - +
95A SER* 1.3 76.0 - - - +
97A MET* 1.3 58.6 + - + +
99A VAL* 3.3 2.3 + - - +
100A PHE* 2.9 28.8 + - - +
345A VAL* 3.8 22.7 - - + +
349A VAL* 4.1 10.7 - - + +
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 2.9 25.5 + - + +
94A THR* 3.8 7.9 - - - +
95A SER 3.3 0.2 - - - -
96A ALA* 1.3 77.2 - - + +
98A ALA* 1.3 57.5 + - - +
100A PHE* 3.3 12.3 + - - +
101A PHE* 2.9 47.3 + - + -
244A GLN* 4.3 0.4 - - - +
248A THR* 4.5 17.9 - - + +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR 2.8 17.8 + - - +
95A SER 3.2 4.9 + - - +
97A MET* 1.3 73.7 - - - +
99A VAL* 1.3 59.5 + - - +
101A PHE* 3.3 1.5 + - - -
102A GLY 2.9 24.4 + - - -
244A GLN* 3.2 28.0 + - - +
315A ASP* 3.7 29.6 - - + +
318A ALA* 4.7 0.4 - - + -
319A LEU* 3.3 18.4 - - + +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER 3.0 18.8 + - - +
96A ALA 3.8 4.3 - - - +
98A ALA* 1.3 75.2 - - - +
100A PHE* 1.3 58.4 + - - +
102A GLY* 3.2 1.6 + - - -
103A LEU* 2.9 33.7 + - + +
318A ALA* 3.7 31.0 - - + +
319A LEU* 4.8 1.3 - - - +
322A GLY* 4.4 14.2 - - - -
344A VAL* 4.2 2.7 - - + +
345A VAL* 3.7 30.3 - - + +
348A ALA* 3.9 21.5 - - + -
349A VAL* 4.6 9.4 - - + -
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 2.9 17.8 + - - +
97A MET* 3.7 14.1 - - - +
99A VAL* 1.3 78.4 - - - +
101A PHE* 1.3 73.8 + + - +
103A LEU* 3.2 9.4 + - + +
104A ILE* 2.9 58.0 + - + +
341A GLN* 3.7 29.4 - - + -
345A VAL* 4.7 6.0 - - + +
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A MET* 2.9 40.2 + - + +
98A ALA* 3.7 5.6 - - - +
100A PHE* 1.3 88.7 - + - +
102A GLY* 1.3 58.9 + - - +
104A ILE* 3.3 10.9 + - + +
105A VAL* 2.9 35.1 + - + +
240A GLY 5.1 1.3 - - - +
243A LEU* 3.9 37.2 - - + -
244A GLN* 4.7 8.7 - - - +
247A ILE* 3.5 35.2 - - + -
248A THR* 4.0 17.0 - - - -
319A LEU* 4.2 11.2 - - + -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 2.9 11.3 + - - -
99A VAL* 3.6 3.4 - - - -
100A PHE 3.2 0.2 - - - -
101A PHE* 1.3 77.2 - - - +
103A LEU* 1.3 57.8 + - - +
105A VAL* 3.1 6.5 - - - +
106A GLY* 2.9 24.8 + - - -
319A LEU* 3.6 16.9 - - - +
322A GLY 5.1 0.2 - - - -
323A VAL* 3.4 30.7 - - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 2.9 21.2 + - + +
100A PHE* 3.2 11.9 + - + +
102A GLY* 1.3 75.2 - - - +
104A ILE* 1.3 60.1 + - + +
106A GLY* 3.3 0.9 + - - -
107A ARG* 2.9 34.3 + - + +
322A GLY* 3.2 32.3 - - - +
325A VAL* 6.3 0.2 - - + -
326A LEU* 4.0 23.5 - - + +
336A LEU* 6.0 2.9 - - + -
341A GLN* 3.6 41.7 - - + +
344A VAL* 3.7 27.1 - - + -
345A VAL* 5.5 1.8 - - + -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 2.9 55.5 + - + +
101A PHE* 3.5 14.8 - - + +
102A GLY 3.2 0.4 - - - -
103A LEU* 1.3 77.7 - - + +
105A VAL* 1.3 63.9 + - + +
107A ARG* 3.1 30.9 + - - +
108A LEU* 2.9 35.2 + - + +
243A LEU* 5.5 6.7 - - + -
341A GLN* 6.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 2.9 19.3 + - + +
102A GLY* 3.1 21.3 - - - +
104A ILE* 1.3 77.1 - - + +
106A GLY* 1.3 57.2 + - - +
108A LEU* 3.7 12.4 - - + +
109A PHE* 3.0 38.3 + - + +
236A ALA* 4.2 12.0 - - + +
239A THR* 4.8 8.5 - - + -
240A GLY* 4.0 28.0 - - - +
243A LEU* 3.9 27.8 - - + -
323A VAL* 4.2 9.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY 2.9 16.9 + - - -
103A LEU 3.7 1.8 - - - -
104A ILE 3.1 0.2 - - - -
105A VAL* 1.3 75.9 - - - +
107A ARG* 1.3 59.6 + - - +
110A ASN* 2.8 32.2 + - - -
111A VAL* 3.8 9.2 + - - -
323A VAL* 4.6 14.8 - - - -
326A LEU* 4.4 19.2 - - - +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 2.9 17.8 + - + +
104A ILE* 3.1 29.5 + - - +
106A GLY* 1.3 75.1 - - - +
108A LEU* 1.3 62.1 + - - +
110A ASN* 4.1 7.8 + - - +
326A LEU* 4.5 15.4 - - + +
341A GLN* 5.0 11.4 + - - -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 2.9 22.8 + - + +
105A VAL* 3.7 13.0 - - + +
106A GLY 3.1 0.4 - - - -
107A ARG* 1.3 80.3 - - - +
109A PHE* 1.3 88.5 + - + +
110A ASN* 3.7 1.4 + - - +
243A LEU* 6.5 0.7 - - + -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 3.0 19.2 + - + +
108A LEU* 1.3 99.3 - - + +
110A ASN* 1.3 72.3 + - - +
111A VAL* 4.3 12.6 - - + -
232A LYS* 3.3 34.9 + - - -
235A GLY 3.3 23.8 - - - -
236A ALA* 3.4 24.7 - - + -
239A THR* 3.8 24.7 - - + -
----------------------------------------------------------
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLY 2.8 15.4 + - - -
107A ARG* 4.1 7.4 + - - +
108A LEU 3.4 2.9 - - - +
109A PHE* 1.3 82.6 - - - +
111A VAL* 1.3 62.4 + - - +
112A GLY 3.7 0.9 + - - -
113A ALA* 3.4 29.1 - - - +
232A LYS* 4.7 4.9 + - - +
330A ASN* 3.1 26.9 - - - +
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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