Contacts of the helix formed by residues 92 - 127 (chain A) in PDB entry 3UON
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 GLY 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 2.8 31.6 + - - +
90A PRO 3.5 3.4 + - - -
91A LEU* 1.3 78.4 - - - +
93A PRO* 1.3 71.0 - - - +
94A VAL* 3.5 3.4 - - - -
95A VAL* 3.2 2.4 - - - +
96A CYS* 3.1 14.2 + - - +
173A ASP 5.1 6.5 + - - -
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Residues in contact with PRO 93 (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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92A GLY* 1.3 82.6 - - - +
94A VAL* 1.3 70.2 + - + +
96A CYS* 3.1 6.8 + - + +
97A ASP* 2.8 34.7 + - - +
169A ARG* 3.4 39.9 - - - +
173A ASP* 5.1 15.5 - - + +
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Residues in contact with VAL 94 (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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91A LEU 5.4 2.2 - - - +
92A GLY* 5.0 1.3 - - - -
93A PRO* 1.3 84.3 - - + +
95A VAL* 1.3 72.5 + - + +
97A ASP* 3.3 9.7 + - - +
98A LEU* 3.1 35.9 + - + +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.7 9.6 - - + -
89A TRP* 3.7 6.5 - - + -
91A LEU* 3.0 54.1 - - + +
92A GLY 3.2 6.3 - - - +
94A VAL* 1.3 82.4 - - + +
96A CYS* 1.3 62.4 + - - +
98A LEU* 3.9 11.5 - - + +
99A TRP* 3.0 27.9 + - - +
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Residues in contact with CYS 96 (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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89A TRP* 3.5 15.0 - - + +
92A GLY 3.1 20.9 + - - +
93A PRO* 3.1 8.0 + - + +
95A VAL* 1.3 77.8 - - - +
97A ASP* 1.3 68.4 + - - +
99A TRP* 3.3 3.6 + - - +
100A LEU* 3.1 36.7 + - - +
169A ARG* 4.5 6.1 - - - -
171A VAL* 4.9 1.8 - - - -
175A GLU 4.4 3.4 - - - +
176A CYS* 2.0 56.0 - - - -
177A TYR 4.2 1.6 - - - -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 2.8 17.8 + - - +
94A VAL* 3.8 7.5 - - - +
96A CYS* 1.3 79.1 - - - +
98A LEU* 1.3 64.7 + - + +
100A LEU* 3.5 10.1 + - - +
101A ALA* 3.0 25.5 + - - +
159A ILE* 4.0 12.7 - - - +
160A LEU* 3.7 23.7 - - + +
163A GLN* 3.4 21.3 + - - -
169A ARG* 2.9 28.1 + - - -
171A VAL* 5.8 0.9 - - - +
177A TYR 5.4 1.4 - - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 3.1 32.0 + - + +
95A VAL* 3.9 12.3 - - + +
97A ASP* 1.3 76.9 - - + +
99A TRP* 1.3 57.4 + - - +
101A ALA* 3.7 4.5 - - + +
102A LEU* 2.9 32.7 + - - +
160A LEU* 4.1 23.8 - - + -
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Residues in contact with TRP 99 (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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75A PHE* 4.3 9.2 - - + -
76A SER* 3.3 29.7 + - - +
79A LEU* 3.5 33.2 - - + +
80A TYR* 3.5 50.9 - + + -
83A TYR* 5.0 6.7 - + + -
89A TRP* 3.8 18.6 - + + -
95A VAL 3.0 19.5 + - - +
96A CYS* 3.5 2.9 - - - +
97A ASP 3.2 0.4 - - - -
98A LEU* 1.3 78.0 - - - +
100A LEU* 1.3 80.6 + - + +
102A LEU* 3.7 5.9 - - + +
103A ASP* 3.0 25.4 + - + +
176A CYS* 3.7 28.7 - - + -
426A TYR* 5.7 2.7 - + - -
430A TYR* 4.1 9.9 - - - -
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Residues in contact with LEU 100 (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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96A CYS* 3.1 21.0 + - - +
97A ASP* 3.9 9.0 - - - +
99A TRP* 1.3 96.6 - - + +
101A ALA* 1.3 68.4 + - - +
103A ASP* 3.2 6.3 + - + +
104A TYR* 2.9 36.8 + - + +
159A ILE* 4.1 12.8 - - + -
176A CYS* 3.9 9.2 - - - +
177A TYR* 3.4 45.8 - - - +
178A ILE* 3.6 17.0 - - + +
426A TYR* 6.0 1.3 - - - +
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Residues in contact with ALA 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 ASP 3.0 10.9 + - - +
98A LEU* 3.7 6.7 - - + +
100A LEU* 1.3 77.0 - - - +
102A LEU* 1.3 54.6 + - - +
104A TYR* 3.8 0.5 - - - +
105A VAL* 2.7 43.0 + - + +
156A ALA* 4.4 12.6 - - + -
159A ILE* 3.7 14.7 - - + +
160A LEU* 3.2 34.8 - - + -
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Residues in contact with LEU 102 (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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71A ILE* 3.6 40.2 - - + -
75A PHE* 3.7 33.4 - - + -
76A SER* 5.7 1.1 - - - +
98A LEU 2.9 18.6 + - - +
99A TRP* 3.7 9.0 - - + +
101A ALA* 1.3 74.5 - - - +
103A ASP* 1.3 64.7 + - - +
105A VAL* 4.5 4.9 - - + -
106A VAL* 3.0 40.1 + - + +
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Residues in contact with ASP 103 (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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72A ILE* 3.9 8.1 - - - +
76A SER* 3.5 20.9 + - - +
99A TRP* 3.0 25.0 + - + +
100A LEU* 3.5 8.7 - - + +
102A LEU* 1.3 77.0 - - - +
104A TYR* 1.3 61.4 + - + +
106A VAL* 3.1 7.2 - - - +
107A SER* 2.8 28.8 + - - -
426A TYR* 4.7 2.6 - - - -
430A TYR* 3.1 23.0 + - - -
1162A QNB 3.3 35.3 + - - -
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Residues in contact with TYR 104 (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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100A LEU* 2.9 33.6 + - + +
103A ASP* 1.3 77.1 - - + +
105A VAL* 1.3 61.6 + - - +
107A SER* 3.8 5.4 - - - -
108A ASN* 3.0 29.5 + - - +
155A TRP* 3.5 30.7 + + + -
159A ILE* 3.9 13.9 - - + -
178A ILE* 3.5 29.7 - - + +
181A PHE* 3.7 22.7 - + - -
403A TYR* 4.3 5.9 + - - -
426A TYR* 4.3 7.0 + - - -
1162A QNB 3.5 66.7 - + + +
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Residues in contact with VAL 105 (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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101A ALA* 2.7 31.3 + - + +
102A LEU* 3.9 5.8 - - + +
104A TYR* 1.3 74.4 - - - +
106A VAL* 1.3 62.0 + - + +
108A ASN 3.5 0.2 + - - -
109A ALA* 3.0 25.1 + - - +
148A TRP* 4.9 9.6 - - + +
151A SER* 3.6 6.7 - - - -
152A PHE* 3.7 38.1 - - + +
155A TRP* 3.6 26.2 - - + -
156A ALA* 3.7 18.8 - - + +
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Residues in contact with VAL 106 (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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68A ALA* 4.0 13.4 - - + +
71A ILE* 4.2 16.4 - - + -
72A ILE* 3.7 30.3 - - + -
102A LEU* 3.0 40.8 + - + +
103A ASP* 3.1 8.7 - - - +
105A VAL* 1.3 77.6 - - + +
107A SER* 1.3 64.1 + - - +
109A ALA* 3.3 8.9 + - - +
110A SER* 2.9 32.7 + - - -
148A TRP* 4.1 17.5 - - + -
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Residues in contact with SER 107 (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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72A ILE* 4.7 4.0 - - - +
103A ASP* 2.8 32.4 + - - -
104A TYR* 3.8 4.9 - - - -
105A VAL 3.3 0.2 - - - -
106A VAL* 1.3 80.3 - - - +
108A ASN* 1.3 60.9 + - - +
110A SER* 3.2 7.9 + - - -
111A VAL* 3.1 26.9 + - - +
400A TRP* 3.6 22.6 - - - -
1162A QNB 3.4 29.3 + - - -
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Residues in contact with ASN 108 (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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104A TYR 3.0 10.7 + - - +
105A VAL 3.7 3.8 - - - +
107A SER* 1.3 72.3 - - - +
109A ALA* 1.3 65.8 + - - +
111A VAL* 2.9 24.8 - - - +
112A MET* 3.0 34.4 + - - +
151A SER* 2.6 28.8 + - - +
154A LEU* 4.5 7.4 - - - +
155A TRP* 3.0 38.1 + - + +
194A ALA* 4.8 7.1 - - - +
1162A QNB 3.5 12.3 - - + -
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Residues in contact with ALA 109 (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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68A ALA* 5.2 0.4 - - + -
105A VAL 3.0 15.4 + - - +
106A VAL* 3.4 10.3 - - - +
107A SER 3.3 0.4 - - - -
108A ASN* 1.3 73.9 - - - +
110A SER* 1.3 55.2 + - - +
112A MET* 3.3 4.7 + - - +
113A ASN* 2.3 44.9 + - - +
147A ALA 4.7 1.8 - - - -
148A TRP* 3.9 39.5 - - + +
151A SER* 3.3 13.6 + - - +
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Residues in contact with SER 110 (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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65A LEU* 4.0 13.9 + - - +
68A ALA* 3.5 18.9 - - - +
69A ASP* 4.5 7.5 + - - -
106A VAL 2.9 17.8 + - - -
107A SER* 3.3 12.3 - - - -
108A ASN 3.2 0.2 - - - -
109A ALA* 1.3 76.0 - - - +
111A VAL* 1.3 64.6 + - - +
113A ASN* 3.1 9.2 + - - +
114A LEU* 3.0 27.9 + - - +
396A PHE* 6.1 1.3 - - - -
400A TRP* 5.1 8.5 - - - -
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Residues in contact with VAL 111 (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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107A SER 3.1 9.8 + - - +
108A ASN* 2.9 36.6 - - - +
110A SER* 1.3 76.3 - - - +
112A MET* 1.3 60.7 + - + +
114A LEU* 3.3 13.0 + - - +
115A LEU* 3.0 30.3 + - + +
194A ALA 4.1 17.9 - - - +
195A PHE* 5.0 1.6 - - + -
198A PRO* 5.3 10.5 - - + -
202A MET* 4.8 1.6 - - + +
396A PHE* 3.6 33.7 - - + -
400A TRP* 4.0 13.5 - - + -
1162A QNB 4.1 7.6 - - + -
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Residues in contact with MET 112 (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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108A ASN* 3.0 42.6 + - - +
109A ALA* 3.7 4.0 - - - +
111A VAL* 1.3 77.1 - - + +
113A ASN* 1.3 62.3 + - - +
115A LEU* 3.1 22.6 + - + +
116A ILE* 2.8 35.2 + - + +
147A ALA* 4.1 23.6 - - + +
150A LEU* 4.4 25.8 - - + -
151A SER* 3.7 8.1 - - - +
154A LEU* 4.4 16.8 - - + -
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Residues in contact with ASN 113 (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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61A PHE* 4.3 9.7 - - + +
64A SER* 2.9 34.3 + - - -
65A LEU* 3.4 21.4 - - + +
109A ALA* 2.3 47.5 + - - +
110A SER* 3.1 8.5 + - - +
112A MET* 1.3 73.6 - - - +
114A LEU* 1.3 60.5 + - - +
116A ILE* 3.2 10.7 + - - +
117A ILE* 2.9 37.5 + - + +
144A ILE* 4.6 9.7 - - - +
147A ALA* 4.4 12.8 - - - +
148A TRP* 4.6 1.6 - - - +
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Residues in contact with LEU 114 (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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65A LEU* 4.7 7.9 - - + -
110A SER* 3.0 18.4 + - - +
111A VAL* 3.4 10.5 - - - +
113A ASN* 1.3 75.0 - - - +
115A LEU* 1.3 59.0 + - - +
117A ILE* 3.5 15.2 + - + +
118A SER* 2.8 31.7 + - - -
202A MET* 3.8 14.1 - - + +
206A TYR* 5.3 0.2 + - - -
392A ILE* 3.4 31.6 - - + -
393A LEU* 4.3 14.7 - - + +
396A PHE* 3.4 53.8 - - + -
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Residues in contact with LEU 115 (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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111A VAL* 3.0 20.8 + - + +
112A MET* 3.1 26.2 + - + +
114A LEU* 1.3 74.3 - - - +
116A ILE* 1.3 60.9 + - + +
118A SER* 3.0 7.7 + - - -
119A PHE* 2.9 41.7 + - + -
198A PRO* 3.6 35.0 - - + +
201A ILE* 5.3 6.3 - - + -
202A MET* 3.4 30.1 - - + +
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Residues in contact with ILE 116 (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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61A PHE* 3.5 33.0 - - + -
112A MET* 2.8 22.3 + - + +
113A ASN* 3.6 13.2 - - - +
115A LEU* 1.3 73.4 - - + +
117A ILE* 1.3 57.9 + - - +
119A PHE* 3.2 7.2 + - - +
120A ASP* 2.8 28.2 + - + +
143A MET* 3.4 60.1 - - + +
144A ILE* 4.4 2.7 - - + +
147A ALA* 4.0 14.6 - - + -
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Residues in contact with ILE 117 (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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61A PHE* 3.7 38.6 - - + -
62A LEU* 4.9 13.7 - - + -
65A LEU* 5.1 7.4 - - + -
113A ASN* 2.9 26.8 + - + +
114A LEU* 3.6 18.8 - - + +
116A ILE* 1.3 74.9 - - - +
118A SER* 1.3 63.9 + - - +
120A ASP* 3.2 9.0 + - + +
121A ARG* 3.0 22.6 + - - +
206A TYR* 4.1 6.1 - - - +
389A ILE* 3.5 39.9 - - + -
392A ILE* 5.6 3.8 - - + -
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Residues in contact with SER 118 (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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114A LEU 2.8 18.5 + - - -
115A LEU* 3.0 9.6 + - - -
117A ILE* 1.3 76.7 - - - +
119A PHE* 1.3 57.3 + - - +
121A ARG* 3.2 3.6 + - - +
122A TYR 2.9 23.6 + - - -
202A MET* 3.4 18.2 - - - +
205A LEU* 3.4 35.3 - - - +
206A TYR* 3.0 28.7 + - - -
393A LEU* 5.2 0.9 - - - +
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Residues in contact with PHE 119 (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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115A LEU* 2.9 26.6 + - + +
116A ILE* 3.7 10.1 - - + +
118A SER* 1.3 75.6 - - - +
120A ASP* 1.3 62.8 + - - +
122A TYR* 3.3 9.2 + + - +
123A PHE* 3.0 56.9 + + + -
143A MET* 6.2 3.4 - - + -
201A ILE* 4.4 15.9 - - + -
205A LEU* 3.7 22.4 - - + -
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Residues in contact with ASP 120 (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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58A ASN* 4.1 3.6 - - - +
61A PHE* 4.1 19.2 - - + -
116A ILE* 2.8 14.7 + - + +
117A ILE* 3.4 13.1 - - - +
118A SER 3.2 0.2 - - - -
119A PHE* 1.3 77.2 - - - +
121A ARG* 1.3 73.8 + - - +
123A PHE 3.4 0.2 + - - -
124A CYS* 3.0 28.8 + - - +
131A TYR* 2.6 31.6 + - - +
135A ARG* 2.7 36.3 + - - -
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Residues in contact with ARG 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 3.6 13.9 + - - -
117A ILE* 3.0 14.1 + - - +
118A SER 3.6 5.6 - - - +
120A ASP* 1.3 99.1 + - - +
122A TYR* 1.3 64.5 + - - +
124A CYS* 3.4 30.7 + - - +
125A VAL* 2.9 33.8 + - + +
135A ARG* 3.9 5.7 - - - +
206A TYR* 3.9 12.1 - - + +
209A ILE* 3.5 22.2 - - + -
383A LYS* 5.1 8.7 - - - +
385A VAL* 4.0 25.1 - - - +
386A THR* 5.0 12.0 - - - +
389A ILE* 3.5 31.8 - - + +
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Residues in contact with TYR 122 (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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118A SER 2.9 13.6 + - - +
119A PHE* 3.5 14.4 - + - +
120A ASP 3.3 0.2 - - - -
121A ARG* 1.3 77.5 - - - +
123A PHE* 1.3 77.7 + + - +
125A VAL* 3.7 0.7 - - - +
126A THR* 2.5 69.1 + - + +
127A LYS* 6.3 1.1 - - - -
205A LEU* 4.0 32.5 - - + -
208A HIS* 3.9 27.5 - + + -
209A ILE* 3.5 13.6 - - + +
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.0 47.6 + + + +
122A TYR* 1.3 99.4 - + - +
124A CYS* 1.3 60.6 + - - +
126A THR* 3.4 5.2 - - - -
127A LYS* 2.7 46.1 + - + +
131A TYR* 3.4 46.2 - + + -
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Residues in contact with CYS 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP 3.0 21.0 + - - +
121A ARG* 3.4 42.2 - - - +
123A PHE* 1.3 77.3 - - - +
125A VAL* 1.3 63.9 + - + +
128A PRO* 3.7 20.3 - - - +
131A TYR* 3.3 21.2 - - - -
132A PRO* 4.7 11.4 - - + +
135A ARG* 3.5 16.8 - - - -
1002A ASN* 6.0 0.3 + - - -
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Residues in contact with VAL 125 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 2.9 26.7 + - + +
122A TYR 3.8 2.9 - - - +
124A CYS* 1.3 81.2 - - + +
126A THR* 1.3 61.4 + - + +
128A PRO* 3.7 13.0 - - - +
209A ILE* 3.9 28.5 - - + +
212A ALA* 3.5 27.2 - - + +
213A SER* 3.4 22.9 - - - +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 2.5 67.9 + - + +
123A PHE* 3.4 10.4 - - - -
125A VAL* 1.3 80.0 - - + +
127A LYS* 1.3 84.7 + - - +
128A PRO* 3.3 8.2 - - - +
208A HIS* 5.7 3.6 - - + +
209A ILE* 6.0 0.4 - - + -
212A ALA* 5.3 7.4 - - + -
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 6.3 1.3 - - - -
123A PHE* 2.7 28.7 + - + +
126A THR* 1.3 100.4 + - - +
128A PRO* 1.3 63.8 - - - +
129A LEU 3.2 2.9 - - - -
130A THR* 3.5 20.4 - - - +
131A TYR* 3.1 14.3 + - + +
132A PRO* 3.0 18.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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