Contacts of the helix formed by residues 88 - 111 (chain A) in PDB entry 2C8U
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 THR 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 4.2 0.9 - - - -
87A GLY* 1.3 82.7 + - - +
89A GLU* 1.3 60.1 + - - +
90A GLU* 3.5 8.7 + - - +
91A GLU* 3.0 29.6 + - + +
92A TYR* 2.9 28.9 + - - +
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Residues in contact with GLU 89 (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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88A THR* 1.3 73.6 - - - +
90A GLU* 1.3 57.9 + - - +
92A TYR* 3.5 8.8 + - - +
93A TYR 3.0 22.5 + - - -
77B TYR* 3.2 29.9 + - + +
80B LYS* 4.3 31.1 + - + +
81B LYS* 3.7 40.7 - - - +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 3.2 7.9 + - - +
89A GLU* 1.3 76.2 - - - +
91A GLU* 1.3 67.4 + - + +
93A TYR* 3.5 10.5 + - + +
94A ASN* 2.9 43.8 + - - +
66B LYS* 6.0 1.9 - - - +
77B TYR* 4.0 13.0 - - + +
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Residues in contact with GLU 91 (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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86A GLY* 3.8 7.4 - - - -
87A GLY* 3.0 28.9 + - - +
88A THR* 3.0 26.3 + - - +
90A GLU* 1.3 75.0 - - + +
92A TYR* 1.3 59.9 + - - +
94A ASN* 3.2 5.7 + - - +
95A VAL* 2.8 32.1 + - - +
147A THR* 4.4 6.2 + - - +
152A VAL* 3.7 20.6 - - + +
153A GLY* 4.0 20.5 - - - -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.5 51.2 + - + +
86A GLY 5.3 0.4 - - - +
88A THR 2.9 13.0 + - - +
89A GLU* 3.5 13.2 - - - +
91A GLU* 1.3 75.8 - - - +
93A TYR* 1.3 63.9 + - - +
95A VAL* 3.1 2.1 + - - +
96A GLU* 2.9 34.6 + - + +
76B ARG* 3.5 44.6 - - + +
77B TYR* 4.2 5.2 - - - -
80B LYS* 3.8 29.2 - - + -
85B MET* 3.5 20.8 - - - +
92B TYR* 4.1 14.0 - + - -
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Residues in contact with TYR 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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89A GLU 3.0 9.3 + - - +
90A GLU* 3.8 12.6 - - - +
91A GLU 3.4 0.4 - - - -
92A TYR* 1.3 76.4 - - - +
94A ASN* 1.3 80.8 + - - +
96A GLU* 3.2 6.0 + - - +
97A LYS* 2.7 46.1 + - + +
67B TRP 4.6 3.9 + - - -
68B MET* 3.4 37.2 - - + -
69B VAL* 2.7 45.8 + - - +
73B ALA* 3.7 18.6 - - + -
74B ILE* 3.9 10.5 - - + -
77B TYR* 3.5 30.1 - + + -
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Residues in contact with ASN 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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90A GLU* 2.9 40.0 + - - +
91A GLU* 3.6 9.3 - - - +
93A TYR* 1.3 84.4 - - - +
95A VAL* 1.3 64.8 + - - +
97A LYS* 3.3 28.7 - - - +
98A LEU* 3.3 19.9 + - - +
151A ALA 5.7 0.4 - - - +
152A VAL* 3.5 26.5 - - + +
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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
----------------------------------------------------------
85A MET* 3.8 36.3 - - + +
86A GLY 4.1 0.7 - - - +
91A GLU 2.8 20.4 + - - +
92A TYR 3.1 8.0 + - - +
94A ASN* 1.3 71.8 - - - +
96A GLU* 1.3 58.8 + - - +
98A LEU 3.4 2.1 + - - -
99A ILE* 2.9 46.1 + - + +
152A VAL* 3.8 12.6 - - + -
157A THR* 3.5 35.0 - - + +
158A LEU* 4.5 0.9 - - + -
159A ALA* 3.8 17.6 - - - +
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Residues in contact with GLU 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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76A ARG* 2.6 51.0 + - - -
85A MET* 3.5 15.2 - - + +
92A TYR* 2.9 35.9 + - + +
93A TYR* 3.7 5.8 - - - +
95A VAL* 1.3 74.3 - - - +
97A LYS* 1.3 58.3 + - - +
99A ILE* 3.8 4.9 - - - +
100A GLY* 2.9 27.2 + - - -
1208A BME 4.2 2.8 - - - +
73B ALA* 3.6 23.7 - - + +
76B ARG* 3.3 30.1 + - + -
92B TYR* 4.2 0.2 + - - -
96B GLU* 3.9 1.4 - - - +
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Residues in contact with LYS 97 (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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93A TYR* 2.7 50.6 + - + +
94A ASN* 3.3 27.8 - - - +
96A GLU* 1.3 72.0 - - - +
98A LEU* 1.3 58.5 + - - +
100A GLY* 3.2 3.3 + - - -
101A GLN* 3.0 38.2 + - - +
142A SER* 3.1 36.3 + - - +
145A ALA* 5.4 5.9 - - - +
69B VAL* 3.5 13.9 - - + +
70B GLU* 3.7 20.3 - - + +
73B ALA* 3.5 9.1 - - - +
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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
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94A ASN 3.3 15.0 + - - +
97A LYS* 1.3 76.2 - - - +
99A ILE* 1.3 66.4 + - - +
101A GLN* 3.8 10.0 - - + +
102A ALA* 3.0 23.6 + - + +
139A ILE* 4.4 14.6 - - + -
142A SER* 3.8 28.5 - - - -
143A LEU* 4.2 14.4 - - + +
151A ALA* 3.4 32.3 - - + +
152A VAL* 5.4 0.7 - - + -
159A ALA* 3.5 29.6 - - + +
163A LEU* 4.1 19.1 - - + -
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Residues in contact with ILE 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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72A LEU* 4.7 6.3 - - + -
76A ARG* 3.5 24.9 - - - +
85A MET* 4.6 0.9 - - + -
95A VAL* 2.9 41.5 + - + +
96A GLU* 3.8 17.9 - - - +
98A LEU* 1.3 76.0 - - - +
100A GLY* 1.3 58.5 + - - +
102A ALA* 3.7 1.6 - - - +
103A GLU* 2.9 37.4 + - + +
158A LEU* 3.8 27.1 - - + -
159A ALA* 4.0 15.5 - - - +
162A VAL* 4.3 20.6 - - + +
1208A BME 3.9 6.7 - - + +
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Residues in contact with GLY 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 GLU 2.9 15.6 + - - -
97A LYS 3.2 4.5 + - - -
99A ILE* 1.3 78.4 - - - +
101A GLN* 1.3 55.2 + - - +
103A GLU* 3.4 3.9 + - - +
104A ASP* 3.0 36.1 + - - +
1208A BME 3.7 24.9 - - - +
70B GLU* 4.5 9.2 - - - -
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Residues in contact with GLN 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 LYS* 3.0 29.2 + - - +
98A LEU* 3.8 11.5 - - - +
100A GLY* 1.3 73.4 - - - +
102A ALA* 1.3 65.1 + - - +
104A ASP* 3.3 11.7 + - - +
105A LEU* 3.2 19.2 + - - +
135A LEU* 4.5 5.2 - - + +
138A ILE* 3.3 27.1 + - + +
139A ILE* 4.0 20.3 - - + +
142A SER* 2.7 37.1 + - - -
52B ARG* 4.5 2.7 - - - +
69B VAL* 4.1 5.9 - - - +
70B GLU* 3.2 30.0 - - - +
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Residues in contact with ALA 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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98A LEU* 3.0 17.4 + - + +
99A ILE 3.7 0.2 - - - +
101A GLN* 1.3 77.3 - - - +
103A GLU* 1.3 59.3 + - - +
105A LEU* 3.1 5.6 + - - +
106A GLU* 2.8 26.9 + - - +
139A ILE* 4.2 11.1 - - + +
162A VAL* 3.7 27.4 - - + +
163A LEU* 4.5 17.5 - - + -
166A VAL* 3.5 15.2 - - + +
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Residues in contact with GLU 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 LEU* 3.6 30.8 - - + +
99A ILE* 2.9 26.9 + - + +
100A GLY* 3.8 7.2 - - - +
101A GLN 3.3 0.2 - - - -
102A ALA* 1.3 72.8 - - - +
104A ASP* 1.3 61.4 + - - +
106A GLU* 3.5 24.7 - - - +
107A HIS* 2.9 27.9 + - - +
110A TYR* 4.7 6.2 + - - -
162A VAL* 3.6 21.5 - - - +
166A VAL* 4.4 3.8 - - - +
1208A BME 4.9 9.2 - - + +
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Residues in contact with ASP 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 GLY 3.0 19.5 + - - +
101A GLN* 3.4 9.5 - - - +
102A ALA 3.3 0.2 - - - -
103A GLU* 1.3 76.4 - - - +
105A LEU* 1.3 61.6 + - - +
107A HIS* 3.4 16.6 + - - +
108A GLU* 3.4 12.1 + - - +
135A LEU* 3.5 24.6 - - + +
16B ARG* 6.3 0.2 - - - -
52B ARG* 2.8 35.6 + - - +
70B GLU* 3.7 6.6 - - - +
1207B SO4 5.2 0.7 - - - -
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Residues in contact with LEU 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 GLN 3.2 8.3 + - - +
102A ALA* 3.1 10.8 + - - +
104A ASP* 1.3 77.1 - - - +
106A GLU* 1.3 64.2 + - - +
108A GLU* 3.1 16.0 + - + +
109A TYR* 3.2 11.6 + - - +
132A VAL* 3.9 42.0 - - + +
135A LEU* 3.6 14.7 - - + +
136A LEU* 3.7 27.1 - - + -
139A ILE* 4.0 16.2 - - + -
166A VAL* 3.7 15.9 - - + -
167A ILE* 4.3 6.3 - - + -
170A VAL* 3.9 20.0 - - + -
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Residues in contact with GLU 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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15A GLY 5.6 1.4 - - - +
16A ARG* 5.5 1.7 - - - +
102A ALA 2.8 20.0 + - - +
103A GLU* 3.5 23.4 - - - +
105A LEU* 1.3 72.7 - - - +
107A HIS* 1.3 56.3 + - - +
109A TYR* 3.3 10.4 + - - +
110A TYR* 2.8 71.7 + - + +
165A ALA* 5.5 1.2 - - - +
166A VAL* 3.5 21.1 - - + +
169A HIS* 2.7 43.1 + - - +
1209A BME 4.6 1.2 - - - -
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Residues in contact with HIS 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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103A GLU 2.9 13.7 + - - +
104A ASP* 3.4 13.7 - - - +
105A LEU 3.2 0.4 - - - -
106A GLU* 1.3 73.6 - - - +
108A GLU* 1.3 82.6 + - - +
110A TYR* 3.3 24.4 + - + +
111A LYS* 3.4 27.7 + - + +
107B HIS* 3.5 36.6 + + - -
110B TYR* 6.0 6.3 - + + -
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Residues in contact with GLU 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 ASP 3.4 11.7 + - - +
105A LEU 3.1 7.9 + - - +
107A HIS* 1.3 85.8 - - - +
109A TYR* 1.3 66.2 + - - +
111A LYS* 2.7 55.8 + - - +
112A THR 4.0 0.3 + - - -
127A ILE* 3.3 30.6 - - + +
131A LYS* 3.8 33.0 + - + +
132A VAL* 3.8 23.1 - - + -
135A LEU* 4.2 8.2 - - + +
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Residues in contact with TYR 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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14A ARG* 5.1 2.8 + - - +
105A LEU 3.2 8.5 + - - +
106A GLU* 3.4 25.6 - - - +
108A GLU* 1.3 76.9 - - - +
110A TYR* 1.3 70.3 + + - +
112A THR* 2.8 26.5 + - - -
113A LEU* 3.4 31.2 - - + +
127A ILE* 4.0 8.9 - - - +
132A VAL* 5.4 0.6 - - - +
166A VAL* 5.9 0.7 - - + -
169A HIS* 3.4 61.7 + + + -
170A VAL* 5.3 5.4 - - + +
172A ASP* 4.3 10.0 + - + -
173A LEU* 4.0 24.9 - - + -
1209A BME 3.8 20.3 - - - -
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Residues in contact with TYR 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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16A ARG* 3.5 27.7 - - + +
103A GLU* 4.7 6.8 + - - -
106A GLU* 2.8 52.0 + - + +
107A HIS* 3.4 20.9 - - + +
108A GLU 3.1 0.6 - - - -
109A TYR* 1.3 79.9 - + - +
111A LYS* 1.3 61.1 + - - +
112A THR 3.0 1.5 + - - -
113A LEU* 3.0 37.0 + - + +
115A LYS* 5.9 0.2 + - - -
1209A BME 3.4 36.1 - - + +
107B HIS* 6.0 6.1 - + + -
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Residues in contact with LYS 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 HIS* 3.6 29.6 - - + +
108A GLU* 2.7 52.3 + - - +
110A TYR* 1.3 75.5 - - - +
112A THR* 1.3 58.3 + - - +
113A LEU 3.4 0.6 + - - -
115A LYS* 3.8 13.5 + - - +
123A ILE* 3.5 33.9 - - + +
126A GLU* 5.3 8.8 + - - +
127A ILE* 4.2 8.9 - - + +
131A LYS* 5.5 2.4 - - - +
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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
------------------------------------------------------------
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