Contacts of the helix formed by residues 113 - 145 (chain G) in PDB entry 3ISE
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 ASP 113 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ARG* 4.3 5.0 + - - +
128F GLU* 4.5 3.5 - - - +
4G ASP* 5.9 1.5 + - + -
7G VAL* 3.7 17.6 - - + +
61G ARG* 3.0 24.7 + - - -
65G LEU* 3.8 10.2 - - - +
108G CYS* 2.9 20.6 + - - +
111G VAL* 3.3 15.0 + - + +
112G HIS* 1.3 75.0 - - - +
114G TYR* 1.3 56.4 + - - +
115G VAL* 3.6 1.7 + - - +
116G SER* 2.8 29.8 + - - -
117G ARG* 3.1 19.8 + - - +
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Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ARG* 4.0 15.3 - - + +
105F ILE* 3.4 42.6 - - + +
106F VAL* 3.2 16.6 + - - +
117F ARG* 3.7 15.7 + - - +
121F LYS* 4.2 18.5 - - + +
124F LEU* 4.1 16.2 - - + -
109G GLU* 3.5 34.1 + - - -
112G HIS* 3.0 59.2 + - + -
113G ASP* 1.3 72.3 - - - +
115G VAL* 1.3 60.0 + - - +
117G ARG* 3.5 9.8 - - + +
118G ASP* 3.0 28.2 + - - +
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Residues in contact with VAL 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F LYS* 5.0 2.5 - - + +
124F LEU* 3.9 13.4 - - + +
125F GLU* 3.7 42.8 - - + +
128F GLU* 3.4 24.9 + - + +
61G ARG* 3.5 30.3 - - - +
113G ASP* 3.4 1.2 + - - -
114G TYR* 1.3 75.0 - - - +
116G SER* 1.3 66.6 + - - +
118G ASP* 3.2 7.4 + - + +
119G LEU* 3.2 22.0 + - + +
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Residues in contact with SER 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 4.4 2.5 - - - -
11G LEU* 4.0 9.8 - - - +
61G ARG* 2.9 27.6 + - - +
65G LEU* 3.7 7.4 - - - +
108G CYS* 3.8 15.0 - - - -
113G ASP* 2.8 34.3 + - - -
115G VAL* 1.3 78.7 - - - +
117G ARG* 1.3 62.8 + - - +
119G LEU* 3.2 7.2 + - - +
120G LEU* 3.2 25.5 + - - +
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Residues in contact with ARG 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ARG* 3.9 22.2 - - - +
105G ILE* 4.1 24.0 - - + +
108G CYS* 3.9 16.3 - - + -
109G GLU* 3.0 41.7 + - - +
113G ASP 3.1 17.5 + - - +
114G TYR* 3.5 12.3 - - + +
115G VAL 3.2 0.4 - - - -
116G SER* 1.3 75.6 - - - +
118G ASP* 1.3 60.6 + - - +
119G LEU 3.2 0.2 + - - -
120G LEU* 3.2 5.9 + - - +
121G LYS* 2.9 36.8 + - + +
109J GLU* 2.9 42.2 + - - -
114J TYR* 3.8 13.9 + - - -
117J ARG* 4.2 15.7 - - - +
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Residues in contact with ASP 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 5.8 0.3 - - - +
121F LYS* 4.0 21.2 - - + +
122F ASP* 5.6 2.4 - - - +
125F GLU* 5.1 8.0 - - - +
114G TYR 3.0 14.6 + - - +
115G VAL* 3.6 9.0 - - + +
117G ARG* 1.3 80.1 - - - +
119G LEU* 1.3 60.7 + - - +
121G LYS* 3.6 8.9 - - - +
122G ASP* 3.2 40.9 + - - +
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Residues in contact with LEU 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 5.5 1.1 - - + -
57G LYS* 4.2 28.9 - - + +
58G LEU* 4.2 20.0 - - + -
61G ARG* 4.1 32.8 - - + -
115G VAL* 3.2 10.0 + - + +
116G SER* 3.4 9.6 - - - +
117G ARG 3.1 0.2 - - - -
118G ASP* 1.3 77.9 - - - +
120G LEU* 1.3 66.0 + - + +
122G ASP* 3.4 9.6 + - + +
123G ILE* 3.1 34.6 + - + +
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Residues in contact with LEU 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 3.8 26.2 - - + -
14G ILE* 4.3 15.0 - - + -
58G LEU* 4.0 18.6 - - + -
101G LEU* 4.3 11.5 - - + +
104G ALA* 3.6 27.6 - - + -
105G ILE* 3.7 20.2 - - + +
108G CYS* 3.9 19.7 - - - -
116G SER 3.2 13.7 + - - +
117G ARG 3.6 6.1 - - - +
119G LEU* 1.3 80.8 - - + +
121G LYS* 1.3 53.9 + - - +
123G ILE* 3.3 6.3 + - + +
124G LEU* 2.7 36.2 + - - +
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Residues in contact with LYS 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ILE* 4.1 6.7 - - + +
117G ARG* 2.9 30.8 + - + +
118G ASP* 3.6 12.6 - - - +
119G LEU 3.3 0.2 - - - -
120G LEU* 1.3 74.7 - - - +
122G ASP* 1.3 60.7 + - - +
124G LEU* 3.2 7.0 + - + +
125G GLU* 3.0 28.9 + - - +
114J TYR* 4.3 28.3 - - + +
115J VAL* 4.8 2.8 - - + +
117J ARG* 6.5 0.9 - - - -
118J ASP* 3.7 23.8 - - + +
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Residues in contact with ASP 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G HIS* 5.0 0.8 + - - -
118G ASP* 3.2 28.8 + - - +
119G LEU* 3.7 9.9 - - + +
121G LYS* 1.3 76.1 - - - +
123G ILE* 1.3 63.4 + - + +
125G GLU* 3.6 10.7 + - - +
126G SER* 3.2 20.6 + - - -
118J ASP* 5.5 4.5 - - - +
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Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ILE* 4.9 2.0 - - + -
18G GLU* 3.5 22.0 - - - +
54G HIS* 3.9 38.6 - - + +
57G LYS* 5.4 0.7 - - + -
58G LEU* 3.9 31.6 - - + -
101G LEU* 4.0 13.0 - - + -
119G LEU* 3.1 28.4 + - + +
120G LEU* 3.6 12.1 - - + +
122G ASP* 1.3 74.6 - - + +
124G LEU* 1.3 59.4 + - - +
126G SER* 2.8 18.4 + - - -
127G GLU* 2.9 23.8 + - + +
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G THR* 3.7 22.2 - - - +
101G LEU* 3.9 28.0 - - + -
102G ARG* 4.1 24.2 - - + +
105G ILE* 4.2 11.7 - - + -
120G LEU 2.7 21.8 + - - +
121G LYS* 3.4 7.2 - - - +
123G ILE* 1.3 72.3 - - - +
125G GLU* 1.3 56.8 + - - +
127G GLU* 3.3 2.4 + - - +
128G GLU* 2.9 34.1 + - + +
114J TYR* 3.9 30.1 - - + -
115J VAL* 3.9 15.7 - - + -
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LYS 3.0 15.0 + - - +
122G ASP* 3.8 11.3 - - - +
124G LEU* 1.3 73.9 - - - +
126G SER* 1.3 67.3 + - - +
128G GLU* 3.3 4.1 + - - +
129G GLU* 3.2 39.6 + - + +
115J VAL* 3.7 30.0 - - + +
118J ASP* 5.4 9.4 - - - +
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Residues in contact with SER 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ASP* 4.8 8.8 + - - +
54G HIS* 2.9 30.8 + - - -
122G ASP 3.2 10.8 + - - -
123G ILE 2.8 9.8 + - - -
125G GLU* 1.3 82.9 - - - +
127G GLU* 1.3 58.7 + - - +
129G GLU* 3.4 13.9 + - - +
130G HIS* 3.1 23.2 + - - +
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Residues in contact with GLU 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G GLU* 2.3 19.6 - - - +
51G GLU* 2.2 44.0 - - - +
54G HIS* 3.1 9.1 + - - -
94G GLU* 2.4 39.9 - - - +
97G ALA* 5.4 6.1 - - + -
98G THR* 4.3 12.1 - - - +
101G LEU* 4.0 12.3 - - + -
123G ILE* 2.9 25.4 + - + +
124G LEU* 3.8 6.7 - - - +
125G GLU 3.2 0.2 - - - -
126G SER* 1.3 76.4 - - - +
128G GLU* 1.3 60.2 + - - +
130G HIS* 3.2 5.9 + - - +
131G ILE* 3.0 29.0 + - - +
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G THR* 4.5 4.7 - - + +
102G ARG* 3.2 28.3 + - - +
124G LEU* 2.9 28.3 + - + +
125G GLU* 3.8 7.0 - - - +
126G SER 3.3 0.2 - - - -
127G GLU* 1.3 75.4 - - - +
129G GLU* 1.3 57.7 + - - +
131G ILE* 3.3 12.7 + - + +
132G ASP* 2.8 28.1 + - - +
61J ARG* 3.0 34.3 + - - +
64J PHE* 3.5 19.3 - - + -
65J LEU* 5.2 0.9 - - - +
113J ASP* 4.5 1.6 - - - +
115J VAL* 3.5 24.6 - - + +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G GLU* 3.2 40.2 + - + +
126G SER* 3.5 14.0 - - - +
128G GLU* 1.3 72.8 - - - +
130G HIS* 1.3 65.7 + - - +
132G ASP* 3.2 9.6 + - + +
133G TYR* 3.0 22.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR* 3.3 36.0 + + - -
44G GLU* 4.2 7.9 + - - -
47G GLU* 3.3 46.6 + - + +
51G GLU* 4.4 1.2 + - - +
90G ASP* 4.5 2.5 - - + -
94G GLU* 3.1 25.4 + - - +
126G SER 3.1 13.9 + - - +
127G GLU* 3.2 9.8 + - - +
129G GLU* 1.3 74.1 - - - +
131G ILE* 1.3 64.4 + - - +
133G TYR* 3.0 13.3 + + - -
134G LEU* 2.9 56.1 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 3.9 13.2 - - + -
94G GLU* 3.8 27.8 - - + +
95G LEU* 4.4 14.8 - - + +
98G THR* 4.0 22.0 - - + +
127G GLU 3.0 17.6 + - - +
128G GLU* 3.3 15.7 + - + +
130G HIS* 1.3 74.3 - - - +
132G ASP* 1.3 58.0 + - - +
134G LEU* 3.3 8.8 + - - +
135G GLU* 2.9 55.0 + - + +
64J PHE* 4.2 12.6 - - + -
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Residues in contact with ASP 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G GLU 2.8 14.2 + - - +
129G GLU* 3.5 13.7 - - - +
131G ILE* 1.3 75.2 - - - +
133G TYR* 1.3 61.3 + - - +
135G GLU* 4.2 2.6 - - - +
136G THR* 2.6 43.2 + - - -
34I ASP* 4.3 10.6 - - - +
64J PHE* 3.6 32.2 - - + +
----------------------------------------------------------
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Residues in contact with TYR 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 3.6 26.5 + - - +
43G HIS* 3.1 56.3 - + + +
44G GLU* 5.0 5.1 + - - -
47G GLU* 4.9 0.7 - - - +
87G LEU* 4.6 5.0 - - + +
129G GLU 3.0 11.3 + - - +
130G HIS* 3.0 26.3 + + + +
132G ASP* 1.3 77.2 - - - +
134G LEU* 1.3 66.2 + - + +
136G THR* 3.3 6.6 - - - -
137G GLN* 2.9 70.6 + - + +
153G HIS* 5.6 1.6 + - - -
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 5.6 0.4 - - - +
87G LEU* 3.8 47.8 - - + +
90G ASP* 4.2 15.0 - - + +
91G LEU* 4.2 20.9 - - + +
94G GLU* 4.6 2.5 - - + -
130G HIS* 2.9 53.3 + - + +
131G ILE* 3.4 11.2 - - - +
132G ASP 3.1 0.2 - - - -
133G TYR* 1.3 84.2 - - + +
135G GLU* 1.3 66.6 + - - +
136G THR 3.1 1.3 - - - -
137G GLN* 3.1 12.4 + - - +
138G LEU* 3.1 21.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 4.2 19.2 - - + +
95G LEU* 5.8 2.8 - - - +
131G ILE* 2.9 37.2 + - + +
132G ASP* 4.3 3.1 - - - +
134G LEU* 1.3 70.8 - - - +
136G THR* 1.3 64.0 + - - +
138G LEU* 3.4 10.3 + - - +
139G GLY* 3.0 19.8 + - - -
64J PHE* 3.9 19.1 - - - +
66J GLU* 3.9 21.0 - - - +
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Residues in contact with THR 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ASP* 2.6 34.0 + - - -
133G TYR* 3.3 7.1 - - - -
135G GLU* 1.3 77.1 - - - +
137G GLN* 1.3 72.5 + - - +
139G GLY* 3.1 2.6 + - - -
140G LEU* 3.0 23.0 + - + +
33I ASN 5.1 0.9 - - - +
34I ASP* 3.5 13.3 + - - +
35I TRP 3.5 31.4 - - - +
36I GLY* 3.6 11.4 - - - -
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Residues in contact with GLN 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G LEU* 3.8 17.3 - - + -
133G TYR* 2.9 66.5 + - + +
134G LEU* 3.1 5.9 + - - +
136G THR* 1.3 83.3 - - - +
138G LEU* 1.3 65.2 + - - +
140G LEU* 3.1 24.6 + - - +
141G ILE* 3.2 19.5 + - - +
149G TYR* 2.1 52.7 + - - +
153G HIS* 3.8 11.7 + - - -
159G FE 4.3 3.2 - - - -
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLN* 4.4 22.0 - - + +
87G LEU* 3.9 40.6 - - + +
88G GLN* 4.4 14.4 - - + +
91G LEU* 4.1 24.2 - - + -
134G LEU 3.1 22.1 + - - +
135G GLU* 3.7 6.3 - - - +
137G GLN* 1.3 78.6 - - - +
139G GLY* 1.3 60.7 + - - +
141G ILE* 3.4 24.8 + - + +
142G GLN* 3.4 17.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G GLU 3.0 15.4 + - - -
136G THR* 3.1 3.8 + - - -
138G LEU* 1.3 74.3 - - - +
140G LEU* 1.3 61.2 + - - +
142G GLN* 3.3 9.7 + - - +
143G LYS* 3.0 43.9 + - - +
35I TRP 5.4 1.6 - - - -
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G THR* 3.0 17.6 + - + +
137G GLN* 3.1 31.8 + - - +
139G GLY* 1.3 75.3 - - - +
141G ILE* 1.3 61.5 + - - +
143G LYS* 4.2 7.9 - - + +
144G VAL* 2.9 40.7 + - + +
149G TYR* 4.0 10.1 - - + -
35I TRP 3.4 25.8 - - - +
36I GLY* 4.1 13.0 - - - +
37I LEU* 3.9 26.2 - - + -
154I MET* 4.0 26.2 - - + -
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Residues in contact with ILE 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G THR* 4.9 4.9 - - + -
84G GLN* 4.2 16.2 - - + +
87G LEU* 4.2 16.4 - - + -
137G GLN 3.2 15.0 - - - +
138G LEU* 3.4 18.6 - - + +
139G GLY 3.1 0.2 - - - -
140G LEU* 1.3 77.5 - - - +
142G GLN* 1.3 69.9 + - - +
145G GLY* 2.9 36.2 + - - -
146G LEU* 3.8 34.3 + - + +
149G TYR* 3.7 33.9 - - + -
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Residues in contact with GLN 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLN* 3.4 27.3 + - - +
138G LEU* 3.4 16.4 + - - +
139G GLY* 3.3 10.0 + - - +
140G LEU 3.2 0.2 - - - -
141G ILE* 1.3 86.8 - - - +
143G LYS* 1.3 63.0 + - + +
144G VAL 3.7 0.2 + - - -
145G GLY* 4.2 2.3 + - - -
147I GLU* 4.3 5.2 - - - +
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Residues in contact with LYS 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G GLY* 3.0 31.1 + - - +
140G LEU* 3.2 10.3 + - + +
142G GLN* 1.3 79.7 - - + +
144G VAL* 1.3 65.2 + - + +
35I TRP* 3.7 54.6 + - + +
37I LEU* 4.5 14.1 - - + -
146I LEU* 5.6 2.1 - - - +
147I GLU* 3.3 13.9 - - - +
150I LEU* 3.7 23.1 - - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU* 2.9 27.8 + - + +
143G LYS* 1.3 80.7 - - + +
145G GLY* 1.3 69.4 + - - +
148G ASN* 2.9 35.3 + - + +
149G TYR* 3.8 19.5 - - + +
147I GLU* 3.5 26.8 - - - +
150I LEU* 3.7 15.0 - - + +
151I GLN* 3.7 25.8 - - + +
154I MET* 4.6 15.3 - - - -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G ILE 2.9 16.9 + - - +
142G GLN 4.2 1.7 + - - -
143G LYS 3.7 0.8 - - - -
144G VAL* 1.3 80.6 - - - +
146G LEU* 1.3 67.1 + - - -
147G GLU 3.2 3.4 - - - -
148G ASN* 4.0 1.1 - - - -
149G TYR* 3.0 25.6 + - - +
147I GLU* 4.2 9.7 + - - -
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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