Contacts of the helix formed by residues 98 - 124 (chain V) in PDB entry 6QY3
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 LYS 98 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96V ALA 3.8 1.8 + - - +
97V TRP* 1.3 76.4 - - - +
99V GLU* 1.3 64.5 + - - +
100V ASN* 4.1 9.9 - - + +
101V VAL* 3.2 15.8 + - + +
102V LYS* 3.0 23.5 + - - +
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Residues in contact with GLU 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97V TRP 4.3 0.4 + - - -
98V LYS* 1.3 74.3 - - - +
100V ASN* 1.3 57.0 + - - +
102V LYS* 3.8 6.7 - - - +
103V CYS* 2.9 32.6 + - - +
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Residues in contact with ASN 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98V LYS* 3.2 6.8 - - + +
99V GLU* 1.3 79.3 - - - +
101V VAL* 1.3 57.3 + - - +
103V CYS* 4.3 3.0 - - - +
104V GLU* 2.9 32.2 + - - +
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Residues in contact with VAL 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97V TRP* 6.1 1.6 - - + -
98V LYS* 3.2 19.6 + - + +
100V ASN* 1.3 76.9 - - - +
102V LYS* 1.3 60.9 + - - +
104V GLU* 3.9 3.9 - - - +
105V VAL* 2.9 32.7 + - - +
276V ALA 5.9 0.2 - - - +
277V LEU* 5.1 11.2 - - + +
280V LEU* 4.9 21.8 - - + -
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Residues in contact with LYS 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97V TRP* 6.0 3.6 - - + -
98V LYS 3.0 16.3 + - - +
99V GLU* 3.9 7.4 - - - +
101V VAL* 1.3 77.0 - - - +
103V CYS* 1.3 58.1 + - - +
105V VAL* 4.1 1.7 - - - -
106V TRP* 2.9 24.6 + - - +
202V GLY 5.2 1.1 - - - +
203V LEU* 3.0 41.6 - - + +
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Residues in contact with CYS 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99V GLU 2.9 19.6 + - - +
100V ASN* 4.3 3.4 - - - +
102V LYS* 1.3 76.7 - - - +
104V GLU* 1.3 56.7 + - - +
106V TRP* 4.1 2.4 - - - +
107V THR* 2.9 30.8 + - - -
142V ARG* 5.4 13.5 - - + +
143V PHE* 5.4 6.5 - - - +
203V LEU 3.8 5.8 + - - -
204V LYS* 5.9 2.2 - - - +
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Residues in contact with GLU 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100V ASN 2.9 21.7 + - - +
101V VAL* 3.9 4.9 - - - +
103V CYS* 1.3 75.2 - - - +
105V VAL* 1.3 60.6 + - - +
107V THR* 3.3 4.8 + - - -
108V ALA* 2.9 30.7 + - - +
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Residues in contact with VAL 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101V VAL 2.9 19.2 + - - +
102V LYS* 4.2 2.7 - - - +
104V GLU* 1.3 75.8 - - - +
106V TRP* 1.3 58.4 + - - +
108V ALA* 3.4 6.1 + - - +
109V ILE* 2.9 29.1 + - - +
203V LEU* 5.8 2.7 - - + -
276V ALA* 6.3 3.6 - - + -
277V LEU* 6.1 6.3 - - + -
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Residues in contact with TRP 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102V LYS 2.9 20.6 + - - +
103V CYS* 4.1 3.6 - - - +
105V VAL* 1.3 77.6 - - - +
107V THR* 1.3 56.7 + - - +
109V ILE* 3.7 6.9 - - - +
110V ILE* 2.9 29.8 + - - +
203V LEU* 3.6 25.5 - - + +
204V LYS* 4.5 10.5 - - + +
217V ASP* 5.8 6.5 - - + -
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Residues in contact with THR 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103V CYS 2.9 21.6 + - - -
104V GLU* 3.7 4.9 - - - -
106V TRP* 1.3 76.9 - - - +
108V ALA* 1.3 57.3 + - - +
110V ILE* 3.4 6.2 + - - +
111V ALA* 2.9 28.6 + - - +
140V LEU* 6.6 0.7 - - - -
141V GLU 5.2 11.9 - - - -
142V ARG* 5.2 8.3 - - - -
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Residues in contact with ALA 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104V GLU 2.9 16.9 + - - +
105V VAL* 3.8 6.5 - - - +
107V THR* 1.3 76.7 - - - +
109V ILE* 1.3 58.0 + - - +
111V ALA* 3.3 8.1 + - - +
112V GLN* 2.9 27.4 + - - +
284V ILE* 4.8 18.2 - - + -
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Residues in contact with ILE 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105V VAL 2.9 17.9 + - - +
106V TRP* 3.7 8.1 - - - +
108V ALA* 1.3 75.4 - - - +
110V ILE* 1.3 59.7 + - - +
112V GLN* 3.1 8.0 + - - +
113V LYS* 2.9 27.1 + - - +
217V ASP* 4.2 18.4 - - + +
218V ILE* 6.1 0.2 - - - -
220V GLU* 5.3 4.0 - - + +
221V PRO* 4.7 7.4 - - + +
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Residues in contact with ILE 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106V TRP 2.9 17.6 + - - +
107V THR* 3.8 6.5 - - - +
109V ILE* 1.3 76.9 - - - +
111V ALA* 1.3 57.5 + - - +
113V LYS* 3.2 7.3 + - - +
114V ILE* 2.9 30.1 + - - +
149V GLU* 5.2 15.0 - - + -
220V GLU* 5.8 3.1 - - - -
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Residues in contact with ALA 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107V THR 2.9 17.8 + - - +
108V ALA* 3.5 9.2 - - - +
109V ILE 3.2 0.2 - - - -
110V ILE* 1.3 77.7 - - - +
112V GLN* 1.3 56.4 + - - +
114V ILE* 4.1 4.1 - - - +
115V LEU* 2.9 30.7 + - - +
137V TYR* 5.0 14.8 - - + +
140V LEU* 5.5 8.5 - - + -
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Residues in contact with GLN 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108V ALA 2.9 14.0 + - - +
109V ILE* 3.1 11.2 + - - +
111V ALA* 1.3 75.1 - - - +
113V LYS* 1.3 59.5 + - - +
115V LEU* 3.8 5.9 - - - +
116V ASN* 2.9 28.8 + - - +
221V PRO* 4.6 12.9 - - + +
285V PRO 5.5 2.7 - - - +
286V GLU* 5.4 7.6 - - + -
287V PHE 4.7 17.7 - - - +
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Residues in contact with LYS 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109V ILE 2.9 13.4 + - - +
110V ILE* 3.6 10.5 - - - +
112V GLN* 1.3 74.6 - - - +
114V ILE* 1.3 59.0 + - - +
116V ASN* 3.1 5.2 + - - +
117V GLN* 2.9 27.4 + - - +
220V GLU* 3.7 30.3 - - + +
221V PRO* 3.8 11.8 - - + +
224V PRO* 5.8 0.7 - - - +
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Residues in contact with ILE 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110V ILE 2.9 16.9 + - - +
111V ALA* 4.1 3.8 - - - +
113V LYS* 1.3 75.8 - - - +
115V LEU* 1.3 57.8 + - - +
117V GLN* 3.2 9.1 + - - +
118V SER* 2.9 28.2 + - - -
133V ILE* 4.8 9.5 - - + +
136V LEU* 5.6 0.9 - - + -
137V TYR* 4.2 23.1 - - + +
149V GLU* 6.2 2.7 - - - -
152V SER* 4.9 17.0 - - - -
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Residues in contact with LEU 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111V ALA 2.9 20.5 + - - +
112V GLN* 3.8 7.0 - - - +
114V ILE* 1.3 77.9 - - - +
116V ASN* 1.3 56.0 + - - +
118V SER* 3.4 7.6 + - - -
119V TYR* 2.9 27.7 + - - +
137V TYR* 4.7 8.0 - - + +
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Residues in contact with ASN 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112V GLN 2.9 18.7 + - - +
113V LYS 3.1 5.8 + - - +
115V LEU* 1.3 73.6 - - - +
117V GLN* 1.3 58.0 + - - +
119V TYR* 3.3 7.9 + - - +
120V TYR* 2.9 27.5 + - - +
221V PRO 4.1 19.3 - - - +
224V PRO* 4.4 11.9 - - + +
287V PHE 4.8 9.6 - - - +
288V ARG* 6.0 1.1 - - - +
289V ILE* 5.3 14.3 - - + +
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Residues in contact with GLN 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113V LYS 2.9 12.9 + - - +
114V ILE* 3.2 12.1 + - - +
116V ASN* 1.3 74.1 - - - +
118V SER* 1.3 58.6 + - - +
120V TYR* 3.2 7.6 + - - +
121V LEU* 2.9 29.5 + - - +
133V ILE* 5.2 8.3 - - + -
152V SER* 5.7 5.2 - - - +
156V TYR* 5.2 15.0 - - + -
224V PRO* 4.9 7.1 - - + +
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Residues in contact with SER 118 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114V ILE 2.9 15.8 + - - -
115V LEU* 3.7 8.3 - - - -
116V ASN 3.3 0.2 - - - -
117V GLN* 1.3 76.1 - - - +
119V TYR* 1.3 56.9 + - - +
122V GLY* 2.9 23.2 + - - -
130V SER* 3.5 34.8 - - - +
133V ILE* 4.4 4.8 - - - +
134V MET* 4.2 18.8 - - - -
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Residues in contact with TYR 119 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115V LEU 2.9 18.0 + - - +
116V ASN* 3.6 9.2 - - - +
117V GLN 3.2 0.2 - - - -
118V SER* 1.3 76.5 - - - +
120V TYR* 1.3 60.2 + - - +
122V GLY* 3.8 1.7 - - - +
123V GLU* 2.9 28.6 + - - +
288V ARG* 6.2 2.0 - - + -
289V ILE* 5.1 15.9 - - + +
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Residues in contact with TYR 120 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116V ASN 2.9 16.8 + - - +
117V GLN* 3.2 8.3 + - - +
119V TYR* 1.3 75.0 - - - +
121V LEU* 1.3 58.1 + - - +
123V GLU* 3.3 7.1 + - - +
124V CYS* 2.9 27.3 + - - +
224V PRO* 4.6 15.3 - - + +
228V ARG* 6.4 1.6 - - + -
289V ILE* 5.7 5.1 - - + +
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Residues in contact with LEU 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117V GLN 2.9 15.9 + - - +
120V TYR* 1.3 74.8 - - - +
122V GLY* 1.3 59.6 + - - +
124V CYS* 3.2 8.5 + - - +
125V SER 3.0 7.1 + - - -
126V PHE* 3.0 34.5 + - + +
129V LYS* 4.7 5.6 - - + -
130V SER* 3.6 30.1 - - - +
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Residues in contact with GLY 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118V SER 2.9 18.5 + - - -
119V TYR* 3.8 2.5 - - - -
120V TYR 3.2 0.2 - - - -
121V LEU* 1.3 75.2 - - - +
123V GLU* 1.3 62.2 + - - +
125V SER* 3.1 13.3 + - - -
126V PHE 4.7 3.1 - - - -
130V SER* 3.8 6.7 - - - -
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Residues in contact with GLU 123 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119V TYR 2.9 18.4 + - - +
120V TYR* 3.3 6.9 + - - +
122V GLY* 1.3 75.5 - - - +
124V CYS* 1.3 58.9 + - - +
125V SER* 3.2 3.0 + - - -
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Residues in contact with CYS 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120V TYR 2.9 17.4 + - - +
121V LEU* 3.6 10.1 - - - +
122V GLY 3.2 0.6 - - - -
123V GLU* 1.3 75.1 - - - +
125V SER* 1.3 70.4 + - - +
126V PHE* 3.4 5.0 + - + +
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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) + - + + + + + -
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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