Contacts of the helix formed by residues 98 - 124 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96S ALA 3.8 1.7 + - - +
97S TRP* 1.3 77.1 - - - +
99S GLU* 1.3 65.7 + - - +
100S ASN* 4.1 9.9 - - + +
101S VAL* 3.3 15.0 + - + +
102S LYS* 3.0 22.2 + - - +
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Residues in contact with GLU 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S TRP 4.3 0.4 + - - -
98S LYS* 1.3 74.1 - - - +
100S ASN* 1.3 56.9 + - - +
102S LYS* 3.9 6.2 - - - +
103S CYS* 2.9 32.2 + - - +
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Residues in contact with ASN 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98S LYS* 3.2 6.6 - - + +
99S GLU* 1.3 78.6 - - - +
101S VAL* 1.3 58.7 + - - +
103S CYS* 3.9 3.2 - - - +
104S GLU* 2.9 32.1 + - - +
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Residues in contact with VAL 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S TRP* 6.1 2.0 - - + -
98S LYS* 3.3 20.0 + - + +
100S ASN* 1.3 75.6 - - - +
102S LYS* 1.3 60.4 + - - +
104S GLU* 3.9 4.8 - - - +
105S VAL* 2.9 33.1 + - - +
277S LEU* 5.1 11.7 - - + +
280S LEU* 4.9 21.5 - - + -
281S GLY 5.5 0.7 - - - +
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Residues in contact with LYS 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S TRP* 6.0 3.8 - - + -
98S LYS 3.0 16.3 + - - +
99S GLU* 3.9 7.0 - - - +
101S VAL* 1.3 77.7 - - - +
103S CYS* 1.3 58.5 + - - +
105S VAL* 4.9 1.3 - - - -
106S TRP* 2.9 25.3 + - - +
202S GLY 5.2 0.7 - - - +
203S LEU* 3.0 39.3 - - + +
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Residues in contact with CYS 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99S GLU 2.9 19.2 + - - +
100S ASN* 4.3 2.7 - - - +
102S LYS* 1.3 77.4 - - - +
104S GLU* 1.3 57.0 + - - +
106S TRP* 4.1 2.8 - - - +
107S THR* 2.9 31.4 + - - -
142S ARG* 5.4 13.7 - - + +
143S PHE* 5.4 5.6 - - - +
203S LEU 3.8 5.8 + - - -
204S LYS* 5.9 2.5 - - - +
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Residues in contact with GLU 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S ASN 2.9 22.1 + - - +
101S VAL* 3.9 4.7 - - - +
103S CYS* 1.3 75.8 - - - +
105S VAL* 1.3 60.6 + - - +
107S THR* 3.3 5.2 + - - -
108S ALA* 2.9 29.8 + - - +
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Residues in contact with VAL 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S VAL 2.9 19.0 + - - +
102S LYS* 4.2 2.5 - - - +
104S GLU* 1.3 76.1 - - - +
106S TRP* 1.3 57.5 + - - +
108S ALA* 3.4 6.7 + - - +
109S ILE* 2.9 29.6 + - - +
203S LEU* 5.8 2.5 - - + -
276S ALA* 6.3 3.4 - - + -
277S LEU* 6.1 6.3 - - + -
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Residues in contact with TRP 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102S LYS 2.9 19.9 + - - +
103S CYS* 4.1 3.8 - - - +
105S VAL* 1.3 78.1 - - - +
107S THR* 1.3 56.0 + - - +
109S ILE* 3.3 6.9 + - - +
110S ILE* 2.9 29.5 + - - +
203S LEU* 3.6 26.2 - - + +
204S LYS* 4.5 10.5 - - + +
217S ASP* 5.8 7.0 - - + -
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Residues in contact with THR 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S CYS 2.9 21.4 + - - -
104S GLU* 3.7 5.4 - - - -
106S TRP* 1.3 78.0 - - - +
108S ALA* 1.3 56.8 + - - +
110S ILE* 3.4 6.3 + - - +
111S ALA* 2.9 28.8 + - - +
140S LEU* 6.6 0.7 - - - -
141S GLU 5.2 11.0 - - - -
142S ARG* 5.2 9.0 - - - -
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Residues in contact with ALA 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S GLU 2.9 17.2 + - - +
105S VAL* 3.8 6.1 - - - +
107S THR* 1.3 76.7 - - - +
109S ILE* 1.3 56.6 + - - +
111S ALA* 3.3 7.8 + - - +
112S GLN* 2.9 27.9 + - - +
284S ILE* 4.8 18.2 - - + -
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Residues in contact with ILE 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105S VAL 2.9 18.5 + - - +
106S TRP* 3.7 7.6 - - - +
108S ALA* 1.3 75.0 - - - +
110S ILE* 1.3 61.0 + - - +
112S GLN* 3.1 8.5 + - - +
113S LYS* 2.9 27.7 + - - +
217S ASP* 4.2 17.9 - - + +
218S ILE* 6.1 0.4 - - - -
220S GLU* 5.3 4.0 - - + +
221S PRO* 4.7 6.6 - - + +
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Residues in contact with ILE 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S TRP 2.9 17.1 + - - +
107S THR* 3.8 7.0 - - - +
109S ILE* 1.3 75.9 - - - +
111S ALA* 1.3 57.1 + - - +
113S LYS* 3.2 7.9 + - - +
114S ILE* 2.9 30.3 + - - +
149S GLU* 5.2 14.6 - - + -
220S GLU* 5.8 2.9 - - - -
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Residues in contact with ALA 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107S THR 2.9 17.8 + - - +
108S ALA* 3.5 9.4 - - - +
110S ILE* 1.3 77.9 - - - +
112S GLN* 1.3 55.2 + - - +
114S ILE* 4.1 4.7 - - - +
115S LEU* 2.9 31.0 + - - +
137S TYR* 5.0 14.1 - - + +
140S LEU* 5.5 9.0 - - + -
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Residues in contact with GLN 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108S ALA 2.9 13.6 + - - +
109S ILE* 3.1 11.6 + - - +
111S ALA* 1.3 76.3 - - - +
113S LYS* 1.3 59.1 + - - +
115S LEU* 3.8 5.8 - - - +
116S ASN* 2.9 28.9 + - - +
221S PRO* 4.6 12.1 - - + +
285S PRO 5.5 2.5 - - - +
286S GLU* 5.4 7.9 - - + -
287S PHE 4.7 18.2 - - - +
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Residues in contact with LYS 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109S ILE 2.9 13.3 + - - +
110S ILE* 3.2 11.2 + - - +
112S GLN* 1.3 74.6 - - - +
114S ILE* 1.3 58.5 + - - +
116S ASN* 3.1 5.5 + - - +
117S GLN* 2.9 27.0 + - - +
220S GLU* 3.7 29.8 - - + +
221S PRO* 3.8 13.4 - - + +
224S PRO* 5.8 0.9 - - - +
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Residues in contact with ILE 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S ILE 2.9 16.5 + - - +
111S ALA* 4.1 4.0 - - - +
113S LYS* 1.3 76.1 - - - +
115S LEU* 1.3 57.4 + - - +
117S GLN* 3.2 9.0 + - - +
118S SER* 2.9 28.3 + - - -
133S ILE* 4.8 9.0 - - + +
136S LEU* 5.6 0.9 - - + -
137S TYR* 4.2 22.9 - - + +
149S GLU* 6.2 2.2 - - - -
152S SER* 4.9 16.8 - - - -
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Residues in contact with LEU 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111S ALA 2.9 21.0 + - - +
112S GLN* 3.8 6.5 - - - +
114S ILE* 1.3 78.5 - - - +
116S ASN* 1.3 56.9 + - - +
118S SER* 3.4 7.7 + - - -
119S TYR* 2.9 27.9 + - - +
137S TYR* 4.7 7.8 - - + +
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Residues in contact with ASN 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112S GLN 2.9 18.9 + - - +
113S LYS 3.1 5.4 + - - +
115S LEU* 1.3 75.3 - - - +
117S GLN* 1.3 60.7 + - - +
119S TYR* 3.3 8.1 + - - +
120S TYR* 2.9 27.7 + - - +
221S PRO* 4.1 19.1 - - + +
224S PRO* 4.4 12.2 - - + +
287S PHE 4.8 10.3 - - - +
288S ARG* 5.6 1.6 - - - +
289S ILE* 5.3 13.8 - - + +
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Residues in contact with GLN 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113S LYS 2.9 13.1 + - - +
114S ILE* 3.5 11.0 - - - +
116S ASN* 1.3 73.3 - - - +
118S SER* 1.3 59.8 + - - +
120S TYR* 3.2 8.3 + - - +
121S LEU* 2.9 29.3 + - - +
133S ILE* 5.2 8.3 - - + -
152S SER* 5.7 5.4 - - - +
156S TYR* 5.2 15.0 - - + -
224S PRO* 4.9 7.5 - - + +
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Residues in contact with SER 118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114S ILE 2.9 16.5 + - - -
115S LEU* 3.7 7.4 - - - -
117S GLN* 1.3 76.9 - - - +
119S TYR* 1.3 58.2 + - - +
122S GLY* 2.9 23.7 + - - -
130S SER* 3.5 34.5 - - - +
133S ILE* 4.4 5.0 - - - +
134S MET* 4.2 18.4 - - - -
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Residues in contact with TYR 119 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115S LEU 2.9 16.6 + - - +
116S ASN* 3.6 8.7 - - - +
117S GLN 3.2 0.2 - - - -
118S SER* 1.3 76.3 - - - +
120S TYR* 1.3 59.4 + - - +
122S GLY* 3.8 1.1 - - - -
123S GLU* 2.9 29.1 + - - +
288S ARG* 6.2 2.7 - - + -
289S ILE* 5.1 16.6 - - + +
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Residues in contact with TYR 120 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116S ASN 2.9 16.7 + - - +
117S GLN* 3.2 8.0 + - - +
119S TYR* 1.3 75.4 - - - +
121S LEU* 1.3 61.2 + - - +
123S GLU* 3.3 6.9 + - - +
124S CYS* 2.9 27.0 + - - +
224S PRO* 4.6 15.0 - - + +
228S ARG* 6.4 2.0 - - + -
289S ILE* 5.7 0.4 - - - +
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Residues in contact with LEU 121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117S GLN 2.9 15.1 + - - +
120S TYR* 1.3 74.8 - - - +
122S GLY* 1.3 58.6 + - - +
124S CYS* 3.2 8.9 + - - +
125S SER 3.0 7.1 + - - -
126S PHE* 3.0 34.3 + - + +
129S LYS* 4.7 5.8 - - + -
130S SER* 3.6 30.5 - - - +
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Residues in contact with GLY 122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S SER 2.9 18.7 + - - -
119S TYR* 3.4 2.9 + - - -
121S LEU* 1.3 74.4 - - - +
123S GLU* 1.3 62.5 + - - +
125S SER* 3.1 13.0 + - - -
126S PHE 4.7 2.7 - - - -
130S SER* 3.8 7.4 - - - -
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Residues in contact with GLU 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119S TYR 2.9 17.7 + - - +
120S TYR* 3.7 7.0 - - - +
122S GLY* 1.3 75.3 - - - +
124S CYS* 1.3 58.6 + - - +
125S SER* 3.2 3.4 + - - -
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Residues in contact with CYS 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120S TYR 2.9 16.5 + - - +
121S LEU* 3.6 10.3 - - - +
122S GLY 3.2 0.4 - - - -
123S GLU* 1.3 74.6 - - - +
125S SER* 1.3 70.0 + - - +
126S 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