Contacts of the helix formed by residues 98 - 124 (chain Z) in PDB entry 6QXT
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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96Z ALA 3.8 1.5 + - - +
97Z TRP* 1.3 76.6 - - - +
99Z GLU* 1.3 61.2 + - - +
100Z ASN* 4.1 10.1 - - + +
101Z VAL* 3.2 18.2 + - + +
102Z LYS* 3.0 28.1 + - - +
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Residues in contact with GLU 99 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Z TRP 4.3 0.2 + - - -
98Z LYS* 1.3 74.2 - - - +
100Z ASN* 1.3 57.2 + - - +
102Z LYS* 3.9 6.7 - - - +
103Z CYS* 2.9 32.2 + - - +
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Residues in contact with ASN 100 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Z LYS* 3.2 7.2 - - + +
99Z GLU* 1.3 79.7 - - - +
101Z VAL* 1.3 57.5 + - - +
103Z CYS* 4.3 2.6 - - - +
104Z GLU* 2.9 31.5 + - - +
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Residues in contact with VAL 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Z TRP* 6.0 1.3 - - + -
98Z LYS* 3.2 20.9 + - + +
100Z ASN* 1.3 76.5 - - - +
102Z LYS* 1.3 61.2 + - - +
104Z GLU* 3.9 4.0 - - - +
105Z VAL* 2.9 33.1 + - - +
277Z LEU* 5.1 11.4 - - + +
280Z LEU* 4.9 21.3 - - + -
281Z GLY 5.6 1.3 - - - +
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Residues in contact with LYS 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Z TRP* 6.0 3.6 - - + -
98Z LYS 3.0 15.9 + - - +
99Z GLU* 3.9 7.0 - - - +
101Z VAL* 1.3 77.9 - - - +
103Z CYS* 1.3 56.9 + - - +
105Z VAL* 4.1 1.7 - - - -
106Z TRP* 2.9 24.9 + - - +
202Z GLY 5.2 1.1 - - - +
203Z LEU* 3.0 41.0 - - + +
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Residues in contact with CYS 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Z GLU 2.9 18.7 + - - +
100Z ASN* 4.3 3.4 - - - +
102Z LYS* 1.3 77.4 - - - +
104Z GLU* 1.3 57.6 + - - +
106Z TRP* 4.2 2.4 - - - +
107Z THR* 2.9 30.8 + - - -
142Z ARG* 5.4 13.6 - - + +
143Z PHE 5.4 5.6 - - - +
203Z LEU 3.8 5.1 + - - -
204Z LYS* 5.9 2.5 - - - +
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Residues in contact with GLU 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100Z ASN 2.9 21.3 + - - +
101Z VAL* 3.9 5.4 - - - +
102Z LYS 3.2 0.2 - - - -
103Z CYS* 1.3 75.8 - - - +
105Z VAL* 1.3 61.6 + - - +
107Z THR* 3.3 5.0 + - - -
108Z ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Z VAL 2.9 18.1 + - - +
102Z LYS* 4.2 3.1 - - - +
104Z GLU* 1.3 76.3 - - - +
106Z TRP* 1.3 58.3 + - - +
108Z ALA* 3.4 6.2 + - - +
109Z ILE* 2.9 29.3 + - - +
203Z LEU* 5.8 2.5 - - + -
276Z ALA* 6.3 2.9 - - + -
277Z LEU* 6.1 6.7 - - + -
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Residues in contact with TRP 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Z LYS 2.9 20.2 + - - +
103Z CYS* 4.2 3.6 - - - +
105Z VAL* 1.3 77.9 - - - +
107Z THR* 1.3 56.4 + - - +
109Z ILE* 3.7 6.7 - - - +
110Z ILE* 2.9 29.6 + - - +
203Z LEU* 3.6 26.8 - - + +
204Z LYS* 4.5 10.8 - - + +
217Z ASP* 5.8 6.5 - - + -
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Residues in contact with THR 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Z CYS 2.9 21.8 + - - -
104Z GLU* 3.7 5.8 - - - -
106Z TRP* 1.3 78.1 - - - +
108Z ALA* 1.3 56.9 + - - +
110Z ILE* 3.4 6.0 + - - +
111Z ALA* 2.9 28.1 + - - +
140Z LEU* 5.7 3.3 - - - +
141Z GLU 5.2 11.2 - - - -
142Z ARG* 5.2 8.7 - - - -
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Residues in contact with ALA 108 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Z GLU 2.9 17.1 + - - +
105Z VAL* 3.8 6.7 - - - +
107Z THR* 1.3 75.7 - - - +
109Z ILE* 1.3 58.3 + - - +
111Z ALA* 3.3 8.2 + - - +
112Z GLN* 2.9 27.2 + - - +
284Z ILE* 4.8 18.4 - - + -
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Residues in contact with ILE 109 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Z VAL 2.9 17.4 + - - +
106Z TRP* 3.7 7.2 - - - +
107Z THR 3.3 0.2 - - - -
108Z ALA* 1.3 73.7 - - - +
110Z ILE* 1.3 60.1 + - - +
112Z GLN* 3.1 9.3 + - - +
113Z LYS* 2.9 28.1 + - - +
217Z ASP 4.3 17.9 - - - +
218Z ILE* 6.1 0.4 - - - -
220Z GLU* 5.6 4.0 - - + -
221Z PRO* 4.7 6.7 - - + +
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Residues in contact with ILE 110 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Z TRP 2.9 17.6 + - - +
107Z THR* 3.8 6.3 - - - +
109Z ILE* 1.3 75.7 - - - +
111Z ALA* 1.3 57.6 + - - +
113Z LYS* 3.2 8.0 + - - +
114Z ILE* 2.9 31.0 + - - +
149Z GLU* 5.2 15.0 - - + -
220Z GLU* 5.7 2.9 - - - -
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Residues in contact with ALA 111 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Z THR 2.9 17.6 + - - +
108Z ALA* 3.5 9.4 - - - +
109Z ILE 3.2 0.2 - - - -
110Z ILE* 1.3 77.0 - - - +
112Z GLN* 1.3 55.9 + - - +
114Z ILE* 3.9 4.7 - - - +
115Z LEU* 2.9 31.2 + - - +
137Z TYR* 5.0 14.7 - - + +
140Z LEU* 5.5 9.3 - - + +
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Residues in contact with GLN 112 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Z ALA 2.9 14.0 + - - +
109Z ILE* 3.1 12.1 + - - +
111Z ALA* 1.3 76.8 - - - +
113Z LYS* 1.3 56.3 + - - +
115Z LEU* 3.5 5.5 + - - +
116Z ASN* 2.9 28.6 + - - +
221Z PRO* 4.5 12.3 - - + +
285Z PRO 5.5 2.9 - - - +
286Z GLU* 5.4 7.9 - - + -
287Z PHE 4.7 17.9 - - - +
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Residues in contact with LYS 113 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Z ILE 2.9 12.7 + - - +
110Z ILE* 3.2 10.5 + - - +
112Z GLN* 1.3 75.1 - - - +
114Z ILE* 1.3 59.8 + - - +
116Z ASN* 3.1 4.9 + - - +
117Z GLN* 2.9 27.0 + - - +
220Z GLU* 3.7 29.8 - - + +
221Z PRO* 3.8 13.6 - - + +
224Z PRO* 5.7 0.7 - - - +
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Residues in contact with ILE 114 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Z ILE 2.9 16.7 + - - +
111Z ALA* 4.1 4.0 - - - +
113Z LYS* 1.3 76.5 - - - +
115Z LEU* 1.3 57.4 + - - +
117Z GLN* 3.2 8.4 + - - +
118Z SER* 2.9 28.8 + - - -
133Z ILE* 4.8 9.9 - - + +
136Z LEU 5.6 0.7 - - - -
137Z TYR* 4.2 23.3 - - + +
149Z GLU* 6.2 2.5 - - - -
152Z SER* 4.9 16.4 - - - -
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Residues in contact with LEU 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Z ALA 2.9 19.9 + - - +
112Z GLN* 3.8 7.4 - - - +
114Z ILE* 1.3 78.3 - - - +
116Z ASN* 1.3 55.8 + - - +
118Z SER* 3.4 7.5 + - - -
119Z TYR* 2.9 27.4 + - - +
137Z TYR* 4.7 8.6 - - + +
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Residues in contact with ASN 116 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Z GLN 2.9 19.3 + - - +
113Z LYS 3.1 4.9 + - - +
115Z LEU* 1.3 72.8 - - - +
117Z GLN* 1.3 60.5 + - - +
119Z TYR* 3.3 8.4 + - - +
120Z TYR* 2.9 27.0 + - - +
221Z PRO 4.1 19.1 - - - +
224Z PRO* 4.4 12.8 - - + +
287Z PHE 4.8 10.3 - - - +
288Z ARG* 5.6 1.1 - - - +
289Z ILE* 5.3 14.1 - - + +
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Residues in contact with GLN 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Z LYS 2.9 13.1 + - - +
114Z ILE* 3.2 11.9 + - - +
116Z ASN* 1.3 74.0 - - - +
118Z SER* 1.3 59.8 + - - +
120Z TYR* 3.2 7.4 + - - +
121Z LEU* 2.9 29.3 + - - +
133Z ILE* 5.2 8.3 - - + -
152Z SER* 5.7 5.4 - - - +
156Z TYR* 5.2 14.6 - - + -
224Z PRO* 4.8 7.6 - - + +
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Residues in contact with SER 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Z ILE 2.9 15.6 + - - -
115Z LEU* 3.7 8.3 - - - -
117Z GLN* 1.3 75.4 - - - +
119Z TYR* 1.3 57.6 + - - +
121Z LEU* 4.6 0.2 - - - -
122Z GLY* 2.9 23.2 + - - -
130Z SER* 3.5 35.3 - - - +
133Z ILE* 4.4 4.6 - - - +
134Z MET* 4.2 18.8 - - - -
137Z TYR* 6.1 0.2 - - - -
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Residues in contact with TYR 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Z LEU 2.9 17.2 + - - +
116Z ASN* 3.6 9.0 - - - +
117Z GLN 3.2 0.4 - - - -
118Z SER* 1.3 76.1 - - - +
120Z TYR* 1.3 59.1 + - - +
122Z GLY* 3.8 1.1 - - - -
123Z GLU* 2.9 28.6 + - - +
288Z ARG* 6.2 2.0 - - + -
289Z ILE* 5.1 17.3 - - + +
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Residues in contact with TYR 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Z ASN 2.9 16.5 + - - +
117Z GLN* 3.2 8.0 + - - +
119Z TYR* 1.3 75.0 - - - +
121Z LEU* 1.3 60.6 + - - +
123Z GLU* 3.3 7.0 + - - +
124Z CYS* 2.9 27.8 + - - +
224Z PRO* 4.7 15.0 - - + +
228Z ARG* 6.4 1.8 - - + -
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Residues in contact with LEU 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Z GLN 2.9 15.3 + - - +
118Z SER* 4.6 0.2 - - - -
120Z TYR* 1.3 75.7 - - - +
122Z GLY* 1.3 57.3 + - - +
124Z CYS* 3.3 8.2 + - - +
125Z SER 3.0 7.6 + - - -
126Z PHE* 2.9 35.0 + - + +
129Z LYS* 4.7 5.2 - - + -
130Z SER* 3.6 30.1 - - - +
133Z ILE* 6.2 0.7 - - + -
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Residues in contact with GLY 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O SER 5.9 2.5 - - - -
147O ASN* 6.1 3.8 - - - +
150O GLY 6.0 0.5 - - - -
151O HIS* 5.3 3.8 + - - +
118Z SER 2.9 17.8 + - - -
119Z TYR* 3.8 2.9 - - - -
120Z TYR 3.2 0.4 - - - -
121Z LEU* 1.3 75.8 - - - +
123Z GLU* 1.3 63.8 + - - +
125Z SER* 3.1 13.2 + - - -
126Z PHE 4.7 2.7 - - - -
130Z SER* 3.8 7.5 - - - -
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Residues in contact with GLU 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Z TYR 2.9 18.4 + - - +
120Z TYR* 3.7 7.4 - - - +
122Z GLY* 1.3 75.9 - - - +
124Z CYS* 1.3 59.3 + - - +
125Z SER* 3.2 3.0 + - - -
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Residues in contact with CYS 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Z TYR 2.9 17.8 + - - +
121Z LEU* 3.7 9.2 - - - +
122Z GLY 3.2 0.4 - - - -
123Z GLU* 1.3 74.9 - - - +
125Z SER* 1.3 69.3 + - - +
126Z PHE* 3.4 5.4 + - + +
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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
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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