Contacts of the helix formed by residues 98 - 124 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R ALA 3.2 5.9 + - - +
97R TRP* 1.3 76.8 - - - +
99R GLU* 1.3 66.5 + - - +
100R ASN* 3.3 9.0 - - + +
101R VAL* 3.5 15.9 + - + +
102R LYS* 3.1 22.2 + - - +
277R LEU 5.9 0.2 + - - -
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Residues in contact with GLU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R TRP 3.9 0.8 + - - -
98R LYS* 1.3 72.1 - - - +
100R ASN* 1.3 59.9 + - - +
102R LYS* 3.8 5.7 - - - +
103R CYS* 2.9 30.7 + - - +
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Residues in contact with ASN 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R LYS* 3.3 7.0 - - + +
99R GLU* 1.3 80.4 - - - +
101R VAL* 1.3 56.3 + - - +
103R CYS* 3.4 4.6 + - - +
104R GLU* 2.9 29.3 + - - +
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Residues in contact with VAL 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R TRP* 6.1 1.8 - - + -
98R LYS* 3.5 19.1 + - + +
99R GLU 3.4 0.2 - - - -
100R ASN* 1.3 75.8 - - - +
102R LYS* 1.3 61.0 + - - +
104R GLU* 3.3 5.9 + - - +
105R VAL* 2.9 31.4 + - - +
277R LEU* 5.1 12.6 - - + +
280R LEU* 4.8 21.3 - - + -
281R GLY* 5.2 4.7 - - - +
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Residues in contact with LYS 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R TRP* 5.7 5.1 - - + +
98R LYS 3.1 17.5 + - - +
99R GLU* 3.8 7.4 - - - +
101R VAL* 1.3 78.1 - - - +
103R CYS* 1.3 55.6 + - - +
105R VAL* 4.1 4.1 - - - +
106R TRP* 2.9 31.9 + - - +
202R GLY 5.5 1.3 - - - +
203R LEU* 4.1 26.1 - - - +
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Residues in contact with CYS 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R GLU 2.9 18.3 + - - +
100R ASN* 3.8 5.8 - - - +
102R LYS* 1.3 74.2 - - - +
104R GLU* 1.3 60.3 + - - +
106R TRP* 3.9 4.6 - - - +
107R THR* 2.9 31.7 + - - -
142R ARG* 5.4 13.8 - - + +
143R PHE 5.7 2.9 - - - +
203R LEU 5.7 0.4 - - - -
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Residues in contact with GLU 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R ASN 2.9 17.9 + - - +
101R VAL* 3.7 7.0 - - - +
103R CYS* 1.3 73.8 - - - +
105R VAL* 1.3 60.7 + - - +
107R THR* 3.4 4.8 + - - -
108R ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R VAL 2.9 17.4 + - - +
102R LYS* 4.1 4.3 - - - +
104R GLU* 1.3 75.9 - - - +
106R TRP* 1.3 58.8 + - - +
108R ALA* 3.4 6.6 + - - +
109R ILE* 2.9 29.5 + - - +
203R LEU* 5.9 3.6 - - + -
277R LEU* 6.5 0.9 - - + -
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Residues in contact with TRP 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R LYS 2.9 20.6 + - - +
103R CYS* 3.9 5.6 - - - +
105R VAL* 1.3 78.3 - - - +
107R THR* 1.3 56.4 + - - +
109R ILE* 3.2 7.0 + - - +
110R ILE* 2.9 29.8 + - - +
203R LEU* 4.4 24.1 - - + +
204R LYS* 5.2 2.9 - - - +
217R ASP* 6.4 0.4 - - + -
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Residues in contact with THR 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R CYS 2.9 19.0 + - - -
104R GLU* 3.8 4.9 - - - -
106R TRP* 1.3 76.7 - - - +
108R ALA* 1.3 58.8 + - - +
110R ILE* 3.5 5.4 + - - +
111R ALA* 2.9 30.0 + - - +
140R LEU* 5.9 2.3 - - - +
141R GLU 5.3 4.9 - - - -
142R ARG* 5.3 15.5 - - - -
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Residues in contact with ALA 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R GLU 2.9 17.3 + - - +
105R VAL* 3.7 7.0 - - - +
107R THR* 1.3 76.2 - - - +
109R ILE* 1.3 58.1 + - - +
111R ALA* 3.4 6.4 + - - +
112R GLN* 2.9 28.8 + - - +
284R ILE* 4.7 18.8 - - + -
285R PRO 6.2 0.2 - - - +
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Residues in contact with ILE 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105R VAL 2.9 17.6 + - - +
106R TRP* 3.2 7.8 + - - +
108R ALA* 1.3 74.1 - - - +
110R ILE* 1.3 59.7 + - - +
112R GLN* 3.2 7.7 + - - +
113R LYS* 2.9 29.0 + - - +
217R ASP* 4.1 19.5 - - + +
218R ILE* 5.8 2.0 - - - +
220R GLU* 5.4 6.3 - - + -
221R PRO* 4.6 8.0 - - + +
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Residues in contact with ILE 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106R TRP 2.9 16.7 + - - +
107R THR* 3.9 6.1 - - - +
109R ILE* 1.3 75.8 - - - +
111R ALA* 1.3 57.6 + - - +
113R LYS* 3.3 6.1 + - - +
114R ILE* 2.9 31.7 + - - +
149R GLU* 5.2 15.7 - - + +
220R GLU* 6.0 1.6 - - - -
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Residues in contact with ALA 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R THR 2.9 18.7 + - - +
108R ALA* 3.6 7.9 - - - +
109R ILE 3.2 0.2 - - - -
110R ILE* 1.3 77.5 - - - +
112R GLN* 1.3 57.1 + - - +
114R ILE* 4.1 3.7 - - - +
115R LEU* 2.9 31.4 + - - +
137R TYR* 5.0 14.4 - - + +
140R LEU* 5.6 9.1 - - + +
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Residues in contact with GLN 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R ALA 2.9 17.4 + - - +
109R ILE* 3.2 6.9 + - - +
111R ALA* 1.3 78.4 - - - +
113R LYS* 1.3 55.9 + - - +
115R LEU* 3.5 5.1 + - - +
116R ASN* 2.9 30.5 + - - +
221R PRO* 4.0 19.0 - - + +
286R GLU* 5.7 4.3 - - + -
287R PHE 4.4 20.3 - - - +
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Residues in contact with LYS 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109R ILE 2.9 15.4 + - - +
110R ILE* 3.8 5.6 - - - +
112R GLN* 1.3 77.3 - - - +
114R ILE* 1.3 56.8 + - - +
116R ASN* 3.2 5.7 + - - +
117R GLN* 2.9 27.9 + - - +
220R GLU* 3.6 32.1 - - + +
221R PRO* 4.1 8.4 - - - +
224R PRO* 5.4 1.9 - - - +
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Residues in contact with ILE 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110R ILE 2.9 17.5 + - - +
111R ALA* 4.1 3.1 - - - +
113R LYS* 1.3 76.0 - - - +
115R LEU* 1.3 58.7 + - - +
117R GLN* 3.2 7.9 + - - +
118R SER* 2.9 29.5 + - - -
133R ILE* 4.8 7.0 - - + +
136R LEU* 5.8 0.9 - - + -
137R TYR* 4.3 21.5 - - + +
149R GLU* 6.0 4.7 - - + -
152R SER* 5.1 14.8 - - - -
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Residues in contact with LEU 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111R ALA 2.9 19.9 + - - +
112R GLN* 3.8 6.3 - - - +
114R ILE* 1.3 77.2 - - - +
116R ASN* 1.3 56.7 + - - +
118R SER* 3.5 5.4 + - - +
119R TYR* 2.9 30.7 + - - +
137R TYR* 4.7 10.2 - - + +
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Residues in contact with ASN 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R GLN 2.9 18.9 + - - +
113R LYS 3.2 5.1 + - - +
115R LEU* 1.3 73.6 - - - +
117R GLN* 1.3 60.4 + - - +
119R TYR* 3.8 5.4 - - - +
120R TYR* 2.9 30.1 + - - +
221R PRO 4.2 17.0 - - - +
224R PRO* 4.5 13.8 - - + +
287R PHE 5.4 3.8 - - - +
288R ARG* 5.6 1.3 - - - +
289R ILE* 4.9 23.7 - - + +
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Residues in contact with GLN 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R LYS 2.9 13.6 + - - +
114R ILE* 3.2 11.6 + - - +
116R ASN* 1.3 75.0 - - - +
118R SER* 1.3 60.0 + - - +
120R TYR* 3.3 6.0 + - - +
121R LEU* 2.9 28.6 + - - +
133R ILE* 5.2 5.4 - - + -
152R SER* 6.2 2.9 - - - -
156R TYR* 4.6 21.8 - - + +
224R PRO* 4.6 10.0 - - + +
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Residues in contact with SER 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R ILE 2.9 16.2 + - - -
115R LEU* 3.9 5.6 - - - -
117R GLN* 1.3 75.9 - - - +
119R TYR* 1.3 58.4 + - - +
121R LEU* 3.3 1.2 + - - -
122R GLY* 2.9 23.4 + - - -
130R SER* 3.2 37.2 - - - +
133R ILE* 3.8 18.1 - - - +
134R MET* 3.8 13.9 - - - -
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Residues in contact with TYR 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R LEU 2.9 19.0 + - - +
116R ASN* 3.9 6.3 - - - +
118R SER* 1.3 77.2 - - - +
120R TYR* 1.3 56.6 + - - +
122R GLY* 3.1 3.6 + - - +
123R GLU* 2.9 26.3 + - - +
289R ILE* 5.7 8.7 - - + +
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Residues in contact with TYR 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116R ASN 2.9 19.6 + - - +
117R GLN* 3.7 5.8 - - - +
119R TYR* 1.3 76.1 - - - +
121R LEU* 1.3 58.6 + - - +
123R GLU* 3.2 8.8 + - - +
124R CYS* 2.9 26.9 + - - +
224R PRO* 5.0 11.7 - - + +
228R ARG* 6.1 4.7 - - + -
289R ILE* 6.0 0.8 - - - +
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Residues in contact with LEU 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117R GLN 2.9 16.7 + - - +
118R SER* 3.3 5.8 + - - +
120R TYR* 1.3 77.3 - - - +
122R GLY* 1.3 58.7 + - - +
124R CYS* 3.3 9.0 + - - +
125R SER 3.1 6.9 + - - -
126R PHE* 3.0 34.0 + - + +
129R LYS* 4.8 4.7 - - + -
130R SER* 3.6 21.1 - - - +
156R TYR* 6.5 0.9 - - - -
159R THR* 5.5 7.0 - - - -
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Residues in contact with GLY 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R SER 2.9 14.5 + - - -
119R TYR* 3.1 5.3 + - - -
121R LEU* 1.3 75.0 - - - +
123R GLU* 1.3 60.2 + - - +
125R SER* 3.1 17.8 + - - -
126R PHE 4.5 3.4 - - - -
127R PHE* 6.0 0.7 - - - -
130R SER* 3.7 8.0 - - - -
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Residues in contact with GLU 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119R TYR 2.9 13.7 + - - +
120R TYR* 3.2 11.6 + - - +
122R GLY* 1.3 76.8 - - - +
124R CYS* 1.3 59.1 + - - +
125R SER* 3.2 3.0 + - - -
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Residues in contact with CYS 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R TYR 2.9 15.7 + - - +
121R LEU* 3.7 9.4 - - - +
122R GLY 3.2 0.4 - - - -
123R GLU* 1.3 74.1 - - - +
125R SER* 1.3 70.3 + - - +
126R PHE* 3.4 4.3 + - + +
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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