Contacts of the helix formed by residues 98 - 124 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Y ALA 3.3 5.3 + - - +
97Y TRP* 1.3 77.1 - - - +
99Y GLU* 1.3 63.8 + - - +
100Y ASN* 3.3 9.4 - - + +
101Y VAL* 3.5 16.5 + - + +
102Y LYS* 3.1 23.0 + - - +
277Y LEU 5.9 0.2 + - - -
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Residues in contact with GLU 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Y TRP 3.9 0.6 + - - -
98Y LYS* 1.3 71.3 - - - +
100Y ASN* 1.3 60.9 + - - +
102Y LYS* 3.8 6.3 - - - +
103Y CYS* 2.9 30.7 + - - +
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Residues in contact with ASN 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Y LYS* 3.3 5.9 - - + +
99Y GLU* 1.3 79.5 - - - +
101Y VAL* 1.3 55.9 + - - +
103Y CYS* 3.4 5.5 + - - +
104Y GLU* 2.9 29.5 + - - +
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Residues in contact with VAL 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Y TRP* 6.1 1.6 - - + -
98Y LYS* 3.5 19.1 + - + +
99Y GLU 3.4 0.2 - - - -
100Y ASN* 1.3 75.8 - - - +
102Y LYS* 1.3 61.1 + - - +
104Y GLU* 3.3 4.9 + - - +
105Y VAL* 2.9 31.5 + - - +
277Y LEU* 5.1 12.8 - - + +
280Y LEU* 4.8 20.6 - - + -
281Y GLY* 5.2 5.4 - - - +
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Residues in contact with LYS 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Y TRP* 5.7 5.1 - - + +
98Y LYS 3.1 17.2 + - - +
99Y GLU* 3.8 7.6 - - - +
101Y VAL* 1.3 78.5 - - - +
103Y CYS* 1.3 56.4 + - - +
105Y VAL* 3.9 4.2 - - - +
106Y TRP* 2.9 31.6 + - - +
203Y LEU* 4.2 25.6 - - + +
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Residues in contact with CYS 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Y GLU 2.9 19.1 + - - +
100Y ASN* 3.9 5.6 - - - +
102Y LYS* 1.3 73.1 - - - +
104Y GLU* 1.3 61.1 + - - +
106Y TRP* 3.9 4.8 - - - +
107Y THR* 2.9 31.7 + - - -
142Y ARG* 5.4 13.6 - - + +
143Y PHE 5.7 3.8 - - - +
203Y LEU 5.7 0.4 - - - -
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Residues in contact with GLU 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100Y ASN 2.9 18.6 + - - +
101Y VAL* 3.7 7.0 - - - +
103Y CYS* 1.3 75.6 - - - +
105Y VAL* 1.3 60.0 + - - +
107Y THR* 3.4 5.0 + - - -
108Y ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Y VAL 2.9 17.2 + - - +
102Y LYS* 4.1 4.0 - - - +
104Y GLU* 1.3 76.9 - - - +
106Y TRP* 1.3 57.4 + - - +
108Y ALA* 3.4 6.8 + - - +
109Y ILE* 2.9 29.6 + - - +
203Y LEU* 5.9 3.6 - - + -
277Y LEU* 6.5 0.9 - - + -
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Residues in contact with TRP 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y LYS 2.9 20.6 + - - +
103Y CYS* 3.9 5.6 - - - +
105Y VAL* 1.3 77.7 - - - +
107Y THR* 1.3 57.0 + - - +
109Y ILE* 3.2 7.1 + - - +
110Y ILE* 2.9 30.1 + - - +
203Y LEU* 4.4 24.4 - - + +
204Y LYS* 5.2 2.9 - - - +
217Y ASP* 6.5 0.4 - - + -
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Residues in contact with THR 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Y CYS 2.9 20.0 + - - -
104Y GLU* 3.8 4.3 - - - -
106Y TRP* 1.3 75.3 - - - +
108Y ALA* 1.3 59.1 + - - +
110Y ILE* 3.5 6.0 + - - +
111Y ALA* 2.9 29.6 + - - +
140Y LEU* 5.9 2.4 - - - +
141Y GLU 5.3 5.2 - - - -
142Y ARG* 5.3 14.8 - - - -
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Residues in contact with ALA 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Y GLU 2.9 17.6 + - - +
105Y VAL* 3.7 7.2 - - - +
107Y THR* 1.3 77.1 - - - +
109Y ILE* 1.3 58.2 + - - +
111Y ALA* 3.4 6.9 + - - +
112Y GLN* 2.9 28.8 + - - +
284Y ILE* 4.7 18.8 - - + -
285Y PRO 6.2 0.2 - - - +
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Residues in contact with ILE 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Y VAL 2.9 17.6 + - - +
106Y TRP* 3.6 7.2 - - - +
108Y ALA* 1.3 75.7 - - - +
110Y ILE* 1.3 59.7 + - - +
112Y GLN* 3.1 6.8 + - - +
113Y LYS* 2.9 29.9 + - - +
217Y ASP* 4.1 20.2 - - + +
218Y ILE* 5.8 1.6 - - - +
220Y GLU* 5.0 6.2 - - + +
221Y PRO* 4.6 7.7 - - + +
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Residues in contact with ILE 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Y TRP 2.9 16.5 + - - +
107Y THR* 3.9 6.3 - - - +
109Y ILE* 1.3 75.7 - - - +
111Y ALA* 1.3 58.2 + - - +
113Y LYS* 3.8 6.0 - - - +
114Y ILE* 2.9 31.9 + - - +
149Y GLU* 5.2 15.1 - - + +
220Y GLU* 6.0 1.1 - - - -
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Residues in contact with ALA 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Y THR 2.9 18.1 + - - +
108Y ALA* 3.6 7.6 - - - +
110Y ILE* 1.3 77.7 - - - +
112Y GLN* 1.3 56.1 + - - +
114Y ILE* 3.9 4.5 - - - +
115Y LEU* 2.9 31.4 + - - +
137Y TYR* 5.0 14.5 - - + +
140Y LEU* 5.6 7.6 - - + -
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Residues in contact with GLN 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y ALA 2.9 17.0 + - - +
109Y ILE* 3.6 6.3 - - - +
111Y ALA* 1.3 77.0 - - - +
113Y LYS* 1.3 57.3 + - - +
115Y LEU* 3.5 5.9 + - - +
116Y ASN* 2.9 30.2 + - - +
221Y PRO* 4.0 18.6 - - + -
286Y GLU* 5.7 3.8 - - + -
287Y PHE 4.4 20.1 - - - +
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Residues in contact with LYS 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y ILE 2.9 16.3 + - - +
110Y ILE* 3.3 6.0 + - - +
112Y GLN* 1.3 77.2 - - - +
114Y ILE* 1.3 57.8 + - - +
116Y ASN* 3.2 6.7 + - - +
117Y GLN* 2.9 28.5 + - - +
220Y GLU* 3.6 31.9 - - + +
221Y PRO* 4.1 7.3 - - - +
224Y PRO* 5.4 1.6 - - - +
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Residues in contact with ILE 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y ILE 2.9 17.4 + - - +
111Y ALA* 4.1 2.7 - - - +
113Y LYS* 1.3 76.2 - - - +
115Y LEU* 1.3 58.7 + - - +
117Y GLN* 3.2 8.0 + - - +
118Y SER* 2.9 30.1 + - - -
133Y ILE* 4.8 8.4 - - - +
136Y LEU* 5.8 0.7 - - + -
137Y TYR* 4.3 21.8 - - + +
149Y GLU* 6.0 5.4 - - + -
152Y SER* 5.1 15.3 - - - -
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Residues in contact with LEU 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Y ALA 2.9 20.1 + - - +
112Y GLN* 3.8 6.3 - - - +
114Y ILE* 1.3 76.8 - - - +
116Y ASN* 1.3 56.9 + - - +
118Y SER* 3.5 5.6 + - - -
119Y TYR* 2.9 30.0 + - - +
137Y TYR* 4.7 10.2 - - + +
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Residues in contact with ASN 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Y GLN 2.9 18.4 + - - +
113Y LYS* 3.6 4.7 - - - +
115Y LEU* 1.3 74.1 - - - +
117Y GLN* 1.3 60.3 + - - +
119Y TYR* 3.8 5.8 - - - +
120Y TYR* 2.9 29.8 + - - +
221Y PRO 4.2 16.4 - - - +
224Y PRO* 4.5 13.8 - - + +
287Y PHE 5.4 4.0 - - - +
288Y ARG* 5.6 1.3 - - - +
289Y ILE* 4.9 23.3 - - + +
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Residues in contact with GLN 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Y LYS 2.9 13.8 + - - +
114Y ILE* 3.5 10.5 - - - +
116Y ASN* 1.3 75.2 - - - +
118Y SER* 1.3 60.7 + - - +
120Y TYR* 3.3 5.5 + - - +
121Y LEU* 2.9 28.1 + - - +
133Y ILE* 5.2 5.4 - - + -
152Y SER* 6.2 2.9 - - - -
156Y TYR* 4.6 22.0 - - + +
224Y PRO* 4.6 10.2 - - + +
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Residues in contact with SER 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Y ILE 2.9 16.0 + - - -
115Y LEU* 3.9 5.2 - - - -
117Y GLN* 1.3 75.8 - - - +
119Y TYR* 1.3 58.1 + - - +
121Y LEU* 3.3 1.2 + - - -
122Y GLY* 2.9 23.2 + - - -
130Y SER* 3.2 36.9 - - - +
133Y ILE* 3.8 17.6 - - - +
134Y MET* 3.8 14.6 - - - -
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Residues in contact with TYR 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Y LEU 2.9 19.0 + - - +
116Y ASN* 3.9 6.5 - - - +
118Y SER* 1.3 77.3 - - - +
120Y TYR* 1.3 56.8 + - - +
122Y GLY* 3.1 3.4 + - - +
123Y GLU* 2.9 27.3 + - - +
289Y ILE* 5.7 8.7 - - + +
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Residues in contact with TYR 120 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y ASN 2.9 19.4 + - - +
117Y GLN* 3.7 5.8 - - - +
118Y SER 3.3 0.2 - - - -
119Y TYR* 1.3 76.9 - - - +
121Y LEU* 1.3 58.5 + - - +
123Y GLU* 3.2 9.5 + - - +
124Y CYS* 2.9 26.9 + - - +
224Y PRO* 5.0 11.4 - - + +
228Y ARG* 6.1 4.7 - - + -
289Y ILE* 5.9 5.1 - - + +
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Residues in contact with LEU 121 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Y GLN 2.9 17.5 + - - +
118Y SER* 3.3 5.8 + - - +
120Y TYR* 1.3 75.9 - - - +
122Y GLY* 1.3 58.0 + - - +
124Y CYS* 3.3 8.5 + - - +
125Y SER 3.1 7.1 + - - -
126Y PHE* 3.0 35.2 + - + +
129Y LYS* 4.8 4.9 - - + -
130Y SER* 3.6 20.9 - - - +
133Y ILE* 6.2 0.4 - - + -
156Y TYR* 6.5 0.7 - - - -
159Y THR* 5.5 7.2 - - - -
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Residues in contact with GLY 122 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Y SER 2.9 14.6 + - - -
119Y TYR* 3.1 5.3 + - - -
121Y LEU* 1.3 74.0 - - - +
123Y GLU* 1.3 59.4 + - - +
125Y SER* 3.1 17.4 + - - -
126Y PHE 4.4 3.8 - - - -
127Y PHE* 6.0 0.4 - - - -
130Y SER* 3.7 8.7 - - - -
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Residues in contact with GLU 123 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Y TYR 2.9 12.9 + - - +
120Y TYR* 3.2 12.3 + - - +
122Y GLY* 1.3 76.7 - - - +
124Y CYS* 1.3 58.4 + - - +
125Y SER* 3.2 3.4 + - - -
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Residues in contact with CYS 124 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120Y TYR 2.9 15.5 + - - +
121Y LEU* 3.7 9.4 - - - +
122Y GLY 3.2 0.6 - - - -
123Y GLU* 1.3 74.9 - - - +
125Y SER* 1.3 69.0 + - - +
126Y PHE* 3.4 4.1 + - + +
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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