Contacts of the helix formed by residues 111 - 134 (chain A) in PDB entry 10GS
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 TYR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 2.9 23.0 + - + +
107A ILE* 3.8 25.5 + - + +
110A ASN* 1.3 71.5 - - - +
112A GLU* 1.3 84.7 + - + +
115A LYS* 3.0 64.7 + - + +
165A LEU* 3.9 16.6 - - + -
208A LYS* 3.7 32.8 - - + +
209A GLN* 2.8 32.3 + - - -
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 3.5 1.1 - - - -
111A TYR* 1.3 93.6 + - + +
113A ALA* 1.3 63.5 + - + +
115A LYS* 4.1 6.7 + - - +
116A ASP* 5.3 3.8 + - - +
208A LYS* 3.0 37.8 + - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 3.8 18.1 + - + +
111A TYR 3.4 0.2 - - - -
112A GLU* 1.3 81.1 - - - +
114A GLY* 1.3 61.1 + - - +
115A LYS 3.6 0.2 + - - -
116A ASP* 4.5 9.0 + - - +
117A ASP* 5.3 3.1 + - - +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.5 9.1 - - - +
110A ASN* 2.9 30.5 + - - -
113A ALA* 1.3 72.0 - - - +
115A LYS* 1.3 63.0 + - - +
116A ASP 3.3 3.3 + - - -
117A ASP* 3.4 10.7 + - - +
118A TYR* 3.1 24.6 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.6 11.2 - - + +
111A TYR* 3.0 58.6 + - + +
112A GLU 4.4 5.2 - - - +
113A ALA 3.5 2.0 - - - -
114A GLY* 1.3 76.0 - - - +
116A ASP* 1.3 67.8 + - - +
118A TYR* 3.8 0.9 - - - +
119A VAL* 3.0 39.7 + - + +
165A LEU* 3.0 44.7 + - + +
209A GLN* 4.5 0.4 + - - -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU 5.3 3.4 + - - +
113A ALA 4.5 7.2 + - - +
114A GLY 3.3 0.6 - - - -
115A LYS* 1.3 80.9 - - - +
117A ASP* 1.3 68.4 + - - +
119A VAL* 3.3 6.9 + - - +
120A LYS* 3.1 44.4 + - - +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 5.5 2.1 - - - +
114A GLY* 3.4 12.1 + - - +
116A ASP* 1.3 76.7 - - - +
118A TYR* 1.3 63.0 + - - +
120A LYS* 3.2 28.9 + - - +
121A ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.5 16.9 - - + +
102A LYS* 3.7 31.9 - - + -
103A TYR* 3.4 19.8 - - - +
106A LEU* 3.6 28.5 - - + -
114A GLY 3.1 17.8 + - - +
115A LYS 3.8 4.3 - - - +
117A ASP* 1.3 79.0 - - - +
119A VAL* 1.3 60.1 + - + +
121A ALA* 3.3 6.9 + - - +
122A LEU* 3.0 32.6 + - + +
125A GLN* 6.3 1.1 - - + -
162A HIS* 2.9 28.9 + + - -
165A LEU* 3.6 24.7 - - + -
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LYS* 3.0 33.5 + - + +
116A ASP* 3.8 5.4 - - - +
118A TYR* 1.3 84.1 - - + +
120A LYS* 1.3 63.3 + - + +
122A LEU* 3.3 20.8 - - + +
123A PRO* 3.6 5.2 - - - +
165A LEU* 5.0 7.4 - - + +
166A ALA* 3.8 31.0 - - + -
169A CYS* 6.0 0.7 - - + -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 3.1 29.6 + - - +
117A ASP* 3.2 29.2 + - - +
119A VAL* 1.3 76.5 - - + +
121A ALA* 1.3 57.6 + - - +
123A PRO* 3.3 16.8 - - - +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP 3.0 15.3 + - - +
118A TYR* 3.3 5.8 + - - +
119A VAL 3.3 0.2 - - - -
120A LYS* 1.3 76.0 - - - +
122A LEU* 1.3 65.2 + - - +
123A PRO* 3.4 1.1 - - - -
124A GLY* 3.2 14.1 + - - -
125A GLN* 3.4 20.8 + - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.8 2.7 - - + -
118A TYR* 3.0 25.2 + - + +
119A VAL* 3.3 18.2 - - + +
120A LYS 3.3 0.2 - - - -
121A ALA* 1.3 76.4 - - - +
123A PRO* 1.3 67.4 - - + +
125A GLN* 2.9 26.4 + - + +
126A LEU* 2.9 36.3 + - + +
162A HIS* 3.7 35.7 - - + +
165A LEU* 5.3 0.9 - - + -
166A ALA* 4.1 16.6 - - + -
169A CYS* 3.9 30.1 - - + -
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Residues in contact with PRO 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL 3.6 6.1 - - - +
120A LYS 3.3 17.0 - - - +
121A ALA 3.5 1.3 - - - -
122A LEU* 1.3 93.2 - - + +
124A GLY* 1.3 60.7 + - - +
126A LEU* 3.3 1.0 + - + -
127A LYS* 3.0 39.0 + - - +
169A CYS 6.0 1.1 - - - +
172A ALA* 6.3 0.9 - - + -
173A PHE* 3.5 24.4 - - + -
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Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ALA 3.2 8.1 + - - -
123A PRO* 1.3 79.8 - - - +
125A GLN* 1.3 65.4 + - - +
127A LYS* 3.8 13.2 + - - +
128A PRO* 3.3 18.0 - - - +
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Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.0 36.0 - - + +
102A LYS* 3.1 32.3 + - + +
118A TYR* 6.3 0.9 - - + -
121A ALA* 3.4 22.7 + - + +
122A LEU* 2.9 13.1 + - + +
124A GLY* 1.3 82.3 - - - +
126A LEU* 1.3 58.5 + - - +
128A PRO* 3.4 13.1 - - - +
129A PHE* 3.7 16.8 - - - -
49B TYR* 5.9 0.2 - - - -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.2 19.3 - - + -
122A LEU* 2.9 38.5 + - + +
123A PRO 5.0 0.2 - - - -
125A GLN* 1.3 77.0 - - - +
127A LYS* 1.3 65.0 + - - +
128A PRO* 3.3 1.6 - - - -
129A PHE* 3.1 25.3 + - + +
130A GLU* 3.4 6.8 + - - +
158A LEU* 5.8 1.1 - - + -
159A LEU* 4.1 23.6 - - + -
162A HIS* 5.5 6.5 - - + +
169A CYS* 4.2 12.3 - - + +
170A LEU* 4.1 23.3 - - + -
173A PHE* 4.0 27.1 - - + -
176A LEU* 3.9 10.2 - - + +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 3.0 26.8 + - - +
124A GLY* 4.0 9.9 - - - +
126A LEU* 1.3 75.2 - - - +
128A PRO* 1.4 69.2 - - + +
130A GLU* 3.0 6.3 + - + +
131A THR* 2.9 27.8 + - - +
173A PHE* 3.6 24.2 - - + -
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Residues in contact with PRO 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLY 3.3 18.2 - - - +
125A GLN* 3.4 10.5 - - - +
126A LEU 3.4 4.7 - - - -
127A LYS* 1.4 90.5 - - + +
129A PHE* 1.3 57.8 + - + +
131A THR* 3.4 8.1 - - - +
132A LEU* 3.0 32.8 + - - +
48B LEU* 3.3 32.6 - - + +
49B TYR* 3.8 31.9 - - + -
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 4.0 7.9 - - + -
95A GLY 3.8 24.7 - - - -
96A VAL* 3.8 22.9 - - + -
99A LEU* 4.5 15.5 - - + -
125A GLN 3.7 19.7 - - - -
126A LEU* 3.1 20.4 + - + +
128A PRO* 1.3 73.7 - - + +
130A GLU* 1.3 65.2 + - - +
131A THR 3.2 0.2 - - - -
132A LEU* 3.4 18.0 + - + +
133A LEU* 3.1 25.6 + - - +
143A ILE* 3.9 4.2 - - + +
155A LEU* 4.0 30.1 - - + -
158A LEU* 4.7 1.8 - - + -
176A LEU* 3.9 18.8 - - + -
49B TYR* 4.0 27.1 - + - -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU 3.4 3.1 + - - +
127A LYS* 3.0 11.3 + - + +
129A PHE* 1.3 77.5 - - - +
131A THR* 1.3 57.5 + - - +
133A LEU* 3.4 5.3 + - - +
134A SER* 2.9 28.6 + - - -
173A PHE* 3.2 39.6 - - + +
174A PRO* 3.6 13.7 - - - +
175A LEU* 3.0 35.9 + - + +
176A LEU* 3.0 32.2 + - + +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 2.9 16.7 + - - +
128A PRO* 3.4 12.5 - - - +
130A GLU* 1.3 75.6 - - - +
132A LEU* 1.3 66.1 + - - +
134A SER* 2.7 24.5 + - - +
135A GLN* 3.1 33.6 + - - +
48B LEU* 4.8 10.8 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A MET* 4.4 13.5 - - + -
92A VAL* 3.9 26.0 - - + -
128A PRO 3.0 22.2 + - - +
129A PHE* 3.7 25.8 - - + +
130A GLU 3.4 0.2 - - - -
131A THR* 1.3 76.0 - - - +
133A LEU* 1.3 64.1 + - - +
135A GLN* 3.2 23.7 + - - +
136A ASN* 3.4 14.6 + - - +
143A ILE* 3.9 18.7 - - + +
144A VAL* 6.1 1.1 - - + -
48B LEU* 4.0 24.7 - - + -
49B TYR* 4.2 11.9 - - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE 3.1 11.3 + - - +
130A GLU 3.4 5.6 - - - +
131A THR 3.2 0.2 - - - -
132A LEU* 1.3 77.5 - - - +
134A SER* 1.3 61.3 + - - +
136A ASN* 3.0 12.6 + - - +
139A GLY* 2.9 39.3 + - - +
141A THR 5.2 0.2 - - - +
142A PHE 3.8 21.1 - - - +
143A ILE* 3.6 22.9 - - + -
175A LEU* 3.7 29.8 - - + +
176A LEU* 3.7 29.8 - - + -
179A TYR* 3.8 25.1 - - + -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 2.9 14.8 + - - -
131A THR* 2.7 26.9 + - - +
133A LEU* 1.3 75.2 - - - +
135A GLN* 1.3 62.7 + - - +
136A ASN 3.3 0.4 + - - -
138A GLY* 3.9 14.7 + - - -
139A GLY 4.4 2.5 - - - +
175A LEU* 3.7 20.1 - - - +
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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
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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