Contacts of the helix formed by residues 111 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B LEU* 2.9 24.0 + - + +
107B ILE* 3.8 26.1 + - + +
109B THR 4.1 0.4 - - - -
110B ASN* 1.3 70.3 - - - +
112B GLU* 1.3 86.1 + - + +
115B LYS* 3.0 64.0 + - + +
165B LEU* 3.9 15.7 - - + -
208B LYS* 3.7 33.3 - - + +
209B GLN* 2.8 31.8 + - - -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.5 1.1 - - - -
111B TYR* 1.3 94.6 + - + +
113B ALA* 1.3 63.3 + - - +
115B LYS* 4.1 6.7 + - - +
116B ASP* 5.3 3.6 + - - +
208B LYS* 3.0 37.7 + - - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.8 18.4 + - + +
111B TYR 3.4 0.2 - - - -
112B GLU* 1.3 83.1 - - + +
114B GLY* 1.3 60.4 + - - +
115B LYS 3.6 0.5 + - - -
116B ASP* 4.5 8.7 + - - +
117B ASP* 5.3 3.3 + - - +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 3.5 8.7 - - - +
110B ASN* 2.9 31.2 + - - -
113B ALA* 1.3 72.6 - - - +
115B LYS* 1.3 63.0 + - - +
116B ASP 3.3 3.0 + - - -
117B ASP* 3.4 10.5 + - - +
118B TYR* 3.1 24.4 + - - +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 3.6 11.0 - - + +
111B TYR* 3.0 59.8 + - + +
112B GLU 4.4 5.2 - - - +
113B ALA 3.5 1.8 - - - -
114B GLY* 1.3 75.1 - - - +
116B ASP* 1.3 66.4 + - - +
118B TYR* 3.6 1.0 + - - +
119B VAL* 3.0 41.0 + - + +
165B LEU* 3.0 43.6 + - + +
209B GLN* 4.5 0.4 + - - -
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU 5.3 3.9 + - - +
113B ALA 4.5 7.9 + - - +
114B GLY 3.3 0.6 - - - -
115B LYS* 1.3 81.5 - - - +
117B ASP* 1.3 67.3 + - - +
119B VAL* 3.4 7.3 + - - +
120B LYS* 3.1 44.7 + - - +
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA 5.3 2.7 + - - +
114B GLY* 3.4 11.3 + - - +
116B ASP* 1.3 75.9 - - - +
118B TYR* 1.3 63.9 + - - +
120B LYS* 3.2 28.7 + - - +
121B ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.5 16.7 - - + +
102B LYS* 3.7 32.1 - - + -
103B TYR* 3.4 20.1 - - - +
106B LEU* 3.6 29.8 - - + -
114B GLY 3.1 17.0 + - - +
115B LYS 3.8 3.6 - - - +
117B ASP* 1.3 78.4 - - - +
119B VAL* 1.3 60.8 + - + +
121B ALA* 3.3 6.6 + - - +
122B LEU* 3.0 31.6 + - + +
125B GLN* 6.3 0.9 - - + -
162B HIS* 2.9 28.9 + + - -
165B LEU* 3.6 26.0 - - + -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LYS* 3.0 33.7 + - + +
116B ASP* 3.9 5.2 - - - +
117B ASP 3.3 0.2 - - - -
118B TYR* 1.3 84.5 - - + +
120B LYS* 1.3 62.9 + - + +
122B LEU* 3.3 20.8 - - + +
123B PRO* 3.6 4.9 - - - +
165B LEU* 4.9 7.2 - - + +
166B ALA* 3.8 32.1 - - + -
169B CYS* 6.0 0.9 - - + -
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASP* 3.1 30.2 + - - +
117B ASP* 3.2 29.0 + - - +
119B VAL* 1.3 76.7 - - + +
121B ALA* 1.3 58.8 + - - +
123B PRO* 3.3 16.5 - - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASP 3.0 14.9 + - - +
118B TYR* 3.3 7.2 + - - +
120B LYS* 1.3 76.4 - - - +
122B LEU* 1.3 65.6 + - - +
123B PRO* 3.4 0.9 - - - -
124B GLY* 3.2 14.2 + - - -
125B GLN* 3.4 20.9 + - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.8 3.1 - - + -
118B TYR* 3.0 24.7 + - + +
119B VAL* 3.3 17.7 - - + +
121B ALA* 1.3 76.4 - - - +
123B PRO* 1.3 66.9 - - + +
125B GLN* 2.9 25.4 + - + +
126B LEU* 2.9 31.1 + - + +
162B HIS* 3.7 36.1 - - + +
165B LEU* 5.3 0.7 - - + -
166B ALA* 4.1 16.4 - - + -
169B CYS* 3.9 30.5 - - + -
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Residues in contact with PRO 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL 3.6 6.3 - - - +
120B LYS 3.3 17.5 - - - +
121B ALA 3.5 1.1 - - - -
122B LEU* 1.3 94.3 - - + +
124B GLY* 1.3 61.6 + - - +
126B LEU* 3.3 1.2 + - + -
127B LYS* 3.0 38.9 + - - +
169B CYS 6.0 1.3 - - - +
173B PHE* 3.5 24.3 - - + -
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA 3.2 8.9 + - - -
123B PRO* 1.3 80.6 - - - +
125B GLN* 1.3 65.8 + - - +
127B LYS* 3.8 12.2 + - - +
128B PRO* 3.3 18.2 - - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 5.9 0.2 - - - -
99B LEU* 4.0 37.9 - - + +
102B LYS* 3.2 32.3 + - + +
118B TYR* 6.3 1.1 - - + -
121B ALA* 3.6 22.3 + - + +
122B LEU* 2.9 13.1 + - + +
124B GLY* 1.3 80.4 + - - +
126B LEU* 1.3 57.9 + - - +
128B PRO* 3.4 13.4 - - - +
129B PHE* 3.7 17.0 - - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.2 20.6 - - + -
122B LEU* 2.9 36.6 + - + +
125B GLN* 1.3 77.9 - - - +
127B LYS* 1.3 66.4 + - - +
128B PRO* 3.3 1.3 - - - -
129B PHE* 3.1 22.8 + - + +
130B GLU* 3.4 7.1 + - - +
158B LEU* 5.8 1.6 - - + -
159B LEU* 4.1 23.8 - - + -
162B HIS* 5.5 7.0 - - + +
169B CYS* 4.2 12.6 - - + +
170B LEU* 4.1 22.7 - - + -
173B PHE* 4.0 28.7 - - + -
176B LEU* 3.9 10.5 - - + +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PRO* 3.0 28.7 + - - +
124B GLY* 4.0 10.8 - - - +
126B LEU* 1.3 76.0 - - - +
128B PRO* 1.4 68.7 - - + +
130B GLU* 3.0 5.8 + - + +
131B THR* 2.9 28.0 + - - +
173B PHE* 3.6 22.0 - - + -
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Residues in contact with PRO 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.3 34.4 - - + +
49A TYR* 3.7 31.6 - - + -
124B GLY 3.3 18.8 - - - +
125B GLN* 3.4 10.3 - - - +
126B LEU 3.4 4.0 - - - -
127B LYS* 1.4 90.5 - - + +
129B PHE* 1.3 57.0 + - + +
131B THR* 3.4 7.3 - - - +
132B LEU* 3.0 33.6 + - - +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 4.0 27.1 - + - -
92B VAL* 4.0 7.4 - - + -
95B GLY 3.8 24.7 - - - -
96B VAL* 3.8 22.7 - - + -
99B LEU* 4.5 15.5 - - + -
125B GLN 3.7 18.6 - - - -
126B LEU* 3.1 22.2 + - + +
128B PRO* 1.3 74.3 - - + +
130B GLU* 1.3 65.4 + - - +
131B THR 3.2 0.4 - - - -
132B LEU* 3.4 18.0 + - + +
133B LEU* 3.1 24.6 + - - +
143B ILE* 3.9 4.1 - - + +
155B LEU* 4.0 28.9 - - + -
158B LEU* 4.7 2.0 - - + -
176B LEU* 3.9 18.6 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU 3.4 3.3 + - - +
127B LYS* 3.0 10.9 + - + +
129B PHE* 1.3 77.8 - - - +
131B THR* 1.3 58.3 + - - +
133B LEU* 3.4 5.6 + - - +
134B SER* 2.9 28.8 + - - -
173B PHE* 3.2 40.2 - - + +
174B PRO* 3.6 13.3 - - - +
175B LEU* 3.0 37.6 + - + +
176B LEU* 3.0 32.4 + - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.8 11.4 - - + -
127B LYS* 2.9 17.4 + - - +
128B PRO* 3.4 12.1 - - - +
130B GLU* 1.3 75.5 - - - +
132B LEU* 1.3 64.9 + - - +
134B SER* 2.7 24.1 + - - +
135B GLN* 3.1 34.6 + - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.9 27.4 - - + -
49A TYR* 4.2 12.3 - - - +
91B MET* 4.4 12.8 - - + -
92B VAL* 3.9 25.8 - - + -
128B PRO 3.0 23.3 + - - +
129B PHE* 3.7 25.6 - - + +
131B THR* 1.3 74.0 - - - +
133B LEU* 1.3 62.1 + - - +
135B GLN* 3.2 24.0 + - - +
136B ASN* 3.4 14.6 + - - +
143B ILE* 3.9 18.0 - - + +
144B VAL* 6.1 0.9 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE 3.1 11.5 + - - +
130B GLU 3.4 5.4 - - - +
132B LEU* 1.3 77.2 - - - +
134B SER* 1.3 60.2 + - - +
136B ASN* 3.0 12.3 + - - +
139B GLY* 2.9 40.1 + - - +
141B THR 5.2 0.2 - - - +
142B PHE 3.8 20.0 - - - +
143B ILE* 3.6 23.1 - - + -
175B LEU* 3.7 30.7 - - + +
176B LEU* 3.7 30.3 - - + +
179B TYR* 3.8 24.7 - - + -
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 2.9 14.2 + - - -
131B THR* 2.7 27.6 + - - +
133B LEU* 1.3 76.0 - - - +
135B GLN* 1.3 62.6 + - - +
136B ASN 3.6 0.5 + - - -
138B GLY* 3.9 14.6 + - - -
139B GLY 4.4 2.5 - - - +
175B 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
------------------------------------------------------------
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