Contacts of the helix formed by residues 113 - 125 (chain A) in PDB entry 2OT7
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 GLU 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A TYR* 3.3 10.4 - - - -
112A SER* 1.3 86.3 - - - +
114A PHE* 1.3 60.9 + - - +
115A GLU* 3.2 10.3 - - + +
116A GLU* 2.9 34.3 + - + +
119A ARG* 5.8 2.5 - - - +
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Residues in contact with PHE 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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111A TYR* 4.3 11.5 - + + -
113A GLU* 1.3 68.8 - - - +
115A GLU* 1.3 68.9 + - + +
116A GLU 3.0 0.5 + - - -
117A LEU* 3.0 5.5 + - + -
118A GLU* 2.9 56.1 + - + +
207A SER* 3.1 34.1 - - - -
209A TYR* 5.1 2.0 - + - -
259A LYS* 4.9 15.5 - - + -
260A VAL 6.2 0.7 - - - -
261A THR* 3.7 12.3 - - + -
279A PHE* 4.1 12.6 - + - -
281A HIS* 3.8 22.4 - + - -
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Residues in contact with GLU 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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113A GLU* 3.2 9.1 - - + +
114A PHE* 1.3 83.1 - - + +
116A GLU* 1.3 56.1 + - - +
118A GLU* 3.5 14.5 + - - +
119A ARG* 3.1 51.3 + - - +
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Residues in contact with GLU 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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110A ARG 3.9 1.6 - - - +
111A TYR* 3.8 10.2 - - + -
112A SER* 3.3 32.5 + - - -
113A GLU* 2.9 23.2 + - + +
115A GLU* 1.3 75.9 - - - +
117A LEU* 1.3 62.7 + - - +
119A ARG* 3.5 24.7 + - + +
120A LYS* 3.2 47.6 + - + +
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Residues in contact with LEU 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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108A THR* 3.9 16.8 - - + -
109A PRO* 4.1 10.8 - - + -
111A TYR* 3.6 42.7 - - + -
113A GLU 3.4 2.2 + - - -
114A PHE* 3.0 8.7 + - + +
116A GLU* 1.3 76.5 - - - +
118A GLU* 1.3 62.8 + - - +
120A LYS* 3.3 6.2 + - + +
121A TYR* 3.0 21.9 + - - +
181A TRP* 3.4 33.2 - - + -
279A PHE* 4.8 3.8 - - + -
281A HIS* 3.3 49.1 - - + +
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Residues in contact with GLU 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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114A PHE* 2.9 41.4 + - + +
115A GLU* 3.6 11.8 - - - +
117A LEU* 1.3 76.5 - - - +
119A ARG* 1.3 61.9 + - + +
121A TYR* 3.1 3.3 + - - +
122A TRP* 3.1 36.2 + - + -
209A TYR* 2.2 42.1 + - - +
247A PRO* 4.0 4.4 - - + +
259A LYS* 2.8 33.3 + - - +
279A PHE* 4.3 11.9 - - + -
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Residues in contact with ARG 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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113A GLU* 5.8 2.6 - - - +
115A GLU* 3.1 35.4 + - - +
116A GLU* 3.8 33.4 - - - +
117A LEU 3.4 0.4 - - - -
118A GLU* 1.3 76.3 - - + +
120A LYS* 1.3 58.9 + - + +
122A TRP* 3.2 6.5 + - - +
123A LYS* 2.9 32.0 + - - +
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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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109A PRO* 4.0 26.6 - - + +
110A ARG 3.6 24.2 + - - +
111A TYR* 4.9 2.0 - - + -
116A GLU* 3.2 35.2 + - + +
117A LEU* 3.3 10.7 + - - +
119A ARG* 1.3 78.7 - - + +
121A TYR* 1.3 57.2 + - - +
123A LYS* 4.1 6.7 - - + -
124A ASN* 3.0 50.0 + - - +
181A TRP* 4.6 11.1 - - + -
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Residues in contact with TYR 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 LEU 3.0 13.5 + - - +
118A GLU 3.1 8.5 + - - +
120A LYS* 1.3 75.7 - - - +
122A TRP* 1.3 104.6 + + - +
125A LEU* 3.0 58.5 + - + +
181A TRP* 4.0 13.0 - + + -
182A LYS* 3.9 24.7 - - + -
184A SER* 2.5 36.2 + - - -
244A LEU* 4.2 5.5 - - - +
278A GLY 4.2 3.0 + - - -
279A PHE* 3.5 47.0 - + + +
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Residues in contact with TRP 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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82A PHE* 3.9 31.4 - + - -
118A GLU* 3.1 35.4 + - + +
119A ARG* 3.2 5.1 + - - +
121A TYR* 1.3 104.0 - + - +
123A LYS* 1.3 60.2 + - - +
125A LEU* 3.5 29.7 - - + +
187A TRP* 5.7 0.2 - - - -
209A TYR* 3.1 34.2 + + - -
244A LEU* 4.6 7.2 - - + -
245A ILE 3.6 22.9 - - - -
246A SER* 3.7 32.5 - - - -
247A PRO* 3.7 16.9 - - + +
277A ALA* 6.5 1.3 - - + -
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Residues in contact with LYS 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 ARG 2.9 19.2 + - - +
120A LYS* 3.7 9.9 - - + +
122A TRP* 1.3 79.2 - - - +
124A ASN* 1.3 76.1 + - - +
125A LEU* 3.7 1.7 - - - +
126A THR* 5.1 1.4 + - - -
127A PHE* 3.5 18.6 - - + -
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Residues in contact with ASN 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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120A LYS* 3.0 38.6 + - - +
121A TYR 3.8 0.9 - - - -
123A LYS* 1.3 98.8 - - - +
125A LEU* 1.3 58.1 + - - +
126A THR 3.2 3.6 - - - -
127A PHE* 3.1 44.3 + - + +
181A TRP* 5.6 1.9 - - + -
182A LYS* 3.4 24.2 - - + -
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Residues in contact with LEU 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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73A GLN 5.2 1.7 - - - +
75A VAL* 3.5 26.8 + - + +
82A PHE* 3.7 27.6 - - + -
121A TYR* 3.0 49.5 + - + +
122A TRP* 3.5 38.8 - - + +
123A LYS 4.9 0.9 - - - +
124A ASN* 1.3 77.0 - - - +
126A THR* 1.3 62.3 + - + +
127A PHE 3.3 0.6 + - - -
129A PRO* 5.8 1.0 - - - +
130A PRO* 5.4 1.4 - - - +
182A LYS* 3.7 19.6 + - + +
184A SER* 5.1 1.1 - - - +
244A LEU* 3.8 22.2 - - + -
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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