Contacts of the strand formed by residues 116 - 123 (chain A) in PDB entry 2X7G
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 ARG 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A TRP* 3.3 14.8 - - - -
111A ASP* 3.0 34.0 + - - +
114A GLY* 3.9 12.7 - - - +
115A LYS* 1.3 80.5 - - - +
117A PHE* 1.3 82.6 + - - +
118A VAL* 4.0 8.4 - - - +
160A ILE* 3.5 32.0 - - - +
178A GLU* 3.9 24.9 + - - +
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Residues in contact with PHE 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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95A ILE* 4.4 13.0 - - + -
108A LEU* 4.2 16.4 - - + -
109A CYS 3.4 15.5 - - - +
110A TRP* 3.5 31.7 - + + -
116A ARG* 1.3 87.6 + - - +
118A VAL* 1.3 66.4 + - - +
179A VAL* 3.9 13.1 + - + +
240A VAL* 3.7 30.7 - - + -
241A ARG* 4.4 22.7 - - + -
244A ALA* 3.5 33.2 - - + -
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Residues in contact with VAL 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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92A TYR* 3.8 27.6 - - + -
108A LEU* 3.6 3.1 - - - +
109A CYS* 2.8 51.6 + - + +
111A ASP* 4.2 15.0 - - + +
116A ARG* 4.0 16.4 - - - +
117A PHE* 1.3 80.2 - - - +
119A ALA* 1.3 59.1 + - - +
120A MET* 5.2 0.7 - - + +
160A ILE* 4.1 10.1 - - + -
176A VAL* 3.7 19.5 - - + -
177A PHE 3.4 14.1 - - - +
179A VAL* 3.3 12.6 - - - +
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Residues in contact with ALA 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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98A LEU* 4.2 5.2 - - + -
106A VAL* 4.1 12.8 - - + -
107A TRP 3.4 5.8 - - - -
108A LEU* 4.7 0.4 - - - +
118A VAL* 1.3 73.9 - - - +
120A MET* 1.3 60.4 + - - +
121A LYS 3.9 0.7 + - - -
175A MET 3.9 0.9 - - - +
176A VAL* 3.6 1.6 - - - +
177A PHE* 2.8 38.7 + - - +
178A GLU 4.1 1.8 - - - +
179A VAL* 3.6 7.1 - - + +
800A PVB 3.5 39.7 - - + +
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Residues in contact with MET 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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82A VAL* 4.6 0.9 - - + -
88A PHE* 4.0 27.4 - - + -
92A TYR* 4.9 4.7 - - + -
94A VAL* 4.1 4.3 - - + -
105A THR 3.6 3.3 - - - +
106A VAL* 4.4 1.3 - - - -
107A TRP* 2.8 55.5 + - + +
109A CYS* 3.5 28.7 - - + -
118A VAL* 4.1 1.1 - - + -
119A ALA* 1.3 70.2 - - - +
121A LYS* 1.3 62.4 + - - +
122A VAL* 3.6 24.6 + - + -
163A PHE* 3.6 29.6 - - + -
174A CYS* 4.5 2.2 - - + -
175A MET 3.4 9.6 - - - +
176A VAL* 4.4 13.5 - - + +
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Residues in contact with LYS 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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104A SER* 3.5 28.7 - - - +
105A THR 3.6 4.5 - - - -
106A VAL* 4.3 14.0 - - + +
119A ALA 3.9 2.2 + - - -
120A MET* 1.3 70.9 - - - +
122A VAL* 1.3 59.1 + - - +
123A VAL* 4.1 12.1 - - + -
136A GLU* 2.9 33.3 + - - -
173A VAL 3.9 1.0 - - - +
174A CYS* 3.3 4.3 - - - +
175A MET* 2.9 58.4 + - + +
177A PHE* 4.3 18.6 - - + -
541A ASP* 5.9 1.8 + - - +
543A GLY* 5.9 0.4 - - - -
800A PVB 4.6 9.6 - - + -
1702A SO4 3.9 20.6 + - - +
1708A EDO 4.4 7.1 - - - -
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Residues in contact with VAL 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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81A PRO* 6.2 2.7 - - + -
82A VAL* 4.1 24.2 - - + -
104A SER* 3.3 2.5 - - - -
105A THR* 2.9 41.1 + - - +
107A TRP* 4.2 9.9 - - + +
120A MET* 4.0 22.4 - - + -
121A LYS* 1.3 74.6 - - - +
123A VAL* 1.3 69.4 + - - +
124A LYS 4.0 0.2 + - - -
165A ILE* 4.7 1.8 - - + -
172A HIS* 4.1 22.0 - - + +
173A VAL 3.8 2.7 - - - -
174A CYS* 3.7 22.0 - - - -
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Residues in contact with VAL 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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103A PHE* 3.6 15.0 - - + +
104A SER* 3.8 2.7 - - - -
121A LYS* 4.1 14.8 - - + -
122A VAL* 1.3 76.3 - - - +
124A LYS* 1.3 67.3 + - - +
129A TYR* 3.6 29.6 - - + +
130A THR* 4.5 1.1 - - - +
133A ALA* 4.1 6.7 - - + -
172A HIS* 2.7 34.7 + - - +
173A VAL* 3.0 24.6 + - + +
175A MET* 3.8 26.0 - - + -
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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