Contacts of the strand formed by residues 170 - 177 (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 GLY 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A SER* 3.9 2.6 + - - -
166A SER* 3.5 6.2 - - - -
167A GLY* 2.9 34.3 + - - +
168A MET 3.2 6.5 + - - -
169A ASN* 1.3 79.6 - - - +
171A ILE* 1.3 64.6 + - - -
172A HIS* 4.3 0.2 - - - -
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Residues in contact with ILE 171 (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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125A SER* 3.5 24.3 + - - +
130A THR* 3.7 19.3 + - + +
164A LYS* 4.2 25.4 - - + -
165A ILE 3.6 10.3 - - - +
166A SER* 4.6 9.9 - - - +
169A ASN 4.3 0.2 + - - -
170A GLY* 1.3 74.0 - - - -
172A HIS* 1.3 72.7 + - - +
173A VAL* 4.5 5.2 - - + +
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Residues in contact with HIS 172 (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* 4.8 19.4 - - + +
122A VAL* 4.1 15.8 - - + +
123A VAL 2.7 25.0 + - - +
124A LYS* 4.0 4.0 - - - -
125A SER* 2.9 37.4 + - - -
164A LYS* 3.6 3.6 - - - -
165A ILE* 2.9 51.3 + - + +
167A GLY* 3.9 28.2 - - - -
169A ASN* 4.4 11.6 + - - -
171A ILE* 1.3 75.3 - - - +
173A VAL* 1.3 62.9 + - - +
174A CYS 3.6 0.5 + - - -
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Residues in contact with VAL 173 (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 LYS 3.9 0.3 - - - +
122A VAL* 3.8 0.2 - - - -
123A VAL* 3.0 35.6 + - + +
124A LYS 5.3 0.2 + - - -
130A THR* 3.9 30.4 + - + +
133A ALA* 3.5 35.4 - - + -
134A LEU* 4.4 10.1 - - + -
137A ILE* 4.5 23.8 - - + -
162A ASP* 6.1 0.2 - - + -
163A PHE 4.0 6.7 - - - +
164A LYS* 4.6 20.0 - - + +
171A ILE* 4.2 2.2 + - + -
172A HIS* 1.3 71.2 - - - +
174A CYS* 1.3 62.2 + - - +
175A MET* 4.3 2.6 + - + +
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Residues in contact with CYS 174 (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 MET* 4.5 1.8 - - + -
121A LYS 3.3 7.4 - - - +
122A VAL* 3.7 26.9 - - + -
162A ASP* 3.4 6.1 - - - +
163A PHE* 2.9 81.5 + - + +
165A ILE* 3.9 25.4 - - - -
172A HIS 4.0 2.7 - - - -
173A VAL* 1.3 75.1 - - - +
175A MET* 1.3 63.0 + - - +
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Residues in contact with MET 175 (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 ALA 3.9 0.5 - - - +
120A MET* 3.4 3.3 - - - +
121A LYS* 2.9 54.5 + - + +
123A VAL* 3.8 19.5 - - + -
133A ALA* 4.1 16.2 - - + -
136A GLU* 3.1 36.8 - - - +
137A ILE* 3.4 30.5 - - + -
140A LEU* 4.3 11.2 - - - -
159A LEU* 3.9 5.4 - - + -
161A ASP 3.7 4.0 - - - -
162A ASP* 4.5 0.4 - - - +
173A VAL* 4.6 2.0 - - + -
174A CYS* 1.3 76.2 - - - +
176A VAL* 1.3 62.8 + - - +
177A PHE* 3.6 20.9 - - + -
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Residues in contact with VAL 176 (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 24.9 - - + +
118A VAL* 3.7 38.6 - - + -
119A ALA 3.6 3.4 - - - +
120A MET* 4.4 8.3 - - + -
159A LEU* 3.8 2.3 - - - +
160A ILE* 2.8 33.4 + - + +
161A ASP* 2.8 27.7 + - + +
163A PHE* 3.8 27.8 - - + -
175A MET* 1.3 77.3 - - - +
177A PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 177 (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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118A VAL* 3.4 8.3 - - - +
119A ALA 2.8 35.5 + - - +
121A LYS* 4.3 8.5 - - + -
140A LEU* 4.0 19.1 - - + -
157A VAL* 3.3 33.4 - - + -
158A GLN 3.5 11.0 - - - +
159A LEU* 4.2 10.8 - - + -
160A ILE* 3.5 11.0 - - - -
175A MET* 3.6 36.6 - - + -
176A VAL* 1.3 75.6 - - - +
178A GLU* 1.3 70.6 - - - +
800A PVB 3.7 31.0 - - + -
1708A EDO 3.7 25.8 - - - -
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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