Contacts of the strand formed by residues 157 - 161 (chain A) in PDB entry 2VR2
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 SER 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A HIS* 2.6 32.8 + - - -
133A VAL 3.4 17.0 + - - -
155A VAL* 3.4 12.7 - - - +
156A ASN* 1.3 81.6 - - - +
158A PHE* 1.3 64.7 + - - +
187A ALA* 4.1 0.8 - - - +
188A ILE* 3.4 22.2 - - - -
190A GLN* 3.7 7.0 - - - -
386A PHE* 4.0 7.0 - - - -
465A ARG* 2.6 19.4 + - - -
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.8 0.4 - - + -
133A VAL* 3.0 24.9 - - + +
135A VAL* 3.9 23.6 - - + -
146A MET* 3.5 43.7 - - + -
149A LEU* 3.9 26.0 - - + -
150A VAL* 3.9 15.0 - - + -
155A VAL* 4.0 12.3 - - + -
157A SER* 1.3 79.3 - - - +
159A LYS* 1.3 55.5 - - - +
160A MET* 3.4 6.5 - - - +
182A CYS* 4.1 13.0 - - - -
185A ILE* 3.9 7.4 - - + -
187A ALA* 3.7 28.3 - - + -
188A ILE 3.2 5.7 + - - -
189A ALA* 3.7 0.5 - - - -
190A GLN* 2.7 35.3 + - - +
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Residues in contact with LYS 159 (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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67A HIS* 3.7 5.4 + - - -
69A HIS* 4.0 6.3 + - - -
101A PHE* 3.5 35.2 - - + -
103A ILE* 5.1 0.7 - - + -
133A VAL 3.0 7.3 + - - -
134A ALA* 3.2 12.4 - - + +
135A VAL 2.8 29.6 + - - +
158A PHE* 1.3 72.1 - - - +
160A MET* 1.3 66.2 + - - +
161A PHE* 3.6 30.4 - - + -
190A GLN* 3.2 19.1 + - + +
191A VAL 4.8 0.4 - - - +
192A HIS* 4.2 4.0 - - - -
247A VAL* 3.7 18.8 - - - -
1494A ZN 3.0 18.0 - - - -
1495A ZN 2.6 34.6 - - - -
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Residues in contact with MET 160 (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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135A VAL* 3.6 37.0 - - + +
158A PHE* 3.4 21.1 - - - +
159A LYS* 1.3 83.4 - - - +
161A PHE* 1.3 62.9 + - - +
170A VAL* 4.4 5.8 - - + -
175A LEU* 3.8 21.8 - - + -
178A ALA* 3.8 23.1 - - + -
179A PHE* 3.7 27.4 - - + -
182A CYS* 4.2 9.2 - - - -
189A ALA* 3.7 15.3 - - + -
190A GLN 2.7 13.4 + - - +
191A VAL* 3.3 8.1 - - + +
192A HIS 3.1 24.1 + - - -
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 5.8 0.7 - + - -
103A ILE* 4.1 14.1 - - + -
134A ALA* 3.9 24.7 - - + -
135A VAL 4.6 1.3 + - - -
136A THR* 4.4 6.1 - - + -
159A LYS* 3.6 38.6 - - + -
160A MET* 1.3 78.4 - - - +
162A MET* 1.3 62.3 + - - +
163A ALA 3.6 10.3 - - - +
164A TYR* 3.8 28.0 - + - -
168A TYR* 3.4 46.1 + + + +
169A MET* 3.4 1.2 - - - -
170A VAL* 3.0 34.2 + - - +
192A HIS* 3.9 12.8 - + + -
1495A ZN 4.2 7.6 - - - -
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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