Contacts of the strand formed by residues 188 - 192 (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 ILE 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASN 2.8 19.1 + - - +
157A SER* 3.4 15.9 - - - -
158A PHE 3.2 23.7 + - - -
182A CYS* 4.2 4.1 - - - -
186A GLY 4.4 0.2 + - - -
187A ALA* 1.3 74.6 - - - +
189A ALA* 1.3 68.7 + - - +
190A GLN* 3.9 4.4 + - + -
243A PRO* 3.6 17.5 - - + +
244A LEU 4.2 9.2 - - - +
245A TYR* 3.8 20.2 - - + -
269A TYR* 4.5 8.5 - - + -
385A ILE* 3.8 25.4 - - + +
386A PHE* 4.0 17.0 - - + -
472A ILE* 3.6 23.9 - - + +
473A TYR* 4.4 1.0 - - - -
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Residues in contact with ALA 189 (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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158A PHE 3.7 3.8 - - - -
160A MET* 3.7 9.0 - - + -
179A PHE* 3.6 33.2 - - + -
182A CYS* 4.1 5.3 - - - +
187A ALA 4.0 1.0 + - - -
188A ILE* 1.3 72.3 - - - +
190A GLN* 1.3 56.2 + - - +
242A CYS* 3.9 10.5 - - - -
243A PRO 3.2 16.7 + - - +
244A LEU* 3.6 7.1 - - + +
245A TYR* 2.8 32.9 + - - +
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Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR 4.8 0.6 + - - -
101A PHE* 3.7 16.1 - - - -
132A HIS* 3.2 58.3 + - - +
157A SER* 3.7 14.4 - - - -
158A PHE 2.7 21.3 + - - +
159A LYS* 3.8 11.0 - - + -
160A MET* 2.7 33.0 + - - +
188A ILE* 4.9 2.7 - - + -
189A ALA* 1.3 72.1 - - - +
191A VAL* 1.3 62.3 + - - +
245A TYR* 3.3 29.3 - - + -
247A VAL* 4.1 13.6 - - + +
271A GLU* 5.1 0.2 + - - -
386A PHE* 4.2 3.6 - - + -
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 5.0 0.4 - - - -
160A MET 3.3 12.8 - - - +
162A MET* 3.6 37.9 - - + -
175A LEU* 4.5 6.5 - - + -
179A PHE* 3.6 19.5 - - + -
190A GLN* 1.3 81.4 - - - +
192A HIS* 1.3 63.2 + - - +
193A ALA 3.5 3.4 + - - +
233A ALA* 4.3 10.3 - - + -
244A LEU* 3.6 29.8 - - + -
245A TYR 3.0 7.7 + - - +
246A ILE* 3.9 9.2 - - + +
247A VAL* 3.3 28.1 + - - +
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Residues in contact with HIS 192 (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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159A LYS* 4.2 5.0 - - - +
160A MET 3.1 9.3 + - - +
161A PHE* 3.9 23.1 - + + -
162A MET* 3.2 22.2 + - - +
163A ALA* 3.5 21.5 - - + +
164A TYR* 3.7 21.3 - + - -
191A VAL* 1.3 70.7 - - - +
193A ALA* 1.3 60.0 + - - +
194A GLU* 2.8 31.7 + - + +
247A VAL* 3.9 7.3 - - - +
248A HIS* 3.2 6.1 - + - -
298A GLY* 3.1 30.5 - - - -
299A PRO* 4.2 0.8 - - + +
1495A ZN 2.6 27.6 - - - -
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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