Contacts of the strand formed by residues 189 - 193 (chain A) in PDB entry 1VPE
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 TYR 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 4.6 2.5 - - + -
185A PRO* 4.1 14.4 - - + -
186A GLU 4.1 10.1 - - - +
187A LYS* 4.5 5.2 - - + -
188A PRO* 1.3 72.0 - - - +
190A VAL* 1.3 64.6 + - - +
191A VAL* 4.0 14.5 - - + +
208A LEU* 4.2 7.5 - - + +
211A LYS* 3.3 67.9 + - + +
212A ALA* 3.7 7.6 - - + +
213A ASP* 2.8 41.6 + - - +
214A ARG 3.5 3.1 + - - -
313A THR* 3.3 34.1 - - + -
315A VAL* 3.8 16.4 - - + +
383A LEU* 3.5 25.1 - - - +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 4.8 1.6 - - + -
189A TYR* 1.3 81.1 - - - +
191A VAL* 1.3 74.0 + - - +
192A VAL* 4.2 0.2 - - + -
214A ARG* 3.5 41.1 - - + +
216A LEU* 3.8 21.1 - - + -
307A LYS 4.0 6.1 - - - +
308A LEU* 3.9 21.1 - - + -
311A ALA* 3.9 22.2 - - + -
313A THR 2.8 11.1 + - - +
314A VAL* 3.2 7.2 - - + +
315A VAL 3.0 22.7 + - - -
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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
----------------------------------------------------------
189A TYR* 4.0 15.9 - - + +
190A VAL* 1.3 78.7 - - - +
192A VAL* 1.3 63.4 + - - +
193A LEU* 3.8 32.3 - - + -
208A LEU* 3.9 35.0 - - + -
212A ALA* 4.0 16.4 - - + -
214A ARG 3.1 9.3 + - - +
215A ILE* 3.4 11.7 - - + -
216A LEU 2.9 25.5 + - - +
315A VAL* 3.4 16.6 - - + +
380A LEU* 5.2 0.2 - - + -
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Residues in contact with VAL 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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190A VAL* 4.2 0.9 - - + -
191A VAL* 1.3 79.0 - - - +
193A LEU* 1.3 62.1 + - - +
216A LEU* 3.5 23.3 - - + +
304A PHE* 5.5 0.9 - - + -
308A LEU* 4.0 27.8 - - + -
314A VAL* 4.1 14.1 - - + -
315A VAL 2.7 10.6 + - - +
316A TRP* 3.3 16.9 - - + -
317A ASN 2.8 27.9 + - - -
320A MET* 3.7 30.3 - - + -
335A VAL* 4.5 8.7 - - + -
339A ILE* 4.3 5.8 - - + -
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Residues in contact with LEU 193 (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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191A VAL* 3.8 26.5 - - + -
192A VAL* 1.3 75.2 - - - +
194A GLY* 1.3 60.0 + - - +
201A LYS* 4.8 9.0 - - + +
204A VAL* 4.8 2.9 - - + -
205A ILE* 3.7 36.6 - - + -
208A LEU* 4.5 6.3 - - + -
215A ILE* 4.3 9.9 - - + -
216A LEU 2.9 11.3 + - - +
217A ILE* 3.4 5.6 - - + -
218A GLY 2.8 24.1 + - - -
221A MET* 4.1 19.1 - - + -
315A VAL* 6.3 0.2 - - + -
317A ASN* 3.3 10.3 - - + +
320A MET* 3.7 6.5 - - - +
380A LEU* 3.9 32.1 - - + -
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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