Contacts of the strand formed by residues 191 - 195 (chain A) in PDB entry 3VAS
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 LEU 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLN 3.0 12.4 + - - +
163A VAL* 3.3 9.4 - - + +
164A TYR* 2.7 35.2 + - - +
185A SER* 3.9 1.8 - - - -
190A LYS* 1.3 75.5 - - - +
192A PHE* 1.3 53.1 + - - +
193A CYS* 3.9 21.8 - - - -
217A ASN* 3.5 24.5 - - + -
218A ILE* 4.2 19.1 - - + -
309A ILE* 5.5 0.2 - - + -
312A TYR* 4.8 12.1 - - + -
313A ILE* 4.0 27.6 - - + -
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.7 25.4 - + + -
166A ILE* 3.7 35.0 - - + -
181A ILE* 4.3 2.0 - - + -
182A ALA* 3.8 29.4 - - + -
185A SER* 3.5 13.9 + - - +
191A LEU* 1.3 72.7 - - - +
193A CYS* 1.3 70.5 + - - +
194A PHE* 4.1 6.7 - + + -
212A MET* 3.4 34.8 - - + -
215A TYR 3.6 17.5 - - - +
216A SER* 3.5 28.2 - - - -
217A ASN* 2.8 36.5 + - - +
218A ILE 3.3 5.4 + - - -
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Residues in contact with CYS 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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163A VAL* 4.5 3.6 - - - -
164A TYR 2.8 20.6 + - - +
165A TYR* 3.5 20.7 - - + -
166A ILE 3.1 25.5 + - - +
191A LEU* 3.9 28.0 - - - -
192A PHE* 1.3 80.2 - - - +
194A PHE* 1.3 60.6 + - - +
218A ILE* 3.4 22.4 - - - +
220A PHE* 4.3 6.5 - - + -
309A ILE* 4.0 20.0 - - + -
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Residues in contact with PHE 194 (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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165A TYR* 5.1 0.4 - - - -
166A ILE 3.3 13.9 - - - -
168A GLY* 3.6 30.7 - - - -
171A ILE* 4.3 10.1 - - + -
178A MET* 4.0 8.1 - - + -
192A PHE* 4.1 3.1 - + + -
193A CYS* 1.3 74.9 - - - +
195A ASN* 1.3 67.2 + - - +
196A LEU* 4.2 7.6 - - + -
209A VAL* 4.1 26.2 - - + -
212A MET* 3.7 42.6 - - + -
213A ILE* 4.3 10.8 - - + -
216A SER* 3.1 29.2 - - - +
218A ILE 2.9 7.4 + - - +
219A VAL* 3.3 12.3 - - + +
220A PHE* 2.8 29.8 + - - +
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Residues in contact with ASN 195 (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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165A TYR* 3.0 30.1 + - + +
166A ILE 3.5 6.7 + - - -
167A ALA* 4.1 7.0 - - + -
168A GLY* 2.7 31.0 + - - -
194A PHE* 1.3 81.3 - - - +
196A LEU* 1.3 62.6 + - - +
197A SER* 2.9 34.6 + - - +
220A PHE* 3.5 26.8 - - + +
221A GLY* 4.7 0.7 - - - -
225A GLU* 4.2 5.0 - - - +
301A GLY* 4.6 10.9 + - - -
302A ASP* 5.2 3.9 + - - -
305A ALA* 4.4 5.5 - - - +
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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