Contacts of the strand formed by residues 191 - 196 (chain C) in PDB entry 3V4P
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 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C PHE* 4.0 14.5 - - - -
182C ALA* 2.9 30.9 + - - -
185C SER* 3.3 20.4 - - - -
190C GLY* 1.3 76.9 - - - -
192C LEU* 1.3 88.4 + - - +
193C PHE* 4.9 1.2 - - - -
204C ALA* 4.1 0.5 - - - +
205C PHE* 2.9 26.2 + - - -
218C LEU* 3.2 15.0 + - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C VAL* 4.7 2.5 - - + -
180C MET 3.6 2.2 - - - +
181C GLY* 3.7 4.7 - - - -
191C SER* 1.3 91.3 + - - +
193C PHE* 1.3 65.3 + - - +
194C VAL* 4.1 0.4 - - + -
203C LYS 3.7 0.3 - - - +
204C ALA* 3.1 27.9 - - - +
205C PHE* 3.4 5.9 + - + +
218C LEU* 4.8 3.8 - - + -
219C GLY* 3.5 15.5 - - - +
222C VAL* 3.5 27.4 - - + -
235C VAL* 3.6 30.5 - - + -
236C VAL 4.0 2.0 - - - +
237C GLY* 3.9 13.0 - - - -
251C PHE* 3.8 27.8 - - + -
258C LEU* 3.9 16.3 - - + +
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Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PRO* 3.8 25.4 - - + -
150C CYS* 3.5 31.6 - - - -
162C PHE* 3.7 33.2 - + - -
165C CYS* 4.6 0.4 - - + -
167C ALA* 4.3 8.7 - - + -
178C ILE 3.1 5.0 - - - +
179C VAL* 3.3 2.4 - - - +
180C MET* 2.9 61.1 + - + +
182C ALA* 3.7 20.9 - - + -
185C SER* 4.7 1.8 - - - -
191C SER* 4.9 1.3 - - - -
192C LEU* 1.3 76.9 - - - +
194C VAL* 1.3 62.4 + - - +
195C TYR 3.9 0.2 - - - -
202C TYR* 4.9 11.2 - - + -
203C LYS 3.5 2.7 - - - -
204C ALA* 3.7 22.2 - - + -
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU* 4.0 17.0 - - + -
178C ILE 3.4 2.5 - - - -
179C VAL* 3.8 18.2 - - + -
192C LEU* 4.1 0.4 - - + -
193C PHE* 1.3 76.1 - - - +
195C TYR* 1.3 60.9 + - - +
196C ASN* 3.7 3.0 + - - +
201C LYS 3.8 0.5 - - - +
202C TYR* 3.7 2.8 - - - -
203C LYS* 2.9 64.2 + - + +
235C VAL* 3.7 30.5 - - + -
253C ILE* 4.3 11.4 - - + -
258C LEU* 3.6 20.2 - - + -
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Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LYS* 3.3 21.5 + - + -
147C ILE* 5.2 10.5 - - + -
177C LEU* 3.3 3.5 - - - -
178C ILE* 2.9 56.8 + - + +
180C MET* 4.5 4.0 - - + +
193C PHE 3.9 1.0 - - - -
194C VAL* 1.3 72.5 - - - +
196C ASN* 1.3 62.3 + - - +
197C ILE* 3.3 33.6 + - + -
200C ASN* 3.2 44.6 - - + +
201C LYS 3.8 6.7 - - - -
202C TYR* 3.4 46.4 - + + -
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Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASP* 3.4 24.2 + - - +
177C LEU* 4.8 11.4 - - + +
194C VAL 3.7 2.4 + - - +
195C TYR* 1.3 78.6 - - - +
197C ILE* 1.3 58.8 + - - +
198C THR* 2.9 25.9 + - - -
199C THR* 3.0 38.8 + - - +
201C LYS* 3.2 13.4 + - + +
203C LYS* 5.2 15.5 - - + +
253C ILE* 6.3 0.6 - - - +
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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