Contacts of the strand formed by residues 178 - 182 (chain C) in PDB entry 3VI4
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 VAL 178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.6 24.2 - - + -
137C LEU* 4.1 12.1 - - + -
148C TYR* 4.0 19.7 - - + -
171C GLU 4.2 1.8 - - - -
172C PHE* 3.8 24.0 - - + -
176C GLY 4.2 2.7 - - - +
177C ARG* 1.3 71.9 - - - +
179C VAL* 1.3 62.1 - - - +
180C LEU* 3.6 15.9 - - + -
194C SER* 3.0 21.0 + - - -
195C ALA 2.9 25.7 + - - +
196C THR* 4.8 0.2 - - - +
197C GLN* 4.3 2.2 - - + -
200C ILE* 3.8 21.5 - - + -
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 5.1 0.2 - - - +
170C ALA* 3.3 5.4 - - - -
171C GLU 2.9 43.1 + - - +
173C THR* 3.9 14.6 - - + -
177C ARG* 4.3 0.2 - - + -
178C VAL* 1.3 79.1 - - - +
180C LEU* 1.3 66.3 + - - +
192C ILE* 4.5 10.8 - - + -
193C LEU 3.6 3.6 - - - +
194C SER* 3.8 7.4 - - - +
235C VAL* 4.0 26.4 - - + +
237C VAL* 4.4 4.7 - - + -
248C PHE* 3.4 45.8 - - + -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 4.1 8.3 - - + -
135C CYS* 3.8 28.5 - - - -
148C TYR* 3.7 22.4 - - + -
150C PRO* 3.8 21.5 - - + -
166C GLY* 4.3 3.6 - - - -
167C GLY* 3.8 21.3 - - - +
169C SER 3.6 1.1 - - - -
170C ALA* 4.2 6.3 - - + -
178C VAL* 3.6 22.2 - - + -
179C VAL* 1.3 83.4 - - - +
181C GLY* 1.3 58.2 + - - +
182C GLY 4.0 0.6 + - - -
192C ILE* 3.4 10.6 - - - +
193C LEU* 2.7 48.7 + - + +
235C VAL* 5.0 0.7 - - - -
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C GLN 3.6 0.5 - - - +
166C GLY* 4.4 0.9 - - - -
167C GLY 3.0 21.8 + - - -
168C PHE 3.4 10.0 + - - -
169C SER* 2.6 25.3 + - - -
180C LEU* 1.3 71.3 - - - +
182C GLY* 1.3 58.7 + - - -
183C PRO* 3.6 1.0 - - - +
192C ILE* 3.9 12.3 - - - -
232C GLY 3.4 19.7 - - - -
235C VAL* 4.7 1.6 - - - +
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Residues in contact with GLY 182 (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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164C CYS* 3.2 26.9 - - - -
166C GLY* 4.1 3.1 - - - -
180C LEU 4.0 1.2 + - - -
181C GLY* 1.3 73.4 - - - -
183C PRO* 1.3 56.4 - - - +
184C GLY 3.0 10.7 + - - -
185C SER* 3.5 4.9 + - - -
190C GLY* 3.2 0.3 - - - -
191C GLN* 2.6 43.6 + - - +
193C LEU* 5.0 1.4 - - - +
231C LEU 3.7 0.7 - - - -
232C GLY 4.0 0.2 + - - -
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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