Contacts of the strand formed by residues 178 - 182 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 4.0 20.0 - - + -
137A LEU* 4.4 11.4 - - + -
148A TYR* 4.0 18.4 - - + -
171A GLU 4.2 1.8 - - - -
172A PHE* 3.7 26.5 - - + -
176A GLY 4.1 3.4 - - - +
177A ARG* 1.3 72.3 - - - +
179A VAL* 1.3 59.2 + - - +
180A LEU* 4.0 23.3 - - + -
194A SER* 2.6 26.0 + - - -
195A ALA 3.0 24.2 + - - +
197A GLN* 4.8 1.3 - - + -
200A ILE* 4.0 20.0 - - + -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ALA* 3.2 7.4 - - - +
171A GLU 3.0 39.0 + - - +
173A THR* 4.2 10.8 - - + -
177A ARG 4.8 0.2 - - - -
178A VAL* 1.3 77.8 - - - +
180A LEU* 1.3 67.6 + - - +
192A ILE* 4.1 21.1 - - + -
193A LEU 3.8 0.9 - - - -
194A SER* 3.9 7.0 - - - +
235A VAL* 4.5 19.4 - - + +
237A VAL* 4.1 12.3 - - + -
248A PHE* 3.7 42.2 - - + -
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Residues in contact with LEU 180 (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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113A LEU* 4.2 1.1 - - + -
115A CYS* 4.3 0.4 - - - -
135A CYS* 3.8 30.3 - - - -
148A TYR* 3.8 22.7 - - + -
150A PRO* 3.8 20.2 - - + -
166A GLY 4.5 3.6 - - - -
167A GLY* 4.3 12.3 - - - +
169A SER 3.7 2.7 - - - +
170A ALA* 3.5 20.6 - - + -
178A VAL* 4.0 17.5 - - + -
179A VAL* 1.3 85.5 - - - +
181A GLY* 1.3 60.7 + - - +
192A ILE* 3.3 10.8 - - - +
193A LEU* 2.7 48.3 + - + +
235A VAL* 5.0 1.8 - - - -
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Residues in contact with GLY 181 (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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166A GLY* 4.4 1.6 - - - -
167A GLY 3.0 23.7 + - - -
168A PHE 3.5 8.7 + - - -
169A SER* 2.9 18.8 + - - +
180A LEU* 1.3 73.3 - - - +
182A GLY* 1.3 59.1 + - - -
183A PRO* 3.8 0.7 - - - +
191A GLN 3.5 4.5 - - - -
192A ILE* 3.9 9.0 - - - -
193A LEU* 5.6 0.7 - - - -
232A GLY 3.6 21.1 - - - -
235A VAL* 4.7 0.8 - - - +
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Residues in contact with GLY 182 (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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164A CYS* 3.2 26.5 - - - -
165A GLN 4.0 0.7 - - - -
166A GLY* 4.0 0.7 - - - -
181A GLY* 1.3 73.3 - - - -
183A PRO* 1.4 65.2 - - - +
184A GLY 3.1 4.7 + - - -
185A SER* 3.5 5.2 + - - -
190A GLY* 3.2 1.7 - - - -
191A GLN* 2.7 39.7 + - - +
193A LEU* 5.3 1.5 - - - +
231A LEU 3.7 2.6 + - - -
232A GLY 4.2 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