Contacts of the strand formed by residues 174 - 181 (chain C) in PDB entry 3VD1
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 ALA 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLY 5.0 1.1 - - - +
173C THR* 1.3 79.1 - - - +
175C ILE* 1.3 73.3 + - - +
176C ARG 4.0 0.4 - - - -
237C VAL* 3.4 24.7 - - + -
238C VAL 3.5 7.4 - - - +
239C PRO* 4.9 0.9 - - + -
240C TYR 3.9 0.9 - - - +
276C THR 3.2 1.9 - - - +
277C LEU* 3.3 2.4 - - - -
278C GLU* 2.8 42.4 + - + +
279C MET 5.2 3.4 - - - +
280C ARG* 6.1 0.7 - - - -
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Residues in contact with ILE 175 (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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127C PHE* 4.2 13.7 - - + -
163C ILE* 4.7 8.1 - - + -
174C ALA* 1.3 84.8 - - - +
176C ARG* 1.3 60.1 + - - +
177C ALA 3.9 0.3 + - - -
236C VAL 3.8 1.4 - - - +
237C VAL* 3.5 6.9 - - - -
238C VAL* 3.0 36.8 + - + +
240C TYR* 4.1 25.1 - - + -
250C THR* 6.1 0.2 - - + -
252C ILE* 4.1 24.7 - - + -
254C TYR* 3.6 21.0 + - - +
275C ILE* 3.8 21.8 - - + -
276C THR 3.2 3.1 - - - +
277C LEU* 3.9 20.4 - - + -
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Residues in contact with ARG 176 (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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174C ALA* 4.0 0.6 - - - +
175C ILE* 1.3 73.4 - - - +
177C ALA* 1.3 66.6 + - - +
178C MET* 4.4 17.8 - - + +
226C VAL* 4.2 13.9 - - - +
228C ASP* 5.3 5.5 + - - -
235C SER* 3.5 30.6 + - - -
236C VAL 3.8 3.8 - - - -
237C VAL* 3.1 30.5 - - + +
254C TYR* 4.7 0.9 - - - -
274C ILE 3.1 7.4 - - - +
275C ILE* 3.2 2.8 - - - -
276C THR* 2.7 45.4 + - - -
278C GLU* 2.7 51.1 + - + +
282C GLY* 5.2 2.6 - - - -
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Residues in contact with ALA 177 (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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175C ILE 3.9 0.4 + - - -
176C ARG* 1.3 72.5 - - - +
178C MET* 1.3 60.5 + - - +
215C ILE* 4.0 13.9 - - + +
235C SER* 3.5 2.8 - - - -
236C VAL* 3.1 35.9 + - + +
254C TYR* 3.4 42.8 - - + +
273C ILE* 4.7 2.2 - - + -
274C ILE 3.5 4.7 - - - -
275C ILE* 3.8 9.6 - - + -
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Residues in contact with MET 178 (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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116C PRO* 3.7 33.2 - - + -
176C ARG* 4.5 18.4 - - + -
177C ALA* 1.3 73.2 - - - +
179C PRO* 1.3 74.1 - - + +
180C VAL* 4.3 5.6 - - + -
215C ILE* 3.8 4.8 - - - +
233C ARG* 4.1 29.4 - - + -
234C GLN 3.8 5.4 - - - +
235C SER* 3.5 18.2 - - - +
272C LEU 3.8 0.7 - - - +
273C ILE* 3.6 0.3 - - - -
274C ILE* 2.8 44.5 + - + +
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Residues in contact with PRO 179 (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 ALA 4.5 0.2 - - - +
178C MET* 1.3 86.2 - - + +
180C VAL* 1.3 68.3 + - - +
191C VAL* 3.7 37.8 + - + +
214C LEU* 3.5 30.1 - - + -
215C ILE* 3.2 17.9 - - + +
233C ARG* 4.0 8.3 + - - -
234C GLN* 3.6 17.7 - - + +
235C SER* 5.0 0.4 - - - -
271C ILE* 4.7 3.8 - - + -
272C LEU 3.8 4.9 - - - +
273C ILE* 4.1 7.0 - - + -
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Residues in contact with VAL 180 (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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116C PRO* 3.6 39.9 - - + +
178C MET* 4.3 4.3 - - + -
179C PRO* 1.3 82.0 - - - +
181C TYR* 1.3 84.0 + - - +
187C VAL* 3.6 21.5 - - + -
191C VAL* 3.9 10.3 - - - -
233C ARG* 4.5 9.9 - - - +
271C ILE* 3.0 5.5 - - - +
272C LEU* 2.8 39.6 + - + +
274C ILE* 3.8 17.5 - - + -
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Residues in contact with TYR 181 (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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180C VAL* 1.3 91.8 - - - +
182C LYS* 1.3 62.2 + - - +
183C LYS 4.3 1.3 - - - +
186C HIS* 3.3 24.9 - - + -
187C VAL* 3.6 25.7 - - - +
189C ASP* 3.0 41.5 - - + +
190C VAL 3.8 3.6 + - - -
191C VAL* 3.3 28.6 - - + +
192C LYS 4.5 2.1 + - - -
265C GLY 4.6 0.7 - - - -
266C MET* 4.1 15.1 + - - -
269C ARG* 3.2 54.7 + - + -
270C PRO 3.6 8.1 - - - +
271C ILE* 4.1 13.2 - - + -
272C LEU* 4.6 3.7 - - - +
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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