Contacts of the strand formed by residues 234 - 239 (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 GLN 234 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C MET* 3.8 6.1 - - - +
179C PRO* 3.6 22.5 - - + +
190C VAL* 4.3 5.4 - - + +
191C VAL 3.9 12.6 + - - +
192C LYS* 3.4 38.6 + - - +
212C SER* 3.3 23.7 + - - -
213C HIS* 3.3 46.9 - - + +
214C LEU 4.5 1.4 - - - +
226C VAL 3.2 3.6 - - - +
227C ASP* 3.6 15.1 - - - +
232C GLY 4.1 7.4 - - - +
233C ARG* 1.3 79.5 - - - +
235C SER* 1.3 65.0 + - - +
248L GLU* 5.5 0.2 - - - +
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Residues in contact with SER 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ARG* 3.5 31.2 + - - -
177C ALA 3.5 7.9 - - - -
178C MET* 3.5 24.8 - - - +
179C PRO* 5.0 0.9 - - - -
213C HIS* 4.0 6.9 - - - -
215C ILE* 6.0 0.7 - - - -
225C TYR 3.6 0.2 - - - -
226C VAL* 2.6 47.0 + - - +
228C ASP* 5.5 1.2 + - - -
233C ARG* 5.1 1.6 + - - +
234C GLN* 1.3 78.9 - - - +
236C VAL* 1.3 56.8 + - - +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE 3.8 1.0 - - - +
176C ARG* 3.8 0.3 - - - +
177C ALA* 3.1 38.0 + - + +
213C HIS* 5.0 0.2 + - - -
215C ILE* 3.9 29.0 + - + +
217C VAL* 3.4 37.2 - - + -
223C SER* 4.3 2.2 - - - -
224C GLN 3.7 8.7 - - - +
225C TYR* 3.7 37.7 - - + +
235C SER* 1.3 73.8 - - - +
237C VAL* 1.3 69.5 + - - +
254C TYR* 5.1 0.5 + - - -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ALA* 3.4 30.7 - - + -
175C ILE 3.5 10.8 - - - +
176C ARG* 3.1 41.3 - - + +
217C VAL* 5.5 0.4 - - - -
223C SER* 3.1 6.4 - - - -
224C GLN* 2.9 50.1 + - + +
226C VAL* 4.2 11.2 - - + -
235C SER 4.8 0.4 - - - +
236C VAL* 1.3 80.3 - - - +
238C VAL* 1.3 76.1 + - - +
278C GLU* 6.0 0.2 - - - +
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ALA* 3.5 2.5 - - - -
175C ILE* 3.0 34.4 + - + +
217C VAL* 3.9 17.5 - - + -
220C ASN* 3.7 23.3 - - - +
223C SER* 3.3 24.2 - - - -
237C VAL* 1.3 86.6 - - - +
239C PRO* 1.3 77.9 - - + +
252C ILE* 3.5 35.9 - - + -
254C TYR* 5.1 1.3 - - - +
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Residues in contact with PRO 239 (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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172C GLY* 6.2 1.8 - - - -
173C THR 3.6 9.6 - - - +
174C ALA* 4.5 1.3 - - + -
220C ASN* 5.0 3.3 + - - +
222C LEU* 3.7 49.1 - - + +
224C GLN* 6.3 2.0 - - + +
238C VAL* 1.3 94.9 - - + +
240C TYR* 1.3 68.9 + - - +
241C GLU* 3.5 11.6 + - + +
252C ILE* 5.5 1.7 - - - +
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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