Contacts of the strand formed by residues 247 - 252 (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 ASP 247 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C VAL* 3.2 9.2 - - - +
238C GLY 2.6 34.9 + - - +
239C GLU* 3.1 11.6 - - - +
240C PHE* 3.2 11.0 + - - +
241C SER* 3.1 15.4 + - - -
246C GLU* 1.3 74.2 - - - +
248C PHE* 1.3 64.3 + - - +
249C VAL* 5.2 0.2 - - - +
264C ILE* 4.1 16.6 - - + -
265C LEU 3.3 7.0 - - - +
266C ASN* 3.1 11.2 - - - +
267C GLY 2.6 25.0 + - - +
273C LEU* 4.0 3.8 - - - +
2001C CA 2.3 27.9 - - - -
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Residues in contact with PHE 248 (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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173C THR* 4.4 9.9 - - + -
177C ARG* 4.6 6.3 - - - -
179C VAL* 3.4 39.5 - - + -
192C ILE* 4.5 8.7 - - + -
194C SER* 4.0 16.4 - - - -
217C LEU* 4.7 2.2 - - + -
235C VAL* 5.7 1.3 - - + -
236C ALA 3.6 4.3 - - - +
237C VAL* 3.9 6.3 - - + -
246C GLU 3.8 14.1 - - - -
247C ASP* 1.3 76.7 - - - +
249C VAL* 1.3 63.2 + - - +
250C ALA* 3.7 2.6 + - + -
263C THR 3.5 2.1 - - - +
264C ILE* 3.2 4.9 - - - -
265C LEU* 2.8 51.7 + - + +
267C GLY* 3.8 26.2 - - - -
270C ILE* 3.5 41.1 - - + -
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Residues in contact with VAL 249 (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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235C VAL* 3.2 7.7 - - - +
236C ALA* 2.7 52.0 + - + +
237C VAL* 5.0 1.6 - - - +
240C PHE* 3.9 28.9 - - + -
247C ASP 3.9 0.2 + - - -
248C PHE* 1.3 70.5 - - - +
250C ALA* 1.3 61.8 + - - +
262C VAL* 3.6 18.4 - - + -
263C THR 3.4 3.4 - - - -
264C ILE* 3.9 13.9 - - + -
289C VAL* 3.6 28.0 - - + -
290C ALA 5.1 0.4 - - - +
291C ALA* 4.5 6.7 - - + -
302C LEU* 3.9 16.4 - - + -
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Residues in contact with ALA 250 (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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192C ILE* 3.9 23.6 - - + -
231C LEU* 3.7 25.6 - - + -
232C GLY 4.4 0.2 - - - +
234C SER 3.4 4.3 - - - +
235C VAL* 4.1 1.8 - - + -
248C PHE* 3.7 4.4 + - + +
249C VAL* 1.3 77.5 - - - +
251C GLY* 1.3 64.2 + - - +
252C VAL* 3.8 0.3 - - - +
262C VAL* 3.3 7.1 - - - +
263C THR* 3.1 36.5 + - - +
265C LEU* 5.0 3.1 - - + -
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Residues in contact with GLY 251 (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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230C TYR 3.2 2.8 - - - +
232C GLY 2.9 25.8 + - - -
233C TYR 3.5 2.4 + - - -
234C SER* 2.7 20.2 + - - -
249C VAL 4.3 0.2 - - - -
250C ALA* 1.3 73.4 - - - +
252C VAL* 1.3 60.4 + - - +
253C PRO* 3.7 5.4 - - - -
261C TYR 4.1 2.0 - - - -
262C VAL* 4.5 0.9 - - - -
286C GLY* 3.6 27.4 - - - -
289C VAL* 4.4 5.2 - - - +
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Residues in contact with VAL 252 (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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189C GLN 4.8 0.2 - - - +
229C SER* 3.0 27.8 - - - +
230C TYR 3.7 0.4 - - - -
231C LEU* 3.8 31.0 - - + +
250C ALA 3.8 9.4 - - - +
251C GLY* 1.3 78.6 - - - +
253C PRO* 1.3 69.7 - - - +
254C LYS 3.0 3.9 + - - -
255C GLY* 3.3 7.6 + - - -
261C TYR* 2.8 77.1 + - + +
263C THR* 4.1 3.8 - - - +
286C GLY* 4.5 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