Contacts of the strand formed by residues 239 - 246 (chain B) in PDB entry 2VDY
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 GLY 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B LEU* 5.6 2.0 - - - +
103B MET* 6.2 1.8 - - - -
181B PHE* 4.9 11.5 - - - -
234B ASN* 3.8 2.9 - - - +
235B TYR* 2.8 48.3 + - - +
237B GLY 3.8 1.0 - - - -
238B ASN* 1.3 79.8 - - - +
240B THR* 1.3 59.7 + - - -
365B ILE* 5.5 1.1 - - - -
366B PHE 3.5 8.3 - - - -
367B ASP* 4.8 1.6 - - - -
368B HIS* 4.6 1.6 + - - -
374B LEU* 5.5 2.2 - - - -
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B GLN* 2.9 24.4 + - - +
233B MET 3.1 13.3 + - - -
234B ASN* 3.4 6.7 + - - -
235B TYR* 3.8 3.1 - - - -
239B GLY* 1.3 74.6 - - - -
241B VAL* 1.3 67.1 + - - +
242B PHE* 4.6 4.5 - - + -
364B MET 3.8 0.4 - - - +
365B ILE* 3.4 5.7 - - - +
366B PHE* 2.8 48.0 + - + +
368B HIS* 3.5 19.1 - - + +
1384B HCY 3.8 29.6 - - + -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TRP* 3.5 29.6 - - + -
231B VAL 3.9 0.3 - - - +
232B GLN* 3.2 6.1 - - - +
233B MET* 2.9 49.9 + - + +
235B TYR* 4.0 13.0 - - + +
240B THR* 1.3 77.5 + - - +
242B PHE* 1.3 67.1 + - - +
243B PHE* 3.7 27.2 + - + -
363B ILE* 3.7 26.5 - - + -
364B MET 3.3 6.7 - - - +
365B ILE* 4.0 7.2 - - + -
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 4.4 15.5 - - + -
231B VAL 3.5 4.9 - - - -
232B GLN* 3.4 44.0 - - + -
240B THR* 4.6 5.4 - - + -
241B VAL* 1.3 76.5 - - - +
243B PHE* 1.3 62.2 + - - +
244B ILE* 3.8 6.0 - - + +
263B ILE* 4.6 7.4 - - + -
266B TRP* 5.0 6.7 - + + -
267B SER* 4.5 6.3 - - - -
270B LEU* 3.7 17.3 - - + -
362B ILE 3.5 1.6 - - - +
363B ILE* 3.4 5.9 - - - -
364B MET* 2.8 58.2 + - + +
366B PHE* 3.8 35.7 - + - -
1384B HCY 4.0 22.4 - - + -
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TRP* 3.9 22.0 - + - -
230B LEU* 3.3 5.0 - - - +
231B VAL* 3.0 41.0 + - + -
233B MET* 4.8 9.9 - - + -
241B VAL* 3.7 34.8 - - + -
242B PHE* 1.3 71.0 - - - +
244B ILE* 1.3 61.3 + - - +
279B ILE* 3.6 28.0 - - + -
331B LEU* 3.9 18.8 - - + -
357B PHE* 3.6 24.4 - + + -
361B PHE* 4.1 11.0 - + - -
362B ILE 3.5 1.3 - - - -
363B ILE* 3.7 40.6 - - + -
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B CYS* 4.0 31.0 - - + -
229B GLN 3.9 4.0 - - - +
230B LEU* 3.7 20.9 - - + -
242B PHE* 3.8 21.5 - - + +
243B PHE* 1.3 76.3 - - - +
245B LEU* 1.3 63.4 + - - +
246B PRO* 3.5 2.6 - - - +
254B VAL* 4.1 14.8 - - + -
258B LEU* 5.8 0.2 - - + -
266B TRP* 3.6 31.6 - - + -
357B PHE* 3.8 2.7 - - - -
361B PHE* 3.2 6.1 - - - +
362B ILE* 2.8 61.5 + - + +
364B MET* 4.1 5.4 - - + -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B CYS* 3.3 2.6 - - - -
229B GLN* 2.9 42.6 + - + +
244B ILE* 1.3 72.1 - - - +
246B PRO* 1.3 71.6 - - - +
247B ASP* 4.9 0.7 - - - +
355B LEU* 3.9 21.3 - - + -
356B ARG 3.5 26.2 - - - +
357B PHE* 3.5 30.8 - - + -
359B GLN* 3.9 37.0 - - + +
360B PRO 4.3 3.1 - - - +
361B PHE* 4.2 2.7 - - + -
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Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B PRO 3.4 6.7 - - - +
228B CYS* 3.9 3.8 - - + -
244B ILE 3.5 10.1 - - - +
245B LEU* 1.3 98.9 - - - +
247B ASP* 1.3 65.4 + - - +
248B LYS* 3.6 1.9 + - - -
250B LYS 3.7 26.0 - - - +
251B MET* 3.9 31.9 - - + +
254B VAL* 3.8 12.1 - - + -
359B GLN* 4.5 5.4 - - - +
360B PRO 3.6 18.0 - - - +
361B PHE* 4.2 1.8 - - - -
362B ILE* 4.3 7.6 - - + -
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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