Contacts of the strand formed by residues 228 - 234 (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 CYS 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B HIS* 4.5 1.8 + - - -
223B ASP* 3.1 54.0 + - - +
226B LEU* 2.8 16.6 + - - -
227B PRO* 1.3 74.8 - - - +
229B GLN* 1.3 65.2 + - - +
230B LEU* 4.1 4.5 - - - -
244B ILE* 4.0 22.7 - - + -
245B LEU 3.3 13.9 - - - +
246B PRO* 3.9 1.6 - - + -
247B ASP* 4.2 5.5 + - - +
254B VAL* 3.8 16.2 - - + -
266B TRP* 4.0 11.4 - - - -
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Residues in contact with GLN 229 (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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220B TYR* 2.7 27.0 + - + +
221B LEU 3.5 7.6 - - - +
222B HIS* 3.4 35.6 + - + +
228B CYS* 1.3 78.3 - - - +
230B LEU* 1.3 63.2 + - - +
243B PHE 4.2 0.2 - - - +
244B ILE* 3.9 0.7 - - - +
245B LEU* 2.9 37.7 + - + +
247B ASP* 5.0 8.7 + - - +
353B ILE* 5.1 1.0 - - - +
354B ILE 4.9 5.0 - - - +
355B LEU* 3.4 31.4 - - + +
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Residues in contact with LEU 230 (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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220B TYR* 3.9 1.2 - - - -
221B LEU* 2.9 54.0 + - + +
223B ASP* 4.5 3.1 - - + -
228B CYS* 4.1 12.3 - - - -
229B GLN* 1.3 76.5 - - - +
231B VAL* 1.3 66.0 + - - +
242B PHE* 4.4 10.1 - - + -
243B PHE 3.3 12.6 - - - +
244B ILE* 3.7 15.3 - - + -
266B TRP* 3.5 66.4 - - + +
270B LEU* 4.0 15.6 - - + +
355B LEU* 4.5 3.7 - - - +
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Residues in contact with VAL 231 (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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218B ILE* 3.8 19.1 - - + -
219B SER 3.2 13.7 - - - +
220B TYR* 3.9 13.5 - - + -
230B LEU* 1.3 80.6 - - - +
232B GLN* 1.3 61.8 + - - +
233B MET* 5.1 2.0 - - + -
242B PHE* 3.5 7.6 - - - +
243B PHE* 3.0 52.9 + - + +
270B LEU* 4.4 3.6 - - - -
275B VAL* 4.9 3.8 - - + -
277B LEU* 3.8 28.3 - - + -
355B LEU* 3.7 20.0 - - + -
357B PHE* 4.3 0.2 - - + -
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Residues in contact with GLN 232 (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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187B GLN* 5.7 1.4 + - - -
218B ILE* 4.1 6.4 - - - +
219B SER* 3.1 31.5 + - - -
231B VAL* 1.3 74.6 - - - +
233B MET* 1.3 65.6 + - - +
234B ASN* 4.7 5.7 + - - +
240B THR* 2.9 27.9 + - - +
241B VAL 3.2 8.1 - - - +
242B PHE* 3.4 27.5 - - + -
267B SER* 5.6 0.9 - - - -
270B LEU* 3.4 27.5 - - + +
368B HIS* 4.5 2.6 - - - -
1384B HCY 2.7 32.9 + - - +
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Residues in contact with MET 233 (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* 4.4 12.6 - - + -
187B GLN* 3.7 37.0 - - + +
189B PHE* 4.4 8.7 - - - -
214B GLN* 3.6 31.4 - - - +
218B ILE* 3.9 21.3 - - + -
231B VAL* 5.1 1.3 - - + -
232B GLN* 1.3 79.1 - - - +
234B ASN* 1.3 66.8 + - - +
240B THR* 3.1 4.2 + - - -
241B VAL* 2.9 48.8 + - + +
243B PHE* 4.8 12.1 - - + -
277B LEU* 3.5 23.1 - - + -
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Residues in contact with ASN 234 (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 9.5 - - - -
186B THR* 2.9 42.8 + - + +
187B GLN* 4.6 2.8 + - - +
232B GLN* 4.7 5.7 + - - +
233B MET* 1.3 81.0 - - - +
235B TYR* 1.3 66.3 + - - +
239B GLY 3.8 4.5 - - - +
240B THR* 3.4 14.2 + - - -
368B HIS* 4.2 14.8 - - - -
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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