Contacts of the strand formed by residues 214 - 218 (chain B) in PDB entry 2VK8
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 PRO 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ALA* 3.9 24.0 - - + +
212B LYS 3.5 5.8 - - - -
213B ASN* 1.3 93.2 - - - +
215B VAL* 1.3 64.4 + - - +
240B PHE* 3.5 49.6 - - + +
241B PRO* 3.3 18.2 - - - +
280B ASP* 3.5 0.2 - - - -
281B LEU* 3.3 22.2 - - + +
283B LEU* 5.6 0.7 - - + -
344B TYR* 3.7 11.6 + - + -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASN* 4.2 8.5 - - - +
214B PRO* 1.3 81.2 - - - +
216B ILE* 1.3 67.3 + - - +
217B LEU* 4.2 1.3 + - + +
240B PHE* 4.7 0.7 - - - -
241B PRO* 3.5 15.7 - - + +
243B PHE* 4.1 18.6 - - + -
275B ALA 3.9 20.0 - - - +
276B VAL* 4.1 15.9 - - + +
279B ALA* 3.6 23.3 - - + -
281B LEU 2.9 6.5 + - - -
282B ILE* 3.9 16.6 - - + -
283B LEU* 2.9 28.5 + - - +
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Residues in contact with ILE 216 (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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215B VAL* 1.3 78.7 - - - +
217B LEU* 1.3 65.6 + - - +
218B ALA* 4.7 4.9 - - + +
231B THR* 4.7 7.0 - - - +
234B LEU* 4.1 18.6 - - + -
235B ILE* 3.9 25.8 - - + -
238B THR* 3.8 28.7 - - + -
240B PHE* 3.9 13.9 - - + +
241B PRO 2.9 9.5 + - - +
242B ALA* 3.4 11.1 - - + -
243B PHE* 2.8 31.8 + - - -
252B ILE* 6.0 0.2 - - + -
283B LEU* 3.4 26.9 - - + +
285B VAL* 4.6 13.0 - - + -
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Residues in contact with LEU 217 (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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215B VAL* 4.2 3.3 - - + -
216B ILE* 1.3 75.0 - - - +
218B ALA* 1.3 58.8 + - - +
219B ASP* 3.9 3.3 + - + +
243B PHE* 3.5 29.8 - - + +
244B VAL 4.1 1.3 - - - +
245B THR* 4.0 19.7 - - + -
263B TYR* 3.9 32.8 - - + -
276B VAL* 5.1 4.5 - - + -
282B ILE* 4.6 10.3 - - + -
283B LEU 2.9 12.2 + - - +
284B SER* 3.5 7.6 + - - +
285B VAL 2.9 26.2 + - - -
299B TYR* 4.0 10.3 - - + +
301B TYR* 3.2 30.1 - - + +
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Residues in contact with ALA 218 (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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216B ILE* 4.1 4.2 - - + -
217B LEU* 1.3 71.9 - - - +
219B ASP* 1.3 59.5 + - - +
222B CYS* 4.2 10.5 - - - -
231B THR* 4.8 4.0 - - - +
243B PHE 2.9 12.7 + - - +
244B VAL* 3.4 8.7 - - + +
245B THR* 3.0 25.7 + - - +
251B SER* 3.6 19.7 - - - +
252B ILE* 3.8 23.3 - - + -
285B VAL* 3.9 7.9 - - + -
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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