Contacts of the strand formed by residues 203 - 208 (chain B) in PDB entry 2VKM
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 ILE 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B VAL* 5.2 0.2 - - + -
202B ILE* 1.3 73.3 - - - +
204B VAL* 1.3 61.0 + - - +
205B ARG 3.7 16.6 - - - +
206B VAL* 3.9 17.3 - - + -
217B CYS 4.1 4.5 - - - +
220B TYR* 4.0 12.5 - - + +
221B ASN* 2.7 35.0 + - - +
225B SER* 3.8 21.1 - - - +
236B LEU* 5.8 2.0 - - + -
285B LEU* 4.3 22.4 - - + -
286B TYR 3.3 13.9 - - - +
287B LEU* 3.9 16.8 - - + -
331B THR* 3.8 24.5 - - + +
333B MET* 4.4 5.8 - - - -
382B CYS* 3.8 3.1 - - - +
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Residues in contact with VAL 204 (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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202B ILE* 4.1 15.3 - - + +
203B ILE* 1.3 78.8 - - - +
205B ARG* 1.3 62.8 + - + +
217B CYS* 3.7 17.2 - - - +
220B TYR* 4.2 2.2 - - - -
286B TYR* 2.7 35.1 + - + +
287B LEU 4.3 0.2 - - - +
288B MET* 4.1 7.0 - - + +
295B SER* 4.0 18.6 - - - +
376B THR* 4.5 8.9 - - + +
379B MET* 3.7 37.0 - - + -
382B CYS* 3.9 15.6 - - - -
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Residues in contact with ARG 205 (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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203B ILE* 3.7 3.2 - - - +
204B VAL* 1.3 85.1 - - + +
206B VAL* 1.3 75.0 + - - +
207B GLU* 2.9 31.9 + - - +
210B GLY 4.5 4.9 + - - -
212B ASP* 3.5 47.8 + - - +
220B TYR* 3.8 7.2 - - - -
285B LEU* 3.6 0.5 - - - -
286B TYR* 2.8 54.4 + - + -
376B THR* 5.4 8.1 - - + -
278C ASN* 4.5 8.1 - - - +
365C PHE* 3.7 42.3 - - - +
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Residues in contact with VAL 206 (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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203B ILE* 3.9 9.4 - - + -
205B ARG* 1.3 83.4 - - - +
207B GLU* 1.3 71.3 + - - +
208B ILE* 4.7 7.2 - - + -
212B ASP* 3.6 5.4 - - - +
213B LEU* 3.0 47.0 + - + +
220B TYR* 3.8 36.9 - - + -
236B LEU* 6.1 4.7 - - + -
240B VAL* 5.2 4.3 - - + -
244B ALA* 5.9 1.3 - - + -
283B ILE* 4.8 3.4 - - + -
284B SER 3.3 9.0 - - - +
285B LEU* 3.8 23.1 - - + -
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Residues in contact with GLU 207 (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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205B ARG* 2.9 40.1 + - - +
206B VAL* 1.3 75.2 - - - +
208B ILE* 1.3 67.9 + - - +
209B ASN 4.0 0.4 - - - -
210B GLY* 3.4 33.1 + - - +
211B GLN 3.3 7.9 - - - +
212B ASP* 4.3 1.8 - - - -
283B ILE* 3.6 5.0 - - - +
284B SER* 3.0 44.8 + - - +
286B TYR* 2.5 34.3 + - + -
297B ARG* 4.4 6.2 + - - -
365C PHE* 3.9 7.9 - - - +
366C ARG* 6.0 0.9 - - - +
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Residues in contact with ILE 208 (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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206B VAL* 4.7 5.4 - - + -
207B GLU* 1.3 78.8 - - - +
209B ASN* 1.3 72.7 + - + +
211B GLN* 2.9 25.0 + - - +
213B LEU* 3.9 22.4 - - + -
244B ALA* 4.5 12.8 - - + +
247B SER* 3.3 31.6 - - - +
248B ILE* 4.0 18.4 - - + +
251B ALA* 5.0 1.6 - - + -
281B PRO* 3.5 31.9 - - + -
282B VAL 3.6 3.1 - - - +
283B ILE* 3.9 22.4 - - + -
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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