Contacts of the strand formed by residues 261 - 264 (chain G) in PDB entry 2VT5
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 261 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G ILE* 3.0 5.2 + - - +
209G TYR* 3.4 25.1 - - + -
210G SER* 2.9 28.1 + - - -
226G TYR* 3.4 40.4 - - + +
240G TYR* 5.2 2.0 - - + -
255G THR* 4.1 5.6 + - - +
260G GLY* 1.3 76.3 - - - +
262G PHE* 1.3 62.1 + - - +
263G LEU* 4.0 8.5 - - + -
317G ILE* 3.5 29.2 - - + -
318G LEU 3.4 12.6 - - - +
323G ASP* 3.8 28.0 - - + +
324G VAL* 4.1 3.1 - - + +
327G PHE* 4.1 4.9 - - + -
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Residues in contact with PHE 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G SER* 3.4 24.2 - - - -
244G TYR* 4.0 20.9 - + - -
248G MET* 4.2 20.4 - - + -
251G ASP* 3.7 27.6 - - + +
252G VAL* 4.6 4.3 - - + -
255G THR* 4.0 11.9 + - - +
261G ILE* 1.3 74.7 - - - +
263G LEU* 1.3 73.5 + - - +
264G TYR* 4.5 7.6 - + + -
275G LEU* 3.8 30.5 - - + -
316G VAL* 4.2 10.5 - - + -
317G ILE* 3.4 3.3 - - - -
318G LEU* 2.9 60.2 + - + -
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Residues in contact with LEU 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G TYR* 5.0 0.4 - - + -
210G SER 2.8 22.2 + - - +
211G LEU* 3.3 37.5 - - + +
212G ASN 4.7 1.2 + - - -
223G VAL* 4.8 17.7 - - + -
226G TYR* 4.5 11.2 - - + -
227G ILE* 4.6 8.1 - - + -
244G TYR* 4.9 0.2 - - - -
261G ILE* 4.0 24.2 - - + +
262G PHE* 1.3 90.6 - - - +
264G TYR* 1.3 64.0 + - - +
265G PRO* 3.6 10.9 - - + +
316G VAL 3.4 3.1 - - - -
317G ILE* 3.8 30.1 - - + -
327G PHE* 4.3 19.1 - - + -
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Residues in contact with TYR 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ASN* 5.1 5.9 + - + -
215G TYR* 3.9 24.6 + + - -
244G TYR* 3.5 26.1 + + - -
262G PHE* 4.4 5.8 - + + -
263G LEU* 1.3 74.3 - - - +
265G PRO* 1.3 77.5 - - + +
267G ASN* 3.8 20.1 + - - -
270G SER* 5.5 0.3 + - - -
273G GLY* 4.9 1.2 - - - -
274G LYS* 3.4 46.4 + - + +
275G LEU* 3.8 40.8 - - + +
314G ALA 4.4 1.9 - - - +
315G PRO* 3.6 4.9 - - - +
316G VAL* 2.8 32.4 + - + +
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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
------------------------------------------------------------
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