Contacts of the strand formed by residues 265 - 269 (chain D) in PDB entry 2YWB
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 LEU 265 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D VAL* 3.7 26.5 - - + -
237D LEU* 4.9 1.6 - - - -
238D ALA* 3.3 21.5 - - + +
240D PHE* 4.0 13.0 - - + -
254D VAL* 5.1 0.4 - - + -
255D GLU* 3.4 43.5 - - + +
258D LEU* 4.6 12.3 - - + -
259D ARG* 3.0 38.3 + - + +
263D VAL* 3.0 13.5 + - + +
264D ASN* 1.3 75.7 + - - +
266D LEU* 1.3 61.8 + - - +
267D VAL* 4.0 12.3 - - + -
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D LEU* 4.1 17.5 - - + -
238D ALA 3.0 11.7 + - - +
239D VAL* 3.5 3.9 - - + +
240D PHE* 2.9 24.4 + - - +
259D ARG* 4.2 1.6 - - - +
264D ASN 4.1 0.2 + - - -
265D LEU* 1.3 75.1 - - - +
267D VAL* 1.3 75.6 + - - +
268D VAL* 4.0 4.9 + - + -
302D VAL* 3.5 36.6 - - + -
306D ARG* 4.0 35.4 - - - +
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D PHE* 3.4 22.2 - - + +
242D ASP* 4.6 1.1 - - + -
251D ARG* 3.8 28.7 - - - +
255D GLU* 3.9 22.2 - - + +
259D ARG* 3.9 20.0 - - - +
265D LEU* 4.0 16.8 - - + -
266D LEU* 1.3 87.4 - - - +
268D VAL* 1.3 68.9 + - - +
269D ASP* 4.0 1.7 + - - +
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D VAL* 3.8 19.7 - - + -
240D PHE 2.8 12.6 + - - +
241D VAL* 4.1 12.3 - - + -
242D ASP* 2.8 33.4 + - - +
266D LEU* 4.7 7.2 - - + -
267D VAL* 1.3 76.8 - - - +
269D ASP* 1.3 70.4 + - - +
270D ALA* 3.3 14.2 + - + -
298D ALA* 4.9 9.6 - - + -
302D VAL* 3.7 29.8 - - + -
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Residues in contact with ASP 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ASP* 4.3 6.3 - - - -
267D VAL* 4.0 3.4 + - + +
268D VAL* 1.3 74.4 - - - +
270D ALA* 1.3 57.2 + - - +
271D LYS* 3.3 35.1 + - - +
272D GLU* 4.6 2.4 + - - +
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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