Contacts of the strand formed by residues 265 - 270 (chain B) in PDB entry 2O61
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 GLU 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.5 18.2 + - - -
199A VAL 5.4 1.0 - - - +
200A ASN* 4.9 6.6 + - - +
254B ASP* 3.9 4.1 - - - +
255B ARG* 3.8 14.9 + - - +
263B GLY 3.8 2.4 + - - -
264B GLU* 1.3 73.1 - - - +
266B ILE* 1.3 71.9 + - - +
267B TYR* 3.8 16.0 - - + -
310B VAL* 3.8 20.4 - - + +
311B PHE 3.1 11.4 - - - +
312B LYS* 3.8 25.6 - - + +
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Residues in contact with ILE 266 (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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253B MET* 4.5 14.6 - - + -
254B ASP* 4.0 6.7 - - + -
255B ARG* 3.2 44.6 - - + +
257B ALA 5.1 0.7 - - - +
264B GLU* 4.1 1.3 - - + +
265B GLU* 1.3 81.9 - - - +
267B TYR* 1.3 78.6 + - - +
268B LEU 4.0 0.2 - - - -
309B ILE 3.8 0.2 - - - +
310B VAL* 3.2 6.9 - - - +
311B PHE* 2.6 66.3 + - + +
313B THR* 3.7 29.6 - - + -
345B PHE* 5.0 6.5 - - + -
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Residues in contact with TYR 267 (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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198A ARG* 3.1 32.1 + - - +
199A VAL 3.2 17.8 + - - -
200A ASN* 3.8 17.9 - - - -
213A PHE* 3.6 43.3 - + + -
215A LEU* 3.7 31.0 - - + -
252B ARG 4.0 0.3 - - - +
253B MET* 3.3 2.3 - - - -
254B ASP* 2.8 47.2 + - + +
265B GLU* 3.8 15.9 - - - -
266B ILE* 1.3 82.5 - - - +
268B LEU* 1.3 60.0 + - - +
269B LEU* 5.4 1.6 - - + -
309B ILE 3.9 2.5 - - - -
310B VAL* 3.4 29.2 - - + -
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Residues in contact with LEU 268 (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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250B ILE* 4.1 12.6 - - + -
252B ARG 3.5 4.5 - - - +
253B MET* 4.0 27.1 - - + -
267B TYR* 1.3 74.5 - - - +
269B LEU* 1.3 78.4 + - - +
270B CYS* 3.7 20.2 - - + -
280B ILE* 4.2 8.5 - - + -
308B ALA* 3.3 6.9 - - - +
309B ILE* 2.9 48.1 + - + +
311B PHE* 4.1 24.2 - - + -
331B LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 269 (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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213A PHE* 4.2 14.6 - - + -
215A LEU* 4.6 4.5 - - + -
243A ASP 5.8 0.2 - - - +
245A HIS* 3.8 32.1 - - + +
249A ALA* 3.9 18.4 - - + -
251A VAL* 4.0 27.6 - - + -
250B ILE 3.6 1.0 - - - -
251B VAL* 2.6 34.3 + - + -
252B ARG* 2.6 42.3 + - + +
267B TYR* 5.4 1.6 - - + -
268B LEU* 1.3 83.2 - - - +
270B CYS* 1.3 55.7 + - - +
307B PHE 3.8 1.3 - - - -
308B ALA* 3.8 17.7 - - + -
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Residues in contact with CYS 270 (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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245A HIS* 2.7 27.7 + - - -
249B LYS 3.3 15.3 - - - +
251B VAL* 3.9 3.4 - - - +
268B LEU* 3.7 12.3 - - + -
269B LEU* 1.3 75.5 - - - +
271B ASP* 1.3 75.8 + - - +
273B VAL* 4.0 20.2 - - - -
307B PHE* 3.1 32.6 + - - +
308B ALA 4.3 1.8 - - - -
309B ILE* 4.4 8.7 - - - -
331B LEU* 3.5 19.1 - - + -
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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