Contacts of the strand formed by residues 257 - 264 (chain A) in PDB entry 2OF2
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 GLY 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ALA 3.6 0.3 - - - -
254A GLY* 2.7 39.3 + - - -
255A GLN 3.5 0.6 - - - -
256A PHE* 1.3 81.2 - - - +
258A GLU* 1.3 63.2 + - - -
259A VAL* 5.9 0.2 - - - -
274A SER* 3.2 10.8 - - - -
276A LYS* 3.8 12.7 - - - +
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A ARG* 3.0 27.1 + - - -
252A GLY 3.3 8.5 - - - +
253A ALA* 4.0 14.3 - - + +
254A GLY 4.8 0.7 - - - +
257A GLY* 1.3 79.8 - - - +
259A VAL* 1.3 65.0 + - - +
260A TRP* 2.7 41.0 + - + +
272A VAL 3.6 0.6 - - - +
273A LYS* 3.4 4.2 - - - +
274A SER* 2.8 43.1 + - - +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A 547 3.8 59.9 - - + +
250A ARG* 3.6 1.9 - - - +
251A LEU* 2.7 39.0 + - + -
252A GLY* 2.9 14.7 + - - +
258A GLU* 1.3 80.7 - - - +
260A TRP* 1.3 58.8 + - - +
271A ALA* 4.9 2.7 - - + -
272A VAL 3.2 13.9 - - - +
273A LYS* 4.2 20.9 - - + +
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Residues in contact with TRP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 4.1 44.3 - - + +
248A VAL 4.0 12.8 - - - -
249A GLU* 3.2 15.0 - - - -
250A ARG* 3.3 44.5 - - + +
251A LEU* 4.0 7.3 - - - +
258A GLU* 2.7 42.3 + - + +
259A VAL* 1.3 81.0 - - - +
261A MET* 1.3 64.8 + - - +
271A ALA* 3.4 5.2 - - - +
272A VAL* 2.8 38.2 + - + +
274A SER* 4.7 4.6 + - - -
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Residues in contact with MET 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 3.9 0.9 - - - -
248A VAL* 2.8 48.3 + - + -
249A GLU* 2.5 40.1 + - + +
251A LEU* 3.8 20.1 - - + +
260A TRP* 1.3 74.3 - - - +
262A GLY* 1.3 73.4 + - - +
263A TYR* 4.2 14.4 - - + +
269A LYS* 3.8 23.3 - - - +
270A VAL 3.6 5.4 - - - +
272A VAL* 5.6 0.2 - - - -
318A TYR* 3.7 31.4 - - + +
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LYS 3.1 14.8 - - - -
247A LEU* 4.3 2.0 - - - -
248A VAL* 3.9 3.4 - - - -
260A TRP 4.0 0.8 + - - -
261A MET* 1.3 83.4 - - - +
263A TYR* 1.3 67.1 + - - -
269A LYS* 3.4 6.4 - - - -
270A VAL* 2.8 39.5 + - - +
272A VAL* 5.1 4.6 - - - +
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Residues in contact with TYR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A THR 3.5 4.7 - - - +
245A LEU* 3.5 2.3 - - - +
246A LYS* 2.9 43.6 + - + +
248A VAL* 3.7 26.2 - - + -
261A MET* 4.2 14.4 - - + +
262A GLY* 1.3 74.3 - - - -
264A TYR* 1.3 59.8 + - - +
266A GLY* 3.7 31.8 + - - +
267A HIS 4.0 7.6 - - - -
268A THR 3.3 5.2 - - - -
269A LYS* 3.8 51.0 + - + +
270A VAL* 3.9 4.5 - - - +
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Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 4.2 24.9 - - + +
241A PRO* 5.9 0.2 - - - +
244A THR* 3.2 37.5 - - + +
245A LEU* 3.9 13.5 - - + -
263A TYR* 1.3 69.7 - - - +
265A ASN* 1.3 94.6 + - + +
266A GLY 3.1 1.6 + - - -
267A HIS* 5.1 0.2 - - - +
268A THR* 2.7 45.9 + - + +
270A VAL* 3.9 17.4 - - + +
304A TYR* 5.8 2.0 - + + -
305A ALA* 5.7 2.7 - - + -
315A ILE* 5.9 2.0 - - + -
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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