Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 2COJ
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 MET 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A TYR* 5.3 1.3 - - + -
194A PHE* 4.0 23.1 - - + -
244A GLN* 3.6 31.2 - - + +
257A GLU* 3.4 9.6 + - - +
258A VAL* 2.9 41.4 + - + +
259A GLY 3.4 0.2 - - - -
260A THR* 1.3 81.9 - - - +
262A ASN* 1.3 59.5 + - - +
330A GLY* 4.1 10.1 - - - -
331A SER 3.1 24.5 - - - +
332A GLY* 4.5 0.4 - - - -
335A CYS* 3.7 26.0 - - - -
338A CYS* 4.0 20.0 - - - -
410A PLP 3.8 2.9 + - - -
420A GBN 3.6 18.6 - - - +
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Residues in contact with ASN 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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257A GLU* 3.7 9.8 - - - +
261A MET* 1.3 70.9 - - - +
263A LEU* 1.3 61.2 + - - +
264A PHE* 4.3 3.3 - - + -
278A THR* 5.1 1.6 - - - +
285A ILE* 3.3 19.1 - - - +
286A LEU 2.9 18.3 + - - +
288A GLY* 3.3 34.4 - - - +
291A ARG* 3.5 23.9 - - + +
329A PHE 3.7 0.5 - - - +
330A GLY* 2.9 8.4 - - - -
331A SER* 2.8 43.3 + - - +
410A PLP 3.7 11.7 + - - -
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Residues in contact with LEU 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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246A LEU* 3.9 20.2 - - + -
255A ILE* 3.6 55.6 - - + -
256A THR 3.7 18.7 + - - +
257A GLU* 4.2 1.8 - - - +
258A VAL* 3.8 19.1 - - + -
261A MET 3.7 0.6 + - - -
262A ASN* 1.3 73.5 - - - +
264A PHE* 1.3 76.2 + - - +
265A LEU* 4.3 3.1 - - + +
278A THR* 2.8 23.2 + - - -
279A PRO* 3.3 9.5 - - + +
311A LEU* 4.1 13.0 - - + -
328A MET* 4.9 9.4 - - + -
329A PHE 3.8 2.7 - - - -
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Residues in contact with PHE 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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262A ASN* 4.3 3.1 - - + -
263A LEU* 1.3 78.3 - - - +
265A LEU* 1.3 61.3 + - - +
266A TYR 4.1 1.1 - - - -
276A LEU* 3.7 27.1 - - + -
277A ALA 3.3 2.9 - - - -
278A THR* 3.6 29.8 - - + -
291A ARG* 3.9 27.8 - - + -
294A ILE* 3.7 33.0 - - + -
295A LEU* 4.3 6.1 - - + -
328A MET* 3.3 9.0 - - - +
329A PHE* 2.8 71.2 + + + +
331A SER* 3.4 27.8 - - - -
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Residues in contact with LEU 265 (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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255A ILE* 5.2 3.6 - - + -
263A LEU* 4.6 4.5 - - + -
264A PHE* 1.3 73.9 - - - +
266A TYR* 1.3 60.4 + - - +
267A TRP* 3.5 50.4 + - + +
275A GLU 3.5 0.9 - - - +
276A LEU* 4.3 1.1 - - - -
277A ALA* 2.8 30.2 + - + +
311A LEU* 4.0 29.6 - - + -
315A ASP* 6.3 0.2 - - + -
316A LEU* 3.9 17.5 - - + -
325A VAL* 4.1 14.1 - - + -
327A GLU 3.6 14.6 - - - +
328A MET* 3.9 26.5 - - + -
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Residues in contact with TYR 266 (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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264A PHE 4.1 0.8 - - - -
265A LEU* 1.3 67.3 - - - +
267A TRP* 1.3 65.6 + - - +
274A GLU* 2.6 47.4 + - + -
275A GLU 3.4 16.2 - - - -
276A LEU* 4.3 5.5 - - + +
304A PHE* 4.0 22.5 - + - -
325A VAL* 4.3 0.5 - - - +
326A ARG* 2.9 44.4 + - + +
327A GLU* 2.8 51.4 + - + +
329A PHE* 4.9 2.0 - - + -
360A LYS* 5.9 2.2 - - + -
361A LEU* 3.7 32.1 - - + -
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Residues in contact with TRP 267 (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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265A LEU* 3.7 33.0 - - + -
266A TYR* 1.3 78.0 - - - +
268A ILE* 1.3 67.3 + - - +
269A ASN* 3.9 13.8 - - - +
270A GLU* 4.2 6.1 - - - -
273A GLU 3.3 0.5 - - - +
274A GLU* 3.4 3.0 - - - +
275A GLU* 2.6 75.1 + - + -
277A ALA* 4.2 5.5 - - - +
309A ARG* 4.1 23.3 - - - -
311A LEU* 4.2 9.2 - - + -
315A ASP* 3.4 30.7 - - + -
316A LEU* 4.8 0.4 - - - -
319A ALA* 3.4 35.7 - - + -
324A ARG* 3.1 29.6 - - - +
325A VAL* 4.0 8.1 - - + -
326A ARG* 4.3 6.1 - - - +
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Residues in contact with ILE 268 (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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267A TRP* 1.3 83.3 - - - +
269A ASN* 1.3 65.5 + - - +
272A GLY* 3.5 25.1 - - - +
273A GLU 3.2 10.3 - - - +
274A GLU* 4.8 10.8 - - + +
324A ARG* 2.7 64.8 + - + +
326A ARG* 3.2 44.6 - - + +
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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