Contacts of the strand formed by residues 264 - 272 (chain B) in PDB entry 2WFD
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 TYR 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ALA* 5.1 10.3 - - + -
262B GLN* 3.2 36.9 + - + +
263B GLU* 1.3 75.1 - - - +
265B THR* 1.3 62.3 + - - +
266B LEU 4.0 0.2 - - - -
292B ALA* 4.1 23.1 - - + -
293B THR* 3.9 11.4 - - - +
294B LEU* 3.2 37.3 - - + +
384B LYS* 5.5 8.5 - - + +
495B GLN* 4.7 2.7 - - - -
506B ILE* 3.7 8.1 - - - +
507B TYR* 2.8 44.2 + + + +
509B GLU* 3.7 40.1 + - + -
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Residues in contact with THR 265 (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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264B TYR* 1.3 71.4 - - - +
266B LEU* 1.3 62.1 + - - +
267B LEU* 3.7 4.2 + - + -
291B ALA 3.7 1.0 - - - +
292B ALA* 3.3 3.0 - - - -
293B THR* 2.8 50.9 + - - +
294B LEU* 5.7 0.2 - - - -
296B PRO* 4.1 11.6 - - + +
495B GLN* 2.3 43.3 + - + +
498B MSE 4.3 18.4 - - + -
499B ILE* 5.7 1.1 - - + -
504B ALA* 3.9 24.0 - - + -
505B LEU 3.7 5.6 - - - +
506B ILE* 5.1 0.2 - - - +
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Residues in contact with LEU 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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264B TYR 3.9 1.0 + - - -
265B THR* 1.3 70.3 - - - +
267B LEU* 1.3 62.7 + - - +
268B LYS* 4.6 1.8 - - + +
290B VAL* 3.4 21.8 - - + -
291B ALA 3.4 27.4 - - - +
292B ALA* 3.7 5.6 - - + +
324B PHE* 5.1 2.5 - - + -
334B MSE 3.4 25.4 - - + -
339B PHE* 3.7 22.2 - - + -
386B THR* 3.6 23.6 - - + -
504B ALA* 3.0 6.0 - - - -
505B LEU* 2.7 48.0 + - + +
507B TYR* 3.8 15.5 - - + -
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Residues in contact with LEU 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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265B THR* 4.0 14.1 - - + +
266B LEU* 1.3 75.4 - - - +
268B LYS* 1.3 60.4 + - - +
269B LEU* 3.9 13.5 + - + +
290B VAL* 3.4 18.7 - - - +
291B ALA* 2.8 25.7 + - + +
293B THR* 4.0 27.8 - - + -
299B MSE 3.6 29.6 - - + -
302B GLN* 3.3 29.6 - - - +
365B PRO* 4.4 9.2 - - + +
390B THR* 5.0 2.7 - - - +
498B MSE 4.0 20.4 - - + -
503B ASP 3.9 3.8 - - - +
504B ALA* 3.9 1.8 - - - -
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Residues in contact with LYS 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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266B LEU* 4.6 2.2 - - + +
267B LEU* 1.3 74.6 - - - +
269B LEU* 1.3 65.1 + - - +
270B LYS* 3.7 2.4 + - - +
288B PHE* 3.7 27.4 - - + -
289B LEU 3.9 3.6 - - - -
290B VAL* 4.5 4.3 - - + -
320B ASN* 5.7 1.0 + - - +
322B ASP* 4.0 16.4 + - - -
324B PHE* 3.5 37.7 - - + -
363B SER 4.4 1.6 - - - +
365B PRO* 3.7 18.2 - - - +
502B GLY* 3.0 33.5 + - - -
503B ASP* 2.7 23.5 + - - +
504B ALA* 4.5 7.0 - - - +
505B LEU* 5.0 14.9 - - + +
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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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267B LEU* 4.2 14.4 - - + +
268B LYS* 1.3 72.2 - - - +
270B LYS* 1.3 62.6 + - - +
271B VAL 3.5 0.5 + - - -
288B PHE* 3.2 2.3 - - - -
289B LEU* 2.8 47.4 + - + +
290B VAL 5.3 0.2 - - - +
291B ALA* 5.0 14.1 - - + +
302B GLN* 4.3 15.9 - - - +
305B CYS* 3.3 31.9 - - - -
362B LEU* 3.9 19.8 - - + +
363B SER 4.2 2.2 - - - -
364B ALA* 3.2 31.4 - - + -
365B PRO* 3.5 14.4 - - + -
372B ILE* 5.2 1.1 - - + -
388B VAL* 5.1 0.4 - - + -
390B THR* 5.9 2.2 - - - -
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Residues in contact with LYS 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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268B LYS 3.7 1.6 + - - -
269B LEU* 1.3 71.0 - - - +
271B VAL* 1.3 75.7 + - - +
272B LEU* 3.3 13.5 + - + +
275B TYR* 5.8 2.0 - - - -
286B ASN* 3.0 33.3 + - - +
287B ILE 3.7 8.5 - - - +
288B PHE* 3.5 29.1 - - + -
362B LEU* 3.4 4.1 - - - -
363B SER* 3.1 45.7 + - - +
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Residues in contact with VAL 271 (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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269B LEU 3.5 0.2 + - - -
270B LYS* 1.3 79.6 - - - +
272B LEU* 1.3 64.0 + - - +
275B TYR* 3.4 37.6 + - + -
276B PRO* 4.4 16.6 - - + -
279B LEU* 4.5 9.4 - - + -
287B ILE* 2.9 41.0 + - + +
289B LEU* 4.2 22.2 - - + +
325B ILE* 4.5 2.5 - - + -
360B ALA* 4.7 7.0 - - + -
361B SER 3.6 9.2 - - - +
362B LEU* 3.6 13.2 - - + -
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Residues in contact with LEU 272 (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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270B LYS* 3.7 21.5 - - + +
271B VAL* 1.3 78.0 - - - +
273B GLU* 1.3 70.5 + - - +
274B PRO 3.4 13.5 - - - +
275B TYR* 3.5 6.3 - - - -
361B SER* 2.9 25.5 + - - +
362B LEU* 3.7 9.2 - - - +
363B SER* 3.5 38.1 - - - +
371B VAL* 4.1 21.1 - - + -
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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