Contacts of the strand formed by residues 264 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A GLN* 3.2 33.0 + - + +
263A GLU* 1.3 75.6 - - - +
265A THR* 1.3 61.4 - - - +
266A LEU 3.9 0.2 - - - -
292A ALA* 4.1 24.7 - - + -
293A THR* 3.8 11.2 - - - +
294A LEU* 3.3 35.9 - - + +
384A LYS* 5.5 8.3 - - + +
495A GLN* 4.7 2.7 - - - -
506A ILE* 3.7 8.1 - - - +
507A TYR* 2.9 44.1 + + + +
509A GLU* 3.7 43.7 + - + -
258B ALA* 5.0 10.1 - - + -
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Residues in contact with THR 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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264A TYR* 1.3 73.5 - - - +
266A LEU* 1.3 60.8 + - - +
267A LEU* 3.8 4.9 + - + +
291A ALA 3.7 1.0 - - - +
292A ALA* 3.2 2.6 - - - -
293A THR* 2.8 51.1 + - - +
294A LEU* 5.6 0.2 - - - -
296A PRO* 4.0 11.7 - - + +
495A GLN* 2.4 40.5 + - + +
498A MSE 4.2 20.0 - - + -
499A ILE* 5.7 1.1 - - + -
504A ALA* 4.0 22.4 - - + -
505A LEU 3.7 4.9 - - - +
506A ILE* 5.1 0.2 - - - +
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Residues in contact with LEU 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 TYR 3.9 0.4 + - - -
265A THR* 1.3 70.4 - - - +
267A LEU* 1.3 63.3 + - - +
268A LYS* 4.5 1.8 - - + +
290A VAL* 3.5 19.7 - - + -
291A ALA 3.3 28.7 - - - +
292A ALA* 3.7 5.4 - - + +
324A PHE* 5.2 2.5 - - + -
334A MSE 3.3 26.7 - - + -
339A PHE* 3.7 21.5 - - + -
386A THR* 3.6 22.7 - - + -
504A ALA* 3.1 6.0 - - - -
505A LEU* 2.7 47.6 + - + +
507A TYR* 3.8 16.4 - - + -
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Residues in contact with LEU 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 THR* 4.1 15.3 - - + +
266A LEU* 1.3 76.3 - - - +
268A LYS* 1.3 59.5 + - - +
269A LEU* 3.9 11.6 + - + -
290A VAL* 3.4 10.0 - - - +
291A ALA* 2.7 34.6 + - + +
293A THR* 4.0 27.6 - - + -
299A MSE 3.7 29.4 - - + -
302A GLN* 3.2 29.2 - - - +
365A PRO* 4.3 10.8 - - + +
390A THR* 5.0 2.9 - - - +
498A MSE 3.9 19.5 - - + -
503A ASP 3.9 3.8 - - - +
504A ALA* 4.0 1.8 - - - -
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Residues in contact with LYS 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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266A LEU* 4.5 2.0 - - + +
267A LEU* 1.3 74.9 - - - +
269A LEU* 1.3 63.4 + - - +
270A LYS* 3.7 3.2 + - - +
288A PHE* 3.7 27.4 - - + -
289A LEU 3.9 3.4 - - - -
290A VAL* 4.5 4.7 - - + -
320A ASN* 5.8 0.8 - - - +
322A ASP* 4.2 15.2 + - - -
324A PHE* 3.5 36.2 - - + -
363A SER 4.4 1.9 - - - +
365A PRO* 3.8 17.2 - - - +
502A GLY* 3.0 34.3 + - - -
503A ASP* 2.7 24.2 + - - +
504A ALA* 4.4 6.3 - - - +
505A LEU* 5.0 15.9 - - + +
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Residues in contact with LEU 269 (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 LEU* 4.2 15.9 - - + +
268A LYS* 1.3 72.1 - - - +
270A LYS* 1.3 62.4 + - - +
271A VAL 3.5 0.5 + - - -
288A PHE* 3.2 2.8 - - - -
289A LEU* 2.8 51.6 + - + +
291A ALA* 5.0 14.6 - - + +
302A GLN* 4.3 14.6 - - - +
305A CYS* 3.3 32.3 - - - -
362A LEU* 3.9 16.8 - - + +
363A SER 4.2 2.9 - - - -
364A ALA* 3.3 28.5 - - + -
365A PRO* 3.6 13.9 - - + -
372A ILE* 5.2 1.3 - - + -
388A VAL* 5.0 0.4 - - + -
390A THR* 5.9 2.2 - - - -
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Residues in contact with LYS 270 (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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268A LYS 3.7 0.8 + - - +
269A LEU* 1.3 71.1 - - - +
271A VAL* 1.3 76.4 + - - +
272A LEU* 3.2 13.5 + - + +
275A TYR* 5.7 2.5 - - - -
286A ASN* 3.0 34.4 + - - +
287A ILE 3.8 4.3 - - - +
288A PHE* 3.5 31.6 - - + -
362A LEU* 3.4 4.0 - - - -
363A SER* 3.2 45.7 + - - +
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Residues in contact with VAL 271 (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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270A LYS* 1.3 79.1 - - - +
272A LEU* 1.3 63.7 + - - +
275A TYR* 3.3 36.8 + - + -
276A PRO* 4.3 16.8 - - + -
279A LEU* 4.4 9.6 - - + -
287A ILE* 2.9 41.4 + - + +
289A LEU* 4.1 22.4 - - + +
325A ILE* 4.5 2.5 - - + -
360A ALA* 4.6 7.4 - - + -
361A SER 3.6 9.0 - - - +
362A LEU* 3.7 13.5 - - + -
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Residues in contact with LEU 272 (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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270A LYS* 3.7 23.1 - - + +
271A VAL* 1.3 78.9 - - - +
273A GLU* 1.3 70.3 + - - +
274A PRO 3.4 14.0 - - - +
275A TYR* 3.5 6.5 - - - -
361A SER* 2.9 25.0 + - - +
362A LEU* 3.7 8.7 - - - +
363A SER* 3.5 36.6 - - - +
370A LYS 5.0 0.2 - - - +
371A VAL* 4.1 21.3 - - + -
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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