Contacts of the strand formed by residues 483 - 496 (chain B) in PDB entry 2PY5
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 TRP 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B PHE* 3.7 32.8 - - + -
249B ASP 3.7 3.4 - - - -
250B VAL* 3.5 34.0 - - + +
440B THR* 3.5 22.3 + - + +
441B THR* 3.8 15.7 - - - -
444B ALA* 3.5 29.8 - - + +
458B ASP 3.4 19.3 - - - -
460B ILE* 3.8 31.9 - - + -
471B ILE* 5.4 5.2 - - + -
474B ILE* 2.8 43.4 + - + +
475B VAL* 3.1 21.9 - - + +
476B ASP 2.9 23.8 + - - -
481B GLY 4.9 3.0 + - - -
482B TYR* 1.3 73.4 - - - +
484B ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 484 (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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248B PHE* 3.1 6.5 - - - -
249B ASP* 2.8 38.8 + - + +
251B ASN* 3.4 21.5 - - - +
476B ASP 3.4 13.4 + - - +
477B PRO* 3.9 12.6 - - + +
482B TYR 3.7 1.4 + - - -
483B TRP* 1.3 73.7 - - - +
485B HIS* 1.3 63.6 + - - +
486B GLU* 3.1 5.7 + - - +
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Residues in contact with HIS 485 (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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246B MET* 3.3 31.5 - - + +
247B VAL 3.6 5.8 - - - -
248B PHE* 3.8 18.5 - + + -
465B THR 4.9 2.5 - - - -
467B ILE* 4.7 12.5 - - + +
475B VAL* 4.4 8.8 - - + +
477B PRO* 5.4 1.6 - - - +
483B TRP 3.8 3.2 + - - -
484B ALA* 1.3 71.0 - - - +
486B GLU* 1.3 59.7 + - - +
487B SER 3.1 18.9 + - - -
488B THR* 2.9 21.0 + - - -
517B SER* 6.1 0.7 - - - -
9003B EDO 3.2 43.7 + - - -
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Residues in contact with GLU 486 (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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247B VAL* 2.9 23.9 + - + +
249B ASP* 2.9 47.1 - - + +
484B ALA* 3.1 10.1 + - + +
485B HIS* 1.3 73.7 - - - +
487B SER* 1.3 68.1 + - - +
515B GLU* 3.5 21.8 - - - +
9003B EDO 3.7 6.1 + - - -
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Residues in contact with SER 487 (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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246B MET* 3.4 0.7 - - - -
247B VAL* 2.9 45.4 + - - +
485B HIS* 3.1 12.5 + - - -
486B GLU* 1.3 86.6 + - - +
488B THR* 1.3 63.6 + - - +
489B PHE* 5.5 0.9 - - - -
502B GLN* 4.7 1.6 + - - -
504B ILE* 4.0 31.3 - - - +
515B GLU* 4.2 7.9 - - - -
9003B EDO 3.8 7.6 - - - -
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Residues in contact with THR 488 (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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245B GLY 3.2 17.3 - - - +
246B MET* 4.2 1.7 - - + +
465B THR* 3.5 31.0 + - + +
485B HIS* 2.9 17.5 + - - -
487B SER* 1.3 72.1 - - - +
489B PHE* 1.3 61.2 + - - +
504B ILE* 3.5 7.9 - - - +
505B TYR* 3.0 39.9 + - + +
515B GLU* 5.6 0.2 - - - +
516B GLY 4.0 8.7 + - - -
517B SER* 4.8 1.4 - - - -
518B PRO* 3.8 9.1 - - + +
9003B EDO 2.7 26.4 + - - -
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Residues in contact with PHE 489 (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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242B ILE* 4.1 5.2 - - + -
243B GLY 3.3 22.0 - - - -
244B GLU* 3.2 7.2 - - - +
245B GLY* 2.8 52.9 + - - +
246B MET* 3.7 19.3 - - - -
247B VAL* 4.3 7.6 - - + -
453B ILE* 3.9 22.4 - - + -
461B HIS* 5.1 0.2 - - + -
487B SER* 5.5 0.9 - - - -
488B THR* 1.3 76.4 - - - +
490B LYS* 1.3 59.0 + - - +
491B ARG 3.7 13.9 - - - +
492B ALA* 3.6 13.5 - - + -
494B TYR* 3.7 8.3 - - - -
502B GLN* 3.5 37.9 - - + -
503B ASP 3.2 18.6 - - - +
504B ILE* 4.1 4.7 - - + +
505B TYR* 3.7 8.3 - - - -
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Residues in contact with LYS 490 (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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243B GLY* 3.1 19.5 - - - -
244B GLU* 3.2 6.9 + - + +
489B PHE* 1.3 72.8 - - - +
491B ARG* 1.3 66.6 + - + +
503B ASP* 2.7 23.0 + - + +
505B TYR* 3.6 35.2 - - + +
521B TYR* 4.5 9.8 + - - +
524B ILE* 3.6 32.2 - - + +
8007B EDO 4.7 0.5 + - - -
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Residues in contact with ARG 491 (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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241B GLU* 5.5 0.4 - - - -
242B ILE 3.1 15.7 - - - +
243B GLY 3.3 3.8 - - - -
489B PHE* 3.6 6.5 - - - -
490B LYS* 1.3 86.8 - - + +
492B ALA* 1.3 65.5 + - - +
502B GLN* 3.6 0.9 - - - -
503B ASP* 2.9 54.4 + - + +
543B PHE* 3.6 46.7 - - + +
544B GLU* 5.4 2.2 + - - -
8007B EDO 3.3 35.7 + - - +
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Residues in contact with ALA 492 (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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241B GLU* 3.8 4.9 - - - +
242B ILE* 2.9 34.6 + - + +
489B PHE* 3.6 23.3 - - + -
491B ARG* 1.3 77.4 - - - +
493B LYS* 1.3 64.8 + - - +
494B TYR* 3.6 19.3 - - + -
501B ILE 3.2 15.5 - - - +
502B GLN* 4.0 5.8 - - + -
543B PHE* 3.8 7.8 - - - -
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Residues in contact with LYS 493 (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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239B GLU 4.5 8.1 - - - +
240B LYS 3.6 22.2 - - - +
241B GLU* 3.4 29.9 + - - +
492B ALA* 1.3 75.3 - - - +
494B TYR* 1.3 62.4 + - - +
495B LEU* 3.8 18.6 - - + -
500B TYR* 3.2 3.8 - - - -
501B ILE* 2.9 43.9 + - + +
543B PHE* 2.7 27.8 + - - -
544B GLU 4.8 2.6 + - - -
546B PHE* 2.6 38.1 + - + +
547B LYS* 4.9 5.6 - - + +
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Residues in contact with TYR 494 (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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233B LEU* 3.5 23.6 - - + -
237B PHE 3.6 6.3 + - - +
238B LYS* 3.9 1.2 - - - -
239B GLU* 2.7 32.1 + - - -
240B LYS 4.3 3.4 + - - -
242B ILE* 3.7 20.2 - - + -
453B ILE* 3.8 17.9 - - + -
454B TYR* 3.8 30.1 - + + -
461B HIS* 2.7 38.4 + - + +
489B PHE* 3.7 5.7 - - - -
492B ALA* 3.6 21.1 - - + -
493B LYS* 1.3 76.0 - - - +
495B LEU* 1.3 56.5 + - - +
496B ARG 5.1 1.6 - - - +
499B THR 3.8 3.8 - - - +
500B TYR* 3.4 29.8 - + + -
502B GLN* 2.9 16.7 + - - -
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Residues in contact with LEU 495 (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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233B LEU* 3.8 2.5 - - - -
238B LYS* 3.4 11.4 - - - +
239B GLU* 4.0 21.3 - - + +
493B LYS* 3.8 27.1 - - + -
494B TYR* 1.3 75.9 - - - +
496B ARG* 1.3 90.9 + - + +
499B THR* 2.9 15.1 + - + +
546B PHE* 3.5 35.0 - - + -
547B LYS* 3.6 37.9 - - - +
548B VAL* 3.9 8.7 - - + +
574B ILE* 3.9 13.9 - - + -
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Residues in contact with ARG 496 (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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233B LEU* 3.7 15.7 - - - +
238B LYS* 3.5 22.6 - - - +
239B GLU* 2.9 25.7 + - - -
454B TYR* 4.6 3.1 - - - -
494B TYR* 5.0 2.1 - - - +
495B LEU* 1.3 97.5 + - + +
497B GLN* 1.3 73.5 + - - +
498B LYS 3.3 0.9 + - - -
499B THR* 3.0 27.2 + - - +
500B TYR* 5.3 0.5 - - - +
548B VAL* 3.4 21.2 - - - +
574B ILE* 4.9 6.1 - - + -
575B LYS* 3.0 40.4 + - - +
8002B EDO 3.9 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