Contacts of the strand formed by residues 483 - 496 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A PHE* 3.7 33.9 - - + -
249A ASP 3.7 2.5 - - - -
250A VAL* 3.5 32.8 - - + +
440A THR* 3.6 22.3 + - + +
441A THR* 3.8 16.8 - - - -
444A ALA* 3.5 25.1 - - + +
458A ASP 3.4 20.2 - - - -
460A ILE* 3.9 28.3 - - + -
471A ILE* 5.3 5.2 - - + -
474A ILE* 2.8 47.7 + - + +
475A VAL* 3.1 18.2 - - + +
476A ASP 2.8 23.9 + - - -
481A GLY 4.9 3.1 + - - -
482A TYR* 1.3 73.4 - - - +
484A ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 484 (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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248A PHE* 3.1 6.9 - - - -
249A ASP* 2.8 39.2 + - + +
251A ASN* 3.5 21.3 - - - +
476A ASP 3.4 12.9 + - - +
477A PRO* 4.0 12.8 - - + +
482A TYR 3.7 1.6 + - - -
483A TRP* 1.3 71.5 - - - +
485A HIS* 1.3 64.3 + - - +
486A GLU* 3.1 6.8 + - + +
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Residues in contact with HIS 485 (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 MET* 3.3 31.1 - - + +
247A VAL 3.6 4.7 - - - -
248A PHE* 3.7 19.6 - + + -
465A THR 4.8 2.9 - - - -
467A ILE* 4.7 12.4 - - + +
475A VAL* 4.5 10.1 - - + +
476A ASP 5.4 0.8 - - - -
477A PRO* 5.4 1.6 - - - +
483A TRP 3.8 2.6 + - - -
484A ALA* 1.3 69.9 - - - +
486A GLU* 1.3 59.0 + - - +
487A SER 3.1 20.9 + - - -
488A THR* 2.9 28.7 + - - -
517A SER* 6.2 0.7 - - - -
9012A EDO 3.1 33.4 + - - -
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Residues in contact with GLU 486 (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 VAL* 2.8 33.1 + - + +
249A ASP* 2.8 35.7 - - + +
459A SER* 5.0 1.4 + - - -
484A ALA* 3.1 10.5 + - + +
485A HIS* 1.3 73.6 - - - +
487A SER* 1.3 63.2 + - - +
515A GLU* 3.4 18.7 - - - +
9012A EDO 3.5 5.9 + - - -
9014A EDO 4.3 25.7 - - - -
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Residues in contact with SER 487 (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 MET* 3.4 0.5 - - - -
247A VAL* 2.9 45.4 + - - +
485A HIS* 3.1 13.2 + - - -
486A GLU* 1.3 82.1 - - - +
488A THR* 1.3 64.2 - - - +
489A PHE* 5.4 1.0 - - - -
502A GLN* 4.8 1.0 + - - -
504A ILE* 4.0 26.1 - - - +
515A GLU* 4.2 3.8 - - - -
9012A EDO 3.8 7.6 - - - -
9014A EDO 4.1 18.0 - - - -
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Residues in contact with THR 488 (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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245A GLY 3.2 18.6 - - - +
246A MET* 4.1 2.1 - - + +
465A THR* 3.6 29.5 + - + -
485A HIS* 2.9 29.1 + - - -
487A SER* 1.3 72.4 - - - +
489A PHE* 1.3 61.8 + - - +
504A ILE* 3.6 6.5 - - - +
505A TYR* 3.0 34.6 + - + +
516A GLY 4.3 8.0 + - - -
517A SER* 4.9 0.3 - - - -
518A PRO* 3.8 22.4 - - + +
9012A EDO 4.1 6.1 - - - -
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Residues in contact with PHE 489 (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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242A ILE* 4.1 4.7 - - + -
243A GLY 3.3 23.3 - - - -
244A GLU* 3.2 7.8 - - - +
245A GLY* 2.8 60.0 + - - +
246A MET* 3.7 7.9 - - - -
247A VAL* 4.3 9.9 - - + -
453A ILE* 4.0 16.2 - - + -
461A HIS* 5.0 0.7 - - + -
462A LEU 4.5 0.2 - - - -
487A SER* 5.4 1.1 - - - -
488A THR* 1.3 76.9 - - - +
490A LYS* 1.3 58.4 + - - +
491A ARG 3.6 16.4 - - - +
492A ALA* 3.5 14.1 - - + -
494A TYR* 3.7 13.2 - - - -
502A GLN* 3.5 37.7 - - + -
503A ASP 3.2 17.7 - - - +
504A ILE* 4.1 3.8 - - + +
505A TYR* 3.7 8.3 - - - -
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Residues in contact with LYS 490 (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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243A GLY* 3.1 20.1 - - - -
244A GLU* 3.3 11.2 + - + +
489A PHE* 1.3 72.4 - - - +
491A ARG* 1.3 61.0 + - + +
503A ASP* 2.8 16.5 + - + +
505A TYR* 3.1 39.2 - - + +
524A ILE* 4.4 12.1 - - + -
8010A EDO 2.6 45.8 + - - +
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Residues in contact with ARG 491 (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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242A ILE 3.1 16.8 - - - +
243A GLY* 3.3 5.4 - - - -
489A PHE* 3.5 8.0 - - - -
490A LYS* 1.3 79.4 - - + +
492A ALA* 1.3 65.6 + - - +
503A ASP* 2.8 56.6 + - + +
543A PHE* 3.5 46.6 - - + +
8010A EDO 3.6 37.9 - - - +
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Residues in contact with ALA 492 (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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241A GLU* 3.8 1.9 - - - -
242A ILE* 2.9 34.8 + - + +
489A PHE* 3.5 23.1 - - + -
491A ARG* 1.3 78.6 - - - +
493A LYS* 1.3 62.5 + - - +
494A TYR* 3.7 18.4 - - + -
501A ILE 3.2 14.8 - - - +
502A GLN* 3.9 6.3 - - + -
543A PHE* 3.9 9.2 - - - -
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Residues in contact with LYS 493 (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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239A GLU 4.5 13.8 + - - +
240A LYS 3.7 14.1 - - - +
241A GLU* 4.4 25.6 + - - +
492A ALA* 1.3 76.0 - - - +
494A TYR* 1.3 65.0 + - - +
495A LEU* 3.9 20.2 - - + -
500A TYR* 3.2 3.3 - - - -
501A ILE* 2.9 46.8 + - + +
543A PHE* 4.4 19.2 + - + +
544A GLU 5.7 1.4 + - - -
546A PHE* 3.5 33.2 + - + +
547A LYS* 5.1 5.5 - - - +
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Residues in contact with TYR 494 (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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233A LEU* 3.6 20.9 - - + -
237A PHE 3.6 6.1 + - - +
238A LYS* 3.7 1.4 - - - -
239A GLU* 2.7 32.4 + - - -
240A LYS 4.3 2.8 + - - -
242A ILE* 3.6 21.8 - - + -
453A ILE* 3.7 20.6 - - + -
454A TYR* 3.8 28.3 - + + -
461A HIS* 2.7 38.6 + - - +
489A PHE* 3.7 6.3 - + - -
492A ALA* 3.7 20.6 - - + -
493A LYS* 1.3 76.6 - - - +
495A LEU* 1.3 56.2 + - - +
496A ARG 5.5 0.4 - - - -
499A THR 3.8 4.5 - - - +
500A TYR* 3.3 30.1 - + + -
502A GLN* 2.9 16.7 + - - -
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Residues in contact with LEU 495 (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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233A LEU* 3.8 2.5 - - - -
238A LYS* 3.6 13.2 - - - +
239A GLU* 4.0 21.5 - - + +
493A LYS* 3.9 28.3 - - + -
494A TYR* 1.3 73.9 - - - +
496A ARG* 1.3 90.3 + - + +
499A THR* 2.9 14.4 + - + +
546A PHE* 3.5 34.3 - - + -
547A LYS* 3.7 37.2 - - + +
548A VAL* 3.9 8.1 - - + +
574A ILE* 3.9 16.6 - - + -
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Residues in contact with ARG 496 (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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233A LEU* 3.7 15.2 - - - +
238A LYS* 3.1 26.7 - - - +
239A GLU* 3.0 23.6 + - - -
454A TYR* 4.5 4.0 - - - -
494A TYR* 5.0 1.4 - - - +
495A LEU* 1.3 105.7 + - + +
497A GLN* 1.3 73.4 + - - +
498A LYS 3.3 0.3 + - - -
499A THR* 3.0 28.9 + - + +
500A TYR* 5.3 0.3 - - - +
548A VAL* 3.4 25.4 - - - +
574A ILE* 5.0 3.6 - - + -
575A LYS* 2.9 41.7 + - - +
1Y G 4.3 10.3 - - - -
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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