Contacts of the strand formed by residues 463 - 476 (chain A) in PDB entry 4RYL
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 SER 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A SER* 3.7 15.5 - - - -
430A ILE* 3.3 28.6 - - - +
461A ARG* 2.9 21.0 + - - -
462A THR* 1.3 77.3 - - - +
464A MET* 1.3 60.6 + - - +
509A SER* 3.6 4.4 - - - -
510A VAL* 2.9 31.4 + - - +
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Residues in contact with MET 464 (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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388A SER* 2.5 33.4 + - - +
390A VAL* 3.8 28.0 - - + -
463A SER* 1.3 73.2 - - - +
465A CYS* 1.3 59.2 + - - +
466A THR* 3.5 2.9 + - + +
507A PRO* 3.6 25.6 - - + +
508A PHE* 3.4 29.4 - - - -
509A SER* 3.9 21.5 - - - +
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Residues in contact with CYS 465 (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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386A ALA* 4.3 12.1 - - - -
387A VAL 3.4 7.9 - - - -
430A ILE* 4.0 12.0 - - + +
463A SER 3.9 2.6 + - - -
464A MET* 1.3 69.9 - - - +
466A THR* 1.3 60.6 + - - +
467A ALA 3.7 18.8 - - - -
468A ILE* 4.2 12.3 - - - -
504A LEU* 3.9 17.6 - - - +
507A PRO* 3.1 24.8 - - - +
508A PHE* 2.9 35.6 + - + +
510A VAL* 4.4 6.5 - - + -
516A LEU* 4.9 3.1 - - - -
538A LEU* 4.9 0.2 - - - -
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Residues in contact with THR 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL 2.9 5.3 + - - -
389A ASP 2.9 31.8 + - - +
390A VAL* 4.0 14.8 - - + +
393A HIS* 3.7 17.5 - - + -
464A MET* 3.8 10.8 - - + +
465A CYS* 1.3 77.5 - - - +
467A ALA* 1.3 62.4 + - - +
504A LEU* 3.0 27.3 + - - +
507A PRO* 4.0 18.6 - - + -
601A 3ZG 2.6 33.2 + - - -
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Residues in contact with ALA 467 (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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387A VAL* 3.0 31.9 + - + +
465A CYS* 3.7 2.7 - - - -
466A THR* 1.3 80.8 + - - +
468A ILE* 1.3 70.4 + - - +
501A VAL* 3.8 16.4 - - + -
502A PHE 3.4 14.6 - - - +
503A LEU* 4.1 3.1 - - - -
504A LEU* 3.9 6.4 - - - +
601A 3ZG 3.6 26.2 - - + +
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Residues in contact with ILE 468 (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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384A LEU* 4.1 31.0 - - + -
385A VAL 3.6 6.1 - - - +
386A ALA* 3.9 18.6 - - + -
387A VAL* 4.3 0.9 - - - -
455A PHE* 5.5 2.2 - - + -
457A LEU* 3.9 15.5 - - + -
465A CYS* 4.2 4.9 - - - -
467A ALA* 1.3 84.1 - - - +
469A ALA* 1.3 68.8 + - - +
501A VAL* 3.7 0.6 - - - -
502A PHE* 2.8 41.9 + - + +
504A LEU* 4.5 3.6 - - + -
516A LEU* 5.3 0.4 - - + -
536A LEU* 3.9 26.5 - - + -
538A LEU* 3.7 32.8 - - + -
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Residues in contact with ALA 469 (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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384A LEU* 3.2 8.3 - - - +
385A VAL* 2.8 46.3 + - + +
387A VAL* 3.8 11.3 - - + +
424A LEU* 3.5 32.8 - - + -
468A ILE* 1.3 76.2 - - - +
470A GLY* 1.3 59.9 + - - +
471A TYR* 5.8 0.4 - - + -
499A GLN* 5.0 3.1 - - + -
500A THR 3.2 10.1 - - - +
501A VAL* 4.4 2.5 - - + +
502A PHE* 4.8 0.4 - - - -
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Residues in contact with GLY 470 (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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351A PHE* 3.8 23.5 - - - -
383A SER 3.2 10.3 - - - -
384A LEU* 4.0 2.2 - - - -
468A ILE 4.3 0.2 + - - -
469A ALA* 1.3 76.2 - - - +
471A TYR* 1.3 66.0 + - - +
499A GLN* 3.8 4.9 - - - +
500A THR* 2.7 37.4 + - - -
502A PHE* 4.4 2.1 - - - -
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Residues in contact with TYR 471 (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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351A PHE* 4.1 6.0 - - - +
382A ILE* 3.4 8.3 - - - +
383A SER* 2.9 51.0 + - - +
385A VAL* 4.1 23.8 - - + -
429A LEU* 5.9 0.2 - - + -
433A PRO* 3.1 29.3 - - - +
469A ALA* 5.8 0.4 - - + -
470A GLY* 1.3 78.2 - - - +
472A PHE* 1.3 68.9 + - - +
473A ASP* 3.6 22.2 - - - -
487A SER* 3.8 3.1 - - - -
488A THR* 3.7 20.6 - - - +
489A GLY* 3.4 23.1 - - - -
490A PRO* 3.8 22.4 - - + -
498A LYS 5.0 1.1 - - - +
499A GLN* 4.3 4.9 - - + +
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Residues in contact with PHE 472 (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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348A MET* 4.0 7.9 - - + -
349A GLY 3.4 19.7 - - - -
351A PHE* 4.0 7.6 - - - -
352A LEU* 3.2 45.5 - - + -
381A THR 3.0 17.9 - - - +
382A ILE* 4.3 2.0 - - + +
383A SER* 4.9 0.4 - - - +
471A TYR* 1.3 80.6 - - - +
473A ASP* 1.3 69.2 + - - +
474A ILE* 3.6 29.6 - - + -
486A PHE* 4.7 0.7 - + - -
488A THR* 2.8 44.0 + - + +
497A TRP* 3.5 44.9 - + + -
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Residues in contact with ASP 473 (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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380A CYS* 3.3 5.2 - - - -
381A THR* 2.9 46.3 + - - +
383A SER* 5.1 3.1 + - - -
471A TYR* 3.6 14.9 - - - -
472A PHE* 1.3 82.3 - - - +
474A ILE* 1.3 65.1 + - - +
475A TYR* 3.8 22.3 + - + +
485A VAL* 5.0 2.4 - - + +
486A PHE 3.4 7.6 - - - +
487A SER* 2.7 32.7 + - - -
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Residues in contact with ILE 474 (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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348A MET* 3.7 25.1 - - + -
352A LEU* 4.0 1.6 - - + -
377A PRO* 3.4 30.7 - - + -
379A ILE 3.8 2.0 - - - +
380A CYS* 3.9 17.0 - - - -
472A PHE* 3.6 28.9 - - + -
473A ASP* 1.3 78.3 - - - +
475A TYR* 1.3 63.7 + - - +
476A PHE* 4.0 6.8 - - + -
484A VAL 4.0 0.3 - - - +
485A VAL* 3.2 6.8 - - - +
486A PHE* 2.8 74.6 + - + +
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Residues in contact with TYR 475 (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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377A PRO* 3.4 4.0 - - - +
378A ASP* 3.2 23.7 + - - +
379A ILE* 2.8 45.0 + - + +
380A CYS 4.7 0.2 - - - -
381A THR* 4.1 19.6 + - + +
473A ASP* 3.8 32.3 + - + -
474A ILE* 1.3 76.6 - - - +
476A PHE* 1.3 66.0 + - - +
477A GLU* 4.9 12.6 - - + -
484A VAL 3.5 4.0 - - - -
485A VAL* 3.6 29.5 - - + +
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Residues in contact with PHE 476 (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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259A SER* 4.5 9.6 - - - -
260A TYR* 3.9 37.2 - + - -
263A PHE* 3.3 53.2 - + + -
344A ILE* 6.4 0.2 - - + -
376A TYR* 3.9 3.1 - - + -
377A PRO* 3.6 35.0 - - + -
378A ASP* 3.3 5.2 - - - -
474A ILE* 4.0 15.9 - - + -
475A TYR* 1.3 74.3 - - - +
477A GLU* 1.3 59.2 + - - +
480A CYS* 3.9 3.7 - - - -
483A ARG* 3.5 10.4 - - - +
484A VAL* 2.8 54.0 + - + +
486A PHE* 4.5 11.7 - + - -
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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