Contacts of the strand formed by residues 451 - 470 (chain A) in PDB entry 5C58
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 HIS 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A SER* 3.5 15.6 - - - -
447A LEU* 3.5 6.0 + - + +
448A ALA* 2.8 36.4 + - + +
449A PRO 4.0 9.9 - - - -
450A GLY* 1.3 75.9 - - - +
452A ASP* 1.3 63.6 + - - +
453A PHE* 4.1 7.9 + - + -
495A TYR* 3.0 35.6 + - + +
497A TYR* 3.2 30.4 - + - -
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Residues in contact with ASP 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 2.6 28.2 + - - +
449A PRO* 5.6 0.2 - - - +
450A GLY* 4.3 14.1 + - - +
451A HIS* 1.3 77.9 + - - +
453A PHE* 1.3 64.6 + - - +
494A THR* 3.8 0.7 - - - +
495A TYR* 3.6 3.4 - - - -
496A ASP* 3.0 45.3 + - + +
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Residues in contact with PHE 453 (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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443A SER 4.9 0.2 - - - -
444A ARG* 3.8 6.4 - - - +
445A PHE* 2.9 56.2 + + + +
447A LEU* 3.5 42.2 - - + -
451A HIS* 4.2 8.7 - - + -
452A ASP* 1.3 79.6 - - - +
454A ARG* 1.3 64.8 + - - +
493A LEU* 4.1 25.8 - - + -
494A THR* 3.2 11.0 - - - -
495A TYR* 3.3 39.9 - + + -
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Residues in contact with ARG 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 5.1 8.5 + - - -
442A THR* 5.1 8.3 - - - +
443A SER 3.7 4.3 - - - +
444A ARG* 3.6 39.3 - - + +
453A PHE* 1.3 77.6 - - - +
455A ALA* 1.3 62.8 + - - +
456A ASN* 3.8 7.6 + - + +
492A ASN 3.9 0.3 - - - +
493A LEU* 3.6 4.9 - - - +
494A THR* 2.9 66.6 + - + +
504A GLU* 5.5 3.2 + - - -
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Residues in contact with ALA 455 (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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441A ASN 3.7 1.4 - - - +
442A THR* 3.2 4.2 - - - -
443A SER* 2.8 55.2 + - - +
445A PHE* 4.4 10.2 - - + -
454A ARG* 1.3 72.3 - - - +
456A ASN* 1.3 60.0 + - - +
457A TYR* 3.9 12.1 - - + -
492A ASN 3.8 5.6 - - - +
493A LEU* 3.9 14.1 - - + -
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Residues in contact with ASN 456 (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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215A GLY* 5.3 5.7 - - - -
216A MET 5.4 0.4 - - - +
440A GLN* 3.1 29.7 + - - +
441A ASN 3.2 14.0 - - - +
442A THR* 3.3 17.7 - - + +
454A ARG* 3.8 7.5 + - + +
455A ALA* 1.3 71.0 - - - +
457A TYR* 1.3 59.8 + - - +
490A PHE* 3.6 16.8 - - - -
492A ASN* 2.8 59.7 + - - +
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Residues in contact with TYR 457 (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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397A TRP* 4.5 3.8 + - - +
440A GLN* 3.4 0.8 - - - -
441A ASN* 2.8 61.4 + - + +
443A SER* 3.5 26.7 + - - -
455A ALA* 3.9 17.7 - - + -
456A ASN* 1.3 75.1 - - - +
458A GLY* 1.3 59.5 + - - +
490A PHE* 3.7 13.9 - - - +
491A ALA* 4.2 12.3 - - + -
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Residues in contact with GLY 458 (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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439A ALA 3.2 14.1 - - - -
440A GLN* 3.8 3.1 - - - -
457A TYR* 1.3 77.5 - - - +
459A LEU* 1.3 63.0 + - - -
489A LEU* 3.4 8.9 - - - +
490A PHE* 3.0 43.8 + - - +
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Residues in contact with LEU 459 (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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216A MET* 3.6 7.1 - - - +
437A ALA* 5.3 4.5 - - + +
438A GLN* 4.9 2.0 - - - -
439A ALA* 2.7 57.0 + - + +
458A GLY* 1.3 75.9 - - - +
460A GLU* 1.3 68.8 + - - +
461A PHE* 6.3 0.4 - - + -
488A SER 3.3 17.3 - - - +
489A LEU* 4.1 15.7 - - + +
490A PHE* 4.0 5.1 - - - -
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Residues in contact with GLU 460 (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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179A GLY 5.0 0.2 - - - +
181A ARG* 2.8 37.9 + - - -
216A MET* 3.2 26.3 - - + +
217A GLY* 3.1 25.2 - - - -
218A SER 4.0 0.5 + - - -
219A ALA* 4.7 3.4 + - + +
405A TYR* 4.4 1.8 + - - +
437A ALA 3.4 12.1 - - - +
438A GLN* 3.4 18.5 + - + -
459A LEU* 1.3 80.9 - - - +
461A PHE* 1.3 71.2 + - - +
462A TYR* 4.4 4.8 - - + -
486A VAL 3.9 1.3 - - - +
487A ALA* 3.7 0.3 - - - -
488A SER* 2.8 45.2 + - - +
490A PHE* 5.8 0.9 - - + -
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Residues in contact with PHE 461 (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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435A TYR* 4.6 4.7 - - + -
436A GLY* 3.3 2.3 - - - -
437A ALA* 2.8 50.7 + - + +
459A LEU* 6.3 0.7 - - + -
460A GLU* 1.3 77.4 - - - +
462A TYR* 1.3 61.7 + - - +
463A TYR* 4.1 24.9 - + + -
485A SER* 3.6 33.9 - - - -
486A VAL 3.7 16.4 - - - -
487A ALA* 4.0 17.7 - - + -
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Residues in contact with TYR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 3.3 39.5 + - - -
183A ASN* 3.4 31.0 - - - -
219A ALA* 3.8 10.1 - - + -
220A GLY* 3.9 17.2 + - - -
405A TYR* 3.9 18.2 - - - +
434A THR* 4.2 5.6 - - + -
435A TYR 3.2 7.9 - - - +
460A GLU* 4.4 6.5 - - + +
461A PHE* 1.3 80.8 - - - +
463A TYR* 1.3 60.3 + - - +
464A ASP* 3.8 15.3 - - - -
484A ARG* 3.9 19.3 + - - -
485A SER* 3.3 18.2 - - - -
486A VAL* 3.3 38.3 + - + +
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Residues in contact with TYR 463 (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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433A ARG 3.3 5.0 - - - +
434A THR* 4.5 0.2 - - - -
435A TYR* 2.8 52.9 + + + +
461A PHE* 4.1 17.3 - + + -
462A TYR* 1.3 72.8 - - - +
464A ASP* 1.3 73.9 + - - +
465A LYS* 4.0 21.2 + - + -
483A ASN* 3.1 26.9 + - + +
485A SER* 3.5 26.9 - - - -
515A ARG* 2.9 32.7 + - - -
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Residues in contact with ASP 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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183A ASN* 2.8 43.4 + - - +
432A LEU* 4.0 14.1 - - + -
433A ARG 3.5 3.4 - - - -
434A THR* 3.2 18.4 + - - +
462A TYR* 3.8 10.9 - - - -
463A TYR* 1.3 77.5 - - - +
465A LYS* 1.3 58.8 + - - +
483A ASN* 3.2 9.1 - - - +
484A ARG* 3.1 48.1 + - - +
593A ILE* 4.3 11.2 - - + -
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Residues in contact with LYS 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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431A ARG 3.7 1.4 - - - +
432A LEU* 3.3 6.6 - - - +
433A ARG* 3.0 67.8 + - + +
435A TYR* 4.4 16.2 - - + +
463A TYR* 4.0 24.7 + - + -
464A ASP* 1.3 76.6 - - - +
466A ALA* 1.3 64.0 + - - +
467A THR* 4.0 6.2 + - - -
482A GLY 3.6 10.9 + - - +
483A ASN* 4.7 5.0 - - + +
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Residues in contact with ALA 466 (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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431A ARG 3.7 2.9 - - - +
432A LEU* 3.7 17.2 - - + +
464A ASP 4.3 0.2 - - - -
465A LYS* 1.3 72.7 - - - +
467A THR* 1.3 66.5 + - - +
479A THR* 6.0 1.1 - - - -
480A PRO 4.2 6.7 - - - +
481A ALA* 3.3 12.8 - - - +
482A GLY 2.9 37.6 + - - +
593A ILE* 4.2 15.4 - - + +
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Residues in contact with THR 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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429A ARG* 5.7 0.3 - - - +
430A THR* 3.9 0.9 - - - -
431A ARG* 3.0 53.2 + - - +
433A ARG* 3.3 31.5 + - - +
465A LYS* 4.8 9.6 - - + -
466A ALA* 1.3 79.2 - - - +
468A SER* 1.3 62.6 + - - +
469A ASP* 5.8 0.2 - - - -
480A PRO 4.6 1.3 - - - -
481A ALA* 4.2 4.9 - - + -
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Residues in contact with SER 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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428A THR* 4.9 0.7 + - - -
429A ARG 3.3 13.9 + - - -
430A THR* 4.0 8.4 - - - +
467A THR* 1.3 76.8 - - - +
469A ASP* 1.3 68.7 + - - +
475A MET 3.9 15.9 + - - -
476A GLU* 4.0 19.6 + - - +
479A THR* 3.5 25.6 + - - -
480A PRO 3.8 7.0 - - - -
481A ALA* 4.4 6.7 - - - +
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Residues in contact with ASP 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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427A ALA 4.5 0.2 - - - +
428A THR* 4.0 1.0 + - - -
429A ARG* 2.9 66.6 + - - +
467A THR 5.8 0.3 - - - -
468A SER* 1.3 80.0 + - - +
470A SER* 1.3 68.4 + - - +
476A GLU* 4.1 13.9 - - + +
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Residues in contact with SER 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TYR* 4.1 3.1 - - - -
427A ALA 3.3 16.5 + - - -
428A THR* 3.7 11.4 - - - -
469A ASP* 1.3 82.4 + - - +
471A SER* 1.3 61.5 + - - +
472A ARG* 3.1 19.4 + - - +
475A MET* 3.6 31.7 - - - +
476A GLU* 3.0 28.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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