Contacts of the strand formed by residues 453 - 471 (chain A) in PDB entry 3M8D
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A GLY 4.5 4.9 - - - -
400A GLN* 3.7 41.4 - - + +
405A TYR* 3.0 50.3 + + + +
407A ASN* 3.1 23.2 + - - +
410A LEU* 4.2 3.4 - - + -
444A ILE* 3.7 28.0 - - + -
445A ASP 3.2 9.0 - - - -
446A TYR* 3.3 35.9 - - + +
452A LYS* 1.3 77.1 - - - +
454A TYR* 1.3 65.5 + - - +
701A CNC 4.5 16.3 + - - +
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Residues in contact with TYR 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 3.9 16.8 - - - -
410A LEU* 3.9 7.9 - - - -
444A ILE* 4.3 1.3 - - - -
445A ASP* 2.8 33.3 + - - +
447A ASP* 4.2 11.9 - - + -
450A THR* 3.8 34.6 - - + +
452A LYS* 3.5 24.4 - - + +
453A TYR* 1.3 81.5 - - - +
455A ASN* 1.3 67.6 + - - +
456A GLU* 3.3 18.7 + - + +
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Residues in contact with ASN 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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409A ASN 4.6 0.5 - - - +
410A LEU* 3.4 14.2 - - - +
411A ASP* 2.8 59.3 + - + +
412A PRO 3.9 3.0 + - - -
442A ASP* 3.0 40.7 + - + +
443A LEU 3.7 4.3 - - - -
444A ILE* 3.6 10.7 - - - +
454A TYR* 1.3 73.9 - - - +
456A GLU* 1.3 61.8 + - - +
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Residues in contact with GLU 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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442A ASP* 3.9 6.2 - - - +
443A LEU 3.0 7.4 + - - -
445A ASP* 3.8 26.0 - - + +
446A TYR 4.5 0.5 - - - +
447A ASP* 3.7 30.6 - - - +
454A TYR* 3.9 14.9 - - + +
455A ASN* 1.3 75.1 - - - +
457A GLY* 1.3 69.7 + - - +
458A LYS* 4.5 9.7 + - - +
490A ILE* 5.2 5.4 - - - +
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Residues in contact with GLY 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A SER* 3.6 1.4 - - - -
442A ASP 3.3 11.6 + - - -
443A LEU* 3.0 38.2 + - - +
445A ASP* 3.1 22.2 + - - -
456A GLU* 1.3 78.5 - - - +
458A LYS* 1.3 62.8 + - - +
488A ASN* 6.4 0.2 - - - -
490A ILE* 5.3 2.9 - - - -
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Residues in contact with LYS 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL 3.5 11.9 - - - +
441A SER* 4.1 16.2 - - - -
442A ASP 5.0 0.4 - - - +
443A LEU* 3.8 6.9 - - - +
456A GLU 4.5 6.5 + - - +
457A GLY* 1.3 79.4 - - - +
459A ALA* 1.3 63.5 + - - +
488A ASN* 3.5 13.3 + - - +
489A ALA* 3.0 31.2 + - + -
490A ILE* 4.1 30.2 - - + +
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Residues in contact with ALA 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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438A ASN 4.5 0.4 - - - -
439A ASP* 3.6 4.3 - - - +
440A VAL* 3.0 46.5 + - + +
443A LEU* 4.0 14.4 - - + -
458A LYS* 1.3 77.0 - - - +
460A ARG* 1.3 63.7 + - - +
461A ILE* 4.2 2.5 - - + -
487A ARG 3.2 12.8 - - - +
488A ASN* 4.9 0.7 - - - -
489A ALA* 3.9 5.4 - - - +
495A LEU* 4.3 18.2 - - + -
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Residues in contact with ARG 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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437A ARG* 3.0 34.9 - - - +
438A ASN 3.7 2.5 - - - -
439A ASP* 3.4 18.2 - - - +
459A ALA* 1.3 75.4 - - - +
461A ILE* 1.3 66.6 - - - +
462A LYS* 4.2 24.9 - - + +
485A ASP* 3.4 7.8 + - - +
487A ARG* 3.0 49.0 + - - +
489A ALA* 4.0 24.6 + - + +
492A ASP* 3.3 24.0 + - - -
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Residues in contact with ILE 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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69A ARG 3.3 21.5 - - - +
70A GLY 3.3 31.4 - - - +
71A THR* 3.6 17.9 - - + +
436A TYR* 4.0 12.5 - - + -
437A ARG* 3.4 6.4 - - - +
438A ASN* 2.9 45.9 + - + +
440A VAL* 4.6 9.9 - - + -
459A ALA* 5.0 4.0 - - + -
460A ARG* 1.3 79.7 - - - +
462A LYS* 1.3 65.3 + - - +
463A GLY 4.2 0.2 - - - -
484A VAL* 4.0 20.0 - - + -
485A ASP 3.3 4.0 - - - +
486A ALA* 4.1 8.7 - - + -
487A ARG 5.1 0.2 - - - +
495A LEU* 5.1 3.6 - - + -
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Residues in contact with LYS 462 (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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436A TYR 3.5 3.8 - - - -
437A ARG* 3.5 30.1 - - + +
460A ARG* 4.2 27.7 - - + +
461A ILE* 1.3 81.2 - - - +
463A GLY* 1.3 58.5 + - - +
483A TYR* 3.7 5.7 - - - -
485A ASP* 2.9 50.9 + - + +
706A C8E 4.1 43.3 - - - +
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Residues in contact with GLY 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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435A GLY* 3.3 1.7 - - - -
436A TYR* 2.8 59.9 + - - +
462A LYS* 1.3 75.0 - - - +
464A VAL* 1.3 69.9 + - - +
483A TYR* 3.0 13.7 - - - -
484A VAL* 4.4 0.4 - - - -
706A C8E 3.5 4.1 + - - +
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 4.3 18.4 - - + -
434A SER 3.2 12.8 - - - +
435A GLY* 4.7 2.5 - - - -
436A TYR* 4.0 3.7 - - - -
463A GLY* 1.3 81.7 - - - +
465A GLU* 1.4 65.6 + - - +
466A ALA* 4.8 1.1 - - + +
481A TYR* 3.9 4.4 - - + +
482A ASP* 3.4 3.6 - - - +
483A TYR* 2.7 48.1 + - + +
704A C8E 4.2 30.7 - - - +
706A C8E 4.1 37.7 - - + +
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Residues in contact with GLU 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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25A PRO* 3.8 8.6 - - - +
50A PRO* 3.6 14.1 - - + +
51A GLY* 5.2 0.6 + - - -
69A ARG* 2.7 38.6 + - - +
111A ARG* 2.7 43.4 + - - -
432A ARG* 3.9 5.1 - - - +
433A ILE* 3.3 3.6 - - - +
434A SER* 2.8 43.0 + - - -
436A TYR* 4.7 4.4 - - + -
464A VAL* 1.4 73.5 - - - +
466A ALA* 1.3 61.7 + - - +
467A THR* 4.0 14.6 + - + +
480A SER* 5.8 0.4 - - - -
481A TYR 3.5 4.5 - - - +
482A ASP* 3.9 16.6 - - - +
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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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432A ARG 3.4 6.1 - - - +
433A ILE* 4.3 7.6 - - + -
464A VAL* 5.3 0.9 - - + -
465A GLU* 1.3 74.3 - - - +
467A THR* 1.3 62.7 + - - +
480A SER* 3.2 4.3 - - - -
481A TYR* 2.8 43.5 + - + +
704A C8E 3.4 51.2 - - + +
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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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50A PRO* 3.8 22.2 - - + -
111A ARG* 5.3 0.2 - - - +
431A TRP* 3.2 4.4 - - - +
432A ARG* 2.8 49.3 + - - +
465A GLU* 4.0 16.0 + - + +
466A ALA* 1.3 80.2 - - - +
468A ALA* 1.3 67.4 + - - +
479A VAL 3.4 5.4 - - - +
480A SER* 3.7 18.2 - - - -
704A C8E 3.7 5.7 - - - +
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Residues in contact with ALA 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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429A VAL* 4.2 11.7 - - + -
430A ASN 3.1 12.3 - - - +
431A TRP* 4.1 6.1 - - + -
467A THR* 1.3 79.5 - - - +
469A ASN* 1.3 64.2 - - - +
470A PHE* 4.7 6.1 - - + -
477A HIS 4.2 0.2 - - - +
478A THR* 3.7 1.9 - - - +
479A VAL* 2.9 46.6 + - + +
704A C8E 3.8 16.2 - - - +
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Residues in contact with ASN 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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428A GLY 4.2 1.0 - - - +
429A VAL* 3.7 0.9 - - - -
430A ASN* 3.0 51.2 + - - +
468A ALA* 1.3 76.5 - - - +
470A PHE* 1.3 65.4 + - - +
476A THR* 5.8 2.2 - - + -
477A HIS 3.1 15.5 - - - +
478A THR* 4.2 16.1 - - + +
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Residues in contact with PHE 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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428A GLY 3.9 10.1 - - - +
429A VAL* 3.4 38.4 - - + -
468A ALA* 4.7 2.9 - - + -
469A ASN* 1.3 83.7 + - - +
471A ASP* 1.3 67.3 + - - +
472A THR* 3.8 17.7 - - + -
476A THR* 4.1 1.5 - - - +
477A HIS* 2.8 74.8 + + + +
479A VAL* 4.8 16.6 - - + -
505A TYR* 5.5 2.9 - + - -
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Residues in contact with ASP 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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428A GLY 4.9 1.8 + - - -
470A PHE* 1.3 80.0 - - - +
472A THR* 1.3 68.5 + - - +
473A GLY 4.3 10.3 - - - +
475A LEU 3.2 6.3 - - - +
476A THR* 2.5 39.7 + - - +
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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