Contacts of the strand formed by residues 458 - 470 (chain A) in PDB entry 1FA0
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 LYS 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A ARG* 3.6 4.9 - - - +
370A GLY 3.5 28.2 + - - +
412A SER* 4.8 2.7 - - - +
413A TYR 3.5 13.5 - - - +
414A CYS* 3.9 13.0 - - - -
415A CYS* 4.2 4.1 - - - +
443A VAL* 3.4 35.2 - - + -
448A LYS 5.7 0.4 + - - -
453A ILE* 3.0 28.3 + - - -
454A LYS* 4.5 7.3 + - - +
456A ALA 3.0 12.4 + - - +
457A PRO* 1.3 79.2 - - - +
459A ALA* 1.3 61.9 + - - +
460A TYR* 3.5 35.7 - - + +
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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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368A THR 3.1 6.3 - - - -
369A ARG* 4.3 0.7 - - - +
411A SER 4.2 0.2 - - - +
412A SER* 3.2 3.7 - - - -
413A TYR* 3.0 34.6 + - + +
415A CYS* 3.5 29.6 - - + -
421A TYR* 4.0 18.4 - - + -
424A ILE* 4.5 12.1 - - + -
458A LYS* 1.3 75.2 - - - +
460A TYR* 1.3 62.5 + - - +
461A LEU* 5.4 0.9 - - - +
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Residues in contact with TYR 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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367A TYR* 3.1 7.1 - - - +
368A THR* 2.5 43.9 + - + +
370A GLY 3.8 16.1 + - - -
371A SER 4.2 7.0 - - - -
372A ASP* 3.8 35.0 + - - +
375A HIS* 3.2 42.6 - + + -
411A SER 3.8 4.9 - - - +
412A SER* 3.6 22.9 - - - -
421A TYR* 5.4 0.2 - - - -
458A LYS* 3.5 31.9 - - + +
459A ALA* 1.3 79.3 - - - +
461A LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 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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365A THR* 4.0 6.3 - - + -
366A ALA 2.9 11.2 - - - +
367A TYR* 3.6 32.1 - - + -
375A HIS* 3.7 1.8 - - - -
409A PHE 3.5 3.3 - - - +
410A GLU* 3.8 1.0 - - - +
411A SER* 2.8 58.0 + - - +
413A TYR* 4.4 18.8 - - + -
424A ILE* 4.6 12.3 - - + +
459A ALA 5.7 0.4 - - - +
460A TYR* 1.3 79.5 - - - +
462A SER* 1.3 61.5 - - - +
463A THR* 4.1 15.7 - - - +
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Residues in contact with SER 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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364A ILE 3.7 1.2 - - - +
365A THR* 3.3 2.5 - - - -
366A ALA* 2.8 30.7 + - - -
375A HIS* 2.8 18.6 + - - -
379A SER* 3.5 21.2 + - - -
408A PRO* 4.7 4.9 - - - -
409A PHE 3.5 4.9 - - - -
410A GLU* 2.4 30.4 + - - -
461A LEU* 1.3 72.7 - - - +
463A THR* 1.3 61.0 + - - +
464A MET* 4.0 13.2 - - - +
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Residues in contact with THR 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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363A GLU* 3.4 27.4 - - + -
364A ILE 3.2 2.5 - - - +
365A THR* 3.1 30.1 + - - +
408A PRO* 3.1 5.6 - - - +
409A PHE* 2.6 54.9 + - - +
461A LEU* 4.1 9.4 - - - +
462A SER* 1.3 74.5 - - - +
464A MET* 1.3 65.6 + - - +
465A TYR* 3.8 14.4 - - + +
520A GLU* 5.0 4.5 + - - +
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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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228A PHE* 4.5 11.7 - - + -
362A LEU 3.4 1.4 - - - +
363A GLU* 3.5 3.3 - - - +
364A ILE* 2.7 54.4 + - + +
366A ALA* 5.1 2.5 - - + -
379A SER* 5.0 1.8 - - - +
382A VAL* 4.3 23.1 - - + -
383A GLU* 3.8 35.9 - - + +
386A VAL* 4.0 15.9 - - + -
405A PHE 5.9 1.6 - - - +
407A LYS 5.3 0.7 - - - -
408A PRO* 3.4 29.2 - - + -
409A PHE* 5.5 0.2 - - - -
462A SER* 4.0 26.5 - - - +
463A THR* 1.3 71.6 - - - +
465A TYR* 1.3 67.3 + - - +
466A ILE* 6.4 0.4 - - + -
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Residues in contact with TYR 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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354A PHE* 4.0 9.2 - - + -
355A PHE* 3.6 32.1 - + + -
361A TYR* 4.3 16.4 - - + -
362A LEU 3.2 4.7 - - - -
363A GLU* 2.5 53.1 + - + -
386A VAL* 5.6 0.9 - - - +
404A PRO* 3.6 1.4 - - - +
405A PHE* 3.0 33.2 + + + +
409A PHE* 3.9 20.4 - + - -
463A THR* 3.8 14.3 - - + +
464A MET* 1.3 76.5 - - - +
466A ILE* 1.3 68.4 + - - +
467A GLY 4.2 0.2 - - - -
512A VAL* 5.5 2.0 - - + -
517A LEU* 4.2 15.3 - - + -
518A PRO* 3.6 14.3 - - + +
520A GLU* 4.2 7.8 + - - -
521A VAL* 3.8 19.4 - - + +
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Residues in contact with ILE 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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354A PHE* 4.2 0.9 - - - -
361A TYR* 3.4 4.7 - - - -
362A LEU* 2.9 40.9 + - + +
364A ILE* 4.1 14.6 - - + -
386A VAL* 4.1 22.2 - - + -
389A LEU* 3.9 34.3 - - + -
390A VAL* 4.2 8.3 - - + -
393A LEU* 4.5 3.6 - - + -
402A ALA* 3.9 27.8 - - + +
403A HIS 3.4 6.3 - - - +
404A PRO* 4.4 4.9 - - + -
464A MET* 6.4 0.2 - - + -
465A TYR* 1.3 79.8 - - - +
467A GLY* 1.3 73.9 + - - +
468A LEU* 3.5 9.7 + - + +
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Residues in contact with GLY 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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354A PHE* 3.4 4.5 - - - -
358A TYR* 3.6 27.8 - - - -
361A TYR* 3.7 11.4 - - - -
401A ILE* 3.6 0.7 - - - +
402A ALA* 3.4 6.1 - - - -
403A HIS* 2.6 41.7 + - - +
466A ILE* 1.3 73.4 - - - +
468A LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 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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358A TYR* 3.7 19.9 - - - +
359A LYS 4.4 2.1 + - - -
360A PHE* 3.3 21.6 + - - +
361A TYR* 4.3 2.2 - - - -
362A LEU* 4.2 23.1 - - + +
393A LEU* 4.5 15.0 - - + -
399A ILE* 4.6 13.0 - - + -
401A ILE 3.6 9.2 - - - +
402A ALA* 4.3 13.5 - - + -
466A ILE* 3.8 12.3 - - + +
467A GLY* 1.3 80.5 - - - +
469A ASP* 1.3 59.3 + - - +
470A PHE* 3.8 20.0 - - + -
481A ILE* 4.3 8.5 - - + -
511A PHE* 3.6 30.5 - - + -
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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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358A TYR* 4.5 10.8 - - + -
399A ILE* 3.4 2.9 - - - +
400A LYS* 2.5 58.9 + - + +
401A ILE* 3.2 31.6 + - + +
468A LEU* 1.3 76.8 - - - +
470A PHE* 1.3 60.3 + - - +
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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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360A PHE* 4.0 23.1 - + - -
398A GLY 3.4 9.0 - - - +
399A ILE* 3.4 28.5 - - + +
400A LYS* 4.3 3.8 - - - +
468A LEU* 3.8 24.2 - - + -
469A ASP* 1.3 83.0 + - - +
471A ASN* 1.3 68.7 + - - +
472A ILE* 3.0 8.0 + - - +
478A LYS* 4.2 32.1 - - + -
479A VAL* 4.2 20.0 - - + -
481A ILE* 4.7 4.9 - - + -
511A PHE* 3.7 35.2 - + - -
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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