Contacts of the strand formed by residues 458 - 470 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B ARG* 4.2 1.9 - - - +
370B GLY* 3.5 29.1 + - - +
412B SER* 5.1 1.1 - - - -
413B TYR 3.0 15.9 - - - +
414B CYS* 4.8 0.4 - - - -
415B CYS* 4.1 5.1 - - - +
443B VAL* 4.6 11.4 - - + -
457B PRO* 1.3 75.3 - - - +
459B ALA* 1.3 64.0 + - - +
460B TYR* 4.1 22.9 - - + +
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B TYR* 6.4 0.2 - - + -
368B THR 3.1 13.9 - - - +
369B ARG* 4.4 7.0 - - - -
412B SER* 3.2 7.3 - - - -
413B TYR 3.0 28.5 + - - +
415B CYS* 4.2 16.8 - - + -
421B TYR* 4.4 11.7 - - + -
424B ILE* 4.4 16.2 - - + -
458B LYS* 1.3 75.8 - - - +
460B TYR* 1.3 64.7 + - - +
461B LEU* 4.3 5.4 - - + +
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Residues in contact with TYR 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ALA 3.4 0.9 - - - +
367B TYR* 3.2 8.8 - - - +
368B THR* 2.9 34.9 + - - -
370B GLY 3.4 24.6 + - - -
371B SER* 3.6 11.4 - - - -
372B ASP* 3.0 42.8 + - - -
375B HIS* 3.3 41.1 - + + +
411B SER 3.6 4.5 - - - +
412B SER* 3.7 22.7 - - - -
458B LYS* 4.1 12.8 - - + +
459B ALA* 1.3 79.7 - - - +
461B LEU* 1.3 67.2 + - - +
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR* 4.4 5.6 - - + -
366B ALA 3.6 4.5 - - - -
367B TYR* 3.7 22.4 - - + -
375B HIS* 4.2 1.4 + - - -
409B PHE 4.2 1.1 - - - +
410B GLU* 3.1 26.3 - - - +
411B SER* 2.8 30.9 + - - +
413B TYR* 4.3 18.8 - - + -
424B ILE* 4.3 12.1 - - + -
428B TYR* 3.5 53.8 - - + +
459B ALA* 4.3 9.2 - - + +
460B TYR* 1.3 83.5 - - - +
462B SER* 1.3 64.0 + - - +
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Residues in contact with SER 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE 3.3 1.2 - - - +
365B THR* 3.2 4.9 - - - +
366B ALA* 3.1 30.6 + - - +
375B HIS* 3.1 17.8 - - - -
379B SER* 3.5 20.1 - - - -
383B GLU* 5.4 2.7 - - - -
408B PRO* 5.5 1.6 - - - -
409B PHE 3.6 3.8 - - - -
410B GLU* 3.0 30.8 + - - +
461B LEU* 1.3 70.0 + - - +
463B THR* 1.3 61.2 + - - +
464B MET* 4.5 15.2 - - - +
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLU* 3.9 8.3 - - + +
364B ILE 3.0 15.7 - - - +
365B THR* 2.6 27.1 + - - +
408B PRO* 3.3 2.9 - - - +
409B PHE* 2.7 46.6 + - - +
428B TYR* 3.0 22.7 + - - +
461B LEU 5.0 0.2 - - - -
462B SER* 1.3 75.1 + - - +
464B MET* 1.3 71.9 + - - +
465B TYR* 3.6 28.3 - - + +
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Residues in contact with MET 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 3.7 31.0 - - + -
362B LEU 3.5 3.6 - - - +
363B GLU* 3.8 0.2 - - - -
364B ILE* 3.0 48.1 + - + +
366B ALA* 5.9 0.9 - - + +
379B SER 5.0 1.3 - - - +
382B VAL* 4.2 13.7 - - + -
383B GLU* 3.4 41.1 - - + +
386B VAL* 3.8 20.4 - - + -
405B PHE 5.5 2.7 - - - +
407B LYS 4.6 4.3 - - - +
408B PRO* 3.6 22.0 - - + -
462B SER* 4.5 11.7 - - - +
463B THR* 1.3 79.1 - - - +
465B TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 3.7 9.5 - - + -
355B PHE* 3.5 28.3 - + + -
361B TYR* 4.6 8.7 - - + -
362B LEU 3.7 2.2 - - - -
363B GLU* 3.6 28.2 + - + -
404B PRO* 3.9 0.5 - - - +
405B PHE* 2.8 37.8 + - + +
407B LYS 4.8 0.8 + - - -
409B PHE* 3.7 33.7 - + + -
428B TYR* 4.0 1.0 + - - -
463B THR* 3.6 23.5 - - + +
464B MET* 1.3 78.2 - - - +
466B ILE* 1.3 62.5 + - - +
467B GLY 3.9 0.2 - - - -
517B LEU* 3.8 23.1 - - + -
518B PRO* 4.0 12.5 - - + +
520B GLU* 3.1 21.8 + - - -
521B VAL* 3.5 14.8 - - + +
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Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 4.4 0.4 - - - -
361B TYR* 3.6 1.3 - - - -
362B LEU* 2.9 38.2 + - + +
364B ILE* 3.5 32.1 - - + -
386B VAL* 4.3 13.7 - - + -
389B LEU* 4.0 18.6 - - + -
390B VAL* 4.4 7.6 - - + -
393B LEU* 4.0 13.5 - - + -
402B ALA* 3.7 25.8 - - + +
403B HIS 3.3 10.3 - - - +
404B PRO* 4.7 5.8 - - + -
465B TYR* 1.3 75.1 - - - +
467B GLY* 1.3 76.8 - - - +
468B LEU* 3.4 10.8 + - + +
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Residues in contact with GLY 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 3.5 13.2 - - - -
358B TYR* 3.6 28.3 - - - -
360B PHE 3.9 5.2 - - - -
361B TYR* 4.0 5.2 - - - -
401B ILE* 3.9 0.8 - - - +
402B ALA* 3.5 1.7 - - - -
403B HIS 2.7 34.9 + - - -
466B ILE* 1.3 77.3 - - - +
468B LEU* 1.3 58.5 + - - -
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B TYR* 4.0 7.5 - - - +
359B LYS 4.5 1.0 + - - -
360B PHE* 2.9 36.4 + - + +
362B LEU* 3.7 35.2 - - + +
393B LEU* 4.7 11.4 - - + -
399B ILE* 4.7 11.7 - - + -
401B ILE 3.8 11.4 - - - +
402B ALA* 4.0 15.7 - - + -
466B ILE* 3.4 9.8 + - + +
467B GLY* 1.3 80.2 - - - +
469B ASP* 1.3 60.5 + - - +
470B PHE* 4.2 13.9 - - + -
481B ILE* 4.1 17.3 - - + -
511B PHE* 4.0 19.7 - - + -
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Residues in contact with ASP 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B TYR* 4.0 17.1 - - + -
359B LYS* 6.0 0.8 - - - +
360B PHE* 5.5 1.1 - - - -
399B ILE* 4.0 2.2 - - - +
400B LYS* 2.9 62.1 + - - +
401B ILE* 3.4 26.3 + - + +
468B LEU* 1.3 74.7 - - - +
470B PHE* 1.3 72.7 + - - +
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Residues in contact with PHE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PHE* 3.7 38.8 - + + -
398B GLY 3.7 6.3 - - - +
399B ILE* 4.5 17.7 - - + +
400B LYS* 3.9 5.1 - - - +
468B LEU* 4.3 13.0 - - + -
469B ASP* 1.3 91.6 + - - +
471B ASN* 1.3 64.5 + - - +
472B ILE 4.1 1.5 + - - +
479B VAL* 4.1 33.9 - - + -
481B ILE* 4.4 19.5 - - + -
511B PHE* 3.9 26.9 - + - -
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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