Contacts of the strand formed by residues 485 - 492 (chain B) in PDB entry 4YFI
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 485 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481B ARG* 3.2 13.3 - - - +
482B CYS 2.9 32.3 + - - +
483B ARG* 3.7 28.8 + - - +
484B ASN* 1.3 82.8 - - - +
486B ILE* 1.3 68.7 + - - +
487B VAL* 4.1 4.3 - - + -
525B VAL* 4.5 25.4 - - + +
540B GLN* 6.0 5.4 - - + -
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Residues in contact with ILE 486 (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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479B LYS* 3.8 29.8 - - + +
480B GLY 3.5 12.3 - - - +
481B ARG* 4.3 16.8 - - + +
485B LYS* 1.3 76.9 - - - +
487B VAL* 1.3 63.6 + - - +
540B GLN* 3.9 3.5 - - - +
541B TYR* 3.0 39.8 + - + +
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LYS* 3.5 4.9 - - - +
480B GLY 2.9 50.0 + - - -
481B ARG 3.6 5.6 - - - +
482B CYS* 3.8 24.9 - - + +
485B LYS* 3.9 14.8 - - + +
486B ILE* 1.3 80.1 - - - +
488B ALA* 1.3 60.1 + - - +
489B ILE* 3.5 17.3 - - + -
525B VAL* 4.2 9.2 - - + -
538B VAL* 3.7 18.4 - - + -
539B THR 3.1 15.7 - - - +
540B GLN* 4.6 0.7 - - - -
541B TYR* 3.6 11.7 - - - +
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Residues in contact with ALA 488 (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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469B ILE* 4.4 9.2 - - + -
477B VAL* 4.4 2.0 - - + -
478B TYR 3.3 8.1 - - - +
487B VAL* 1.3 71.9 - - - +
489B ILE* 1.3 60.7 + - - +
537B ILE 3.6 1.6 - - - +
538B VAL* 3.5 2.1 - - - -
539B THR* 2.8 40.4 + - - +
541B TYR* 3.8 3.8 - - + +
801B 4CW 3.3 48.8 - - + +
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Residues in contact with ILE 489 (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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463B ILE* 3.8 23.3 - - + -
465B PHE* 3.6 31.0 - - + -
476B LYS 3.7 0.3 - - - +
477B VAL* 3.3 4.9 - - - -
478B TYR* 2.9 37.7 + - + +
479B LYS 4.3 1.3 - - - -
480B GLY* 3.8 20.6 - - - +
487B VAL* 3.5 25.4 - - + -
488B ALA* 1.3 75.8 - - - +
490B LYS* 1.3 62.2 + - - +
491B ARG* 3.4 4.3 + - + +
536B ALA* 4.0 24.5 - - + -
537B ILE 3.4 4.7 - - - +
538B VAL* 3.9 18.4 - - + -
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Residues in contact with LYS 490 (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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474B PHE* 3.9 39.8 - - + +
476B LYS 3.8 3.1 - - - -
477B VAL* 4.4 7.2 - - + +
489B ILE* 1.3 70.4 - - - +
491B ARG* 1.3 58.1 + - - +
492B TYR* 2.7 41.5 + - + +
509B GLU* 2.8 28.3 + - - +
536B ALA* 3.4 3.1 - - - -
537B ILE* 2.8 37.1 + - + +
606B ASP* 5.1 3.0 + - - -
608B GLY* 4.4 8.5 - - - -
801B 4CW 3.8 34.3 - - + +
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Residues in contact with ARG 491 (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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460B LEU* 3.5 30.5 - - - +
465B PHE* 4.1 26.5 - - - -
474B PHE* 4.1 4.3 - - - +
475B GLY* 3.6 4.0 + - - -
476B LYS 2.8 39.3 + - - +
478B TYR* 3.9 22.8 + - + +
489B ILE* 3.4 3.8 + - + +
490B LYS* 1.3 73.2 - - - +
492B TYR* 1.3 70.7 + - - +
533B SER 3.5 21.3 + - - -
534B GLN* 3.8 12.9 + - - +
535B PHE 3.7 16.3 + - - -
536B ALA* 4.1 10.3 - - - +
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Residues in contact with TYR 492 (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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474B PHE* 3.6 31.0 - - + -
475B GLY* 4.8 2.0 - - - -
490B LYS* 2.7 48.3 + - + -
491B ARG* 1.3 89.0 + - - +
493B ARG* 1.3 66.9 + - - +
502B ASP* 5.5 4.3 - - + -
505B MET 5.6 0.3 - - - -
506B PHE* 3.5 44.8 - + + -
509B GLU* 3.0 12.1 + - - -
532B PRO 5.3 3.4 - - - +
533B SER 4.4 7.0 - - - +
535B PHE* 3.1 36.1 + + + +
537B ILE* 4.4 3.6 - - + -
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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