Contacts of the strand formed by residues 475 - 482 (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 GLY 475 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B SER* 3.9 0.7 + - - -
472B GLY 3.0 30.0 + - - +
473B SER 3.2 5.3 + - - -
474B PHE* 1.3 86.9 - - - +
476B LYS* 1.3 68.1 + - - +
491B ARG 3.6 6.7 - - - -
492B TYR 4.8 0.9 - - - -
493B ARG* 4.7 9.0 - - - -
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Residues in contact with LYS 476 (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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468B ILE* 4.0 31.1 - - + +
470B GLY 3.8 7.6 - - - +
471B SER* 4.2 15.9 - - - +
474B PHE* 4.2 2.0 - - - -
475B GLY* 1.3 79.6 - - - +
477B VAL* 1.3 62.6 + - - +
478B TYR* 3.7 26.6 - - + +
489B ILE 3.7 0.3 - - - +
490B LYS 3.6 0.7 - - - -
491B ARG* 2.8 42.3 + - + +
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 3.5 5.2 - - - +
469B ILE* 2.9 49.2 + - + -
470B GLY* 3.1 21.8 + - - +
471B SER 4.7 0.2 - - - +
474B PHE* 4.0 23.1 - - + -
476B LYS* 1.3 75.7 - - - +
478B TYR* 1.3 63.8 + - - +
488B ALA* 4.4 9.0 - - + -
489B ILE 3.3 14.8 - - - +
490B LYS* 4.6 7.4 - - + -
801B 4CW 4.4 32.5 - - + -
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Residues in contact with TYR 478 (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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465B PHE* 3.7 37.0 - + + -
466B HIS 3.7 19.1 - - - -
467B GLU 3.5 4.5 - - - -
468B ILE* 3.6 27.6 - - + +
469B ILE* 4.1 5.8 - - - +
476B LYS* 3.7 35.7 - - + +
477B VAL* 1.3 76.2 - - - +
479B LYS* 1.3 67.4 + - - +
488B ALA* 3.3 6.8 - - - +
489B ILE* 2.9 39.7 + - + +
491B ARG* 3.9 20.9 + - + +
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Residues in contact with LYS 479 (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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466B HIS* 2.9 36.8 + - + +
467B GLU* 2.8 33.6 + - + +
469B ILE* 3.6 22.5 - - + +
478B TYR* 1.3 77.8 - - - +
480B GLY* 1.3 63.2 + - - +
486B ILE* 3.8 26.0 - - + +
487B VAL 3.5 9.4 - - - +
489B ILE* 4.3 0.4 - - - -
541B TYR* 3.8 37.9 + - + +
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Residues in contact with GLY 480 (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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464B GLU 3.1 14.4 - - - -
466B HIS* 3.8 12.6 + - - -
479B LYS* 1.3 77.9 - - - +
481B ARG* 1.3 61.3 + - - +
486B ILE* 3.5 12.0 - - - +
487B VAL* 2.9 32.7 + - - -
489B ILE* 3.8 8.9 - - - +
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Residues in contact with ARG 481 (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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462B GLU 3.8 0.9 - - - +
463B ILE* 3.7 1.9 - - - +
464B GLU* 2.9 62.7 + - + +
466B HIS* 4.1 12.0 - - + -
480B GLY* 1.3 75.2 - - - +
482B CYS* 1.3 66.8 + - - +
484B ASN* 3.5 41.0 + - - +
485B LYS* 3.2 15.0 + - - +
486B ILE* 4.3 21.2 - - + +
487B VAL* 3.6 2.3 - - - +
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Residues in contact with CYS 482 (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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458B LEU* 3.9 30.1 - - - -
462B GLU* 3.5 18.8 - - - +
463B ILE* 4.2 14.6 - - + -
481B ARG* 1.3 77.7 - - - +
483B ARG* 1.3 81.5 + - - +
484B ASN 3.2 1.6 - - - -
485B LYS* 2.9 26.3 + - - +
487B VAL* 3.8 22.5 - - + +
525B VAL* 4.2 10.3 - - - +
538B VAL* 4.2 3.8 - - + -
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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
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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