Contacts of the strand formed by residues 475 - 482 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A SER* 3.8 1.2 + - - -
472A GLY 3.0 27.7 + - - +
473A SER 3.3 3.6 - - - -
474A PHE* 1.3 87.6 - - - +
476A LYS* 1.3 68.9 + - - +
491A ARG 3.4 10.1 - - - -
492A TYR 4.6 0.2 - - - -
493A ARG* 4.2 9.9 - - - -
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Residues in contact with LYS 476 (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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468A ILE* 4.1 31.9 - - + +
470A GLY 3.8 6.1 - - - +
471A SER* 3.9 20.4 + - - +
472A GLY 5.7 0.7 - - - -
474A PHE* 4.4 1.3 - - - -
475A GLY* 1.3 78.6 - - - +
477A VAL* 1.3 64.8 + - - +
478A TYR* 3.9 26.0 - - + +
489A ILE 3.6 0.9 - - - +
490A LYS* 3.5 1.9 - - - +
491A ARG* 2.8 40.2 + - + +
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Residues in contact with VAL 477 (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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468A ILE* 3.5 4.7 - - - +
469A ILE* 2.8 43.3 + - + -
470A GLY* 2.9 27.0 + - - +
471A SER 4.8 0.2 - - - +
474A PHE* 4.4 13.7 - - + -
476A LYS* 1.3 79.0 - - - +
478A TYR* 1.3 61.8 + - - +
488A ALA* 4.8 0.4 - - + -
489A ILE 3.3 10.3 - - - +
490A LYS* 4.3 12.3 - - + -
801A 4CW 3.7 55.0 - - + +
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Residues in contact with TYR 478 (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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465A PHE* 3.6 40.8 - + + -
466A HIS 4.8 6.1 - - - -
467A GLU 3.3 15.9 - - - -
468A ILE* 3.6 24.1 - - + +
469A ILE* 3.9 6.0 - - - +
476A LYS* 3.9 28.0 - - + +
477A VAL* 1.3 73.7 - - - +
479A LYS* 1.3 69.8 + - - +
488A ALA* 3.3 10.2 - - - +
489A ILE* 2.9 41.7 + - + +
491A ARG* 3.7 26.3 - - + +
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Residues in contact with LYS 479 (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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465A PHE* 4.1 0.2 - - - -
466A HIS* 2.8 38.0 + - - +
467A GLU* 2.8 39.1 + - - +
469A ILE* 3.9 18.9 - - + +
478A TYR* 1.3 81.1 - - - +
480A GLY* 1.3 62.4 + - - +
486A ILE* 4.1 30.4 - - + +
487A VAL 3.6 5.4 - - - +
489A ILE* 4.1 0.2 - - - -
541A TYR* 3.8 40.2 + - + +
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Residues in contact with GLY 480 (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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464A GLU 3.2 13.5 - - - -
466A HIS* 3.7 15.3 + - - -
479A LYS* 1.3 80.6 - - - +
481A ARG* 1.3 58.4 + - - +
486A ILE* 3.3 10.7 - - - +
487A VAL* 2.8 36.2 + - - -
489A ILE* 3.7 5.4 - - - -
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Residues in contact with ARG 481 (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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462A GLU 3.8 0.7 - - - +
463A ILE* 3.6 3.1 - - - +
464A GLU* 2.9 54.6 + - + +
466A HIS* 4.1 16.4 - - + +
480A GLY* 1.3 75.1 - - - +
482A CYS* 1.3 65.3 + - - +
484A ASN* 3.4 50.8 + - - +
485A LYS 3.4 10.8 - - - +
486A ILE* 3.5 31.1 - - - +
487A VAL* 3.9 1.9 - - - +
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Residues in contact with CYS 482 (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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458A LEU* 3.9 39.9 - - - -
462A GLU* 3.6 17.5 - - - +
463A ILE* 4.1 11.7 - - + -
481A ARG* 1.3 78.0 - - - +
483A ARG* 1.3 67.8 + - - +
484A ASN 3.0 3.1 - - - +
485A LYS* 2.8 36.3 + - - +
487A VAL* 3.9 20.1 - - + +
525A VAL* 5.5 5.2 - - + -
538A VAL* 4.7 4.0 - - + -
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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