Contacts of the strand formed by residues 564 - 571 (chain C) in PDB entry 4YOC
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 TYR 564 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560C GLU* 3.3 33.8 + - + -
561C ALA* 3.3 16.4 + - - +
562C HIS* 4.3 0.3 - - - +
563C LEU* 1.3 82.3 - - + +
565C MET* 1.3 63.0 + - - +
566C GLN* 5.0 1.8 - - - +
595C LYS* 3.6 41.3 - - + -
596C VAL 3.3 18.6 - - - -
597C LEU* 3.5 31.6 - - + +
598C LYS* 3.3 18.4 - - - -
656C ASN* 4.3 4.5 + - - -
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Residues in contact with MET 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C TYR* 1.3 78.1 - - - +
566C GLN* 1.3 67.5 + - - +
567C VAL* 3.6 10.9 + - + -
594C PHE 3.3 3.3 - - - +
595C LYS* 3.7 1.2 - - - -
596C VAL* 2.9 42.8 + - + +
598C LYS* 4.1 14.1 - - + -
648C MET* 3.9 24.5 - - - +
649C ILE* 4.0 20.4 - - + -
652C SER* 3.5 28.5 - - - +
655C GLU 3.7 13.5 - - - +
656C ASN* 3.6 15.7 - - + +
658C TRP* 4.1 18.6 - - + -
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Residues in contact with GLN 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C TYR* 5.0 1.4 - - - +
565C MET* 1.3 80.3 + - - +
567C VAL* 1.3 57.3 + - - +
568C GLN* 3.9 3.8 - - + +
593C VAL* 3.9 24.8 - - + +
594C PHE 3.6 3.1 - - - -
595C LYS* 3.1 41.1 + - - +
656C ASN* 2.7 17.8 + - - +
657C PRO* 3.2 23.4 - - + +
658C TRP* 2.6 35.3 + - - +
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Residues in contact with VAL 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565C MET* 4.4 11.0 - - + +
566C GLN* 1.3 74.8 - - - +
568C GLN* 1.3 61.9 + - - +
569C ILE* 3.7 7.2 + - + -
592C THR 3.6 3.1 - - - +
594C PHE* 2.9 40.8 + - - +
596C VAL* 4.4 16.4 - - + -
605C PHE* 3.5 31.0 - - + -
648C MET* 3.8 21.5 - - + -
658C TRP* 3.3 19.3 - - + +
660C ILE* 4.0 19.1 - - + -
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Residues in contact with GLN 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C GLN* 4.8 4.1 - - + +
567C VAL* 1.3 72.9 - - - +
569C ILE* 1.3 62.2 + - - +
586C GLU* 4.6 2.8 - - - +
591C TYR* 3.1 44.9 + - + -
592C THR 3.9 3.4 - - - -
593C VAL* 4.4 20.1 - - + +
657C PRO* 3.7 33.7 - - + +
658C TRP 2.9 9.6 + - - +
659C THR* 3.3 24.1 + - - +
660C ILE 2.9 26.1 + - - -
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Residues in contact with ILE 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C VAL* 4.3 2.7 - - + +
568C GLN* 1.3 73.2 - - - +
570C VAL* 1.3 65.2 + - - +
571C ALA* 4.3 1.3 + - + +
590C LYS 4.5 0.3 - - - +
591C TYR* 3.5 5.1 - - - -
592C THR* 2.9 46.6 + - - +
594C PHE* 3.7 26.7 - - + -
605C PHE* 4.1 12.1 - - + -
609C LEU* 3.7 21.3 - - + -
613C MET* 4.3 9.4 - - + -
622C LEU* 5.3 1.3 - - + -
660C ILE* 3.5 29.4 - - + +
662C LEU* 3.7 37.2 - - + -
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Residues in contact with VAL 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C ILE* 1.3 78.6 - - - +
571C ALA* 1.3 74.6 + - - +
574C GLN* 3.8 21.3 - - + -
575C PHE* 4.1 9.4 - - + -
584C TYR* 4.2 6.5 - - + -
589C VAL* 3.9 14.4 - - + -
590C LYS 4.7 2.0 - - - +
591C TYR* 3.9 13.9 - - + -
625C MET* 3.8 24.7 - - + -
659C THR* 4.1 9.2 - - + -
660C ILE 2.9 19.0 + - - +
661C PHE* 3.5 6.9 - - + -
662C LEU 2.9 24.8 + - - -
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Residues in contact with ALA 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C ILE* 4.3 1.5 - - + +
570C VAL* 1.3 88.0 - - - +
572C GLU* 1.3 65.4 + - - +
573C ASP* 3.2 22.7 - - - +
574C GLN* 3.2 16.0 + - + +
575C PHE* 4.1 3.5 - - - -
590C LYS 5.4 0.6 + - - -
613C MET* 6.1 3.8 - - + -
661C PHE* 4.0 3.1 - - - -
662C LEU* 4.2 17.7 - - + +
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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