Contacts of the strand formed by residues 594 - 601 (chain C) in PDB entry 4YZ9
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 ARG 594 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590C MET* 3.2 8.2 - - - -
591C PHE* 2.8 39.8 + - - +
592C ASP* 3.7 17.0 + - - +
593C ASN* 1.3 78.6 - - - +
595C ASP* 1.3 62.9 + - - +
596C VAL* 3.8 8.7 - - + +
627C ARG* 4.1 25.0 - - - +
629C PHE* 3.8 35.7 - - + -
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Residues in contact with ASP 595 (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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588C ARG* 5.5 8.5 - - + -
589C GLY 3.5 6.3 - - - +
590C MET* 4.2 17.1 - - - +
593C ASN 5.0 2.8 - - - +
594C ARG* 1.3 73.8 - - - +
596C VAL* 1.3 62.5 + - - +
644C LEU* 3.6 30.5 + - + +
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Residues in contact with VAL 596 (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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588C ARG* 3.8 6.1 - - - +
589C GLY 2.8 38.1 + - - +
590C MET 3.7 2.5 - - - +
591C PHE* 3.7 26.2 - - + +
594C ARG* 3.8 18.8 - - + +
595C ASP* 1.3 80.5 - - - +
597C ALA* 1.3 61.5 + - - +
598C VAL* 4.2 7.9 - - + -
629C PHE* 4.0 23.1 - - + -
641C ALA* 4.0 17.9 - - + -
642C ILE 3.3 14.6 - - - +
643C GLU* 5.2 0.2 - - - -
644C LEU* 3.9 13.3 - - - +
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Residues in contact with ALA 597 (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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577C LEU* 4.0 14.4 - - + -
586C VAL* 3.7 20.4 - - + -
587C TYR 3.4 4.7 - - - -
596C VAL* 1.3 75.5 - - - +
598C VAL* 1.3 61.9 + - - +
641C ALA* 3.4 1.9 - - - -
642C ILE* 2.7 54.3 + - + +
643C GLU 4.4 3.1 - - - +
644C LEU* 4.1 8.2 - - + +
712C PHE* 4.2 9.2 - - + -
714C LEU* 5.9 0.2 - - + -
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Residues in contact with VAL 598 (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* 4.1 14.4 - - + -
570C SER 3.9 10.8 - - - +
571C PHE* 3.9 38.4 - - + -
585C ILE 3.6 0.3 - - - +
586C VAL* 3.3 6.5 - - - +
587C TYR* 2.8 35.7 + - + +
589C GLY* 4.0 10.1 - - - -
596C VAL* 4.2 9.6 - - + -
597C ALA* 1.3 76.4 - - - +
599C LYS* 1.3 62.5 + - - +
600C ARG 3.6 1.4 + - - -
639C TYR* 3.9 31.2 - - + -
640C ILE 3.4 7.0 - - - +
641C ALA* 4.8 2.2 - - - -
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Residues in contact with LYS 599 (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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584C THR* 4.1 12.1 - - + -
585C ILE 3.7 3.8 - - - -
586C VAL* 4.2 15.9 - - + -
597C ALA 4.0 0.2 + - - -
598C VAL* 1.3 71.0 - - - +
600C ARG* 1.3 59.8 + - - +
601C ILE* 3.9 5.2 + - + +
626C ILE* 5.7 0.2 - - - -
638C GLN 3.4 1.9 - - - +
639C TYR* 3.2 6.8 - - - -
640C ILE* 2.6 48.1 + - + +
642C ILE* 3.6 29.2 - - + -
711C ASP* 2.8 39.4 + - - +
712C PHE* 4.3 10.8 - - + -
1001C 4K7 2.8 54.5 + - - +
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Residues in contact with ARG 600 (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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571C PHE* 5.8 0.4 - - - -
583C GLY 4.3 3.8 + - - +
584C THR* 3.5 6.4 - - - -
585C ILE* 2.8 55.0 + - - +
587C TYR* 2.7 39.1 + - + -
598C VAL 3.6 1.2 + - - -
599C LYS* 1.3 70.8 - - - +
601C ILE* 1.3 61.8 + - - +
602C LEU* 4.4 13.0 - - - +
637C PHE* 3.8 48.1 - - + -
638C GLN 3.6 2.7 - - - -
639C TYR* 3.5 26.9 - - + -
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Residues in contact with ILE 601 (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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584C THR* 4.0 24.7 - - + +
599C LYS* 4.4 10.3 - - + +
600C ARG* 1.3 77.7 - - - +
602C LEU* 1.3 61.3 + - - +
605C CYS* 4.3 10.8 - - + +
606C PHE* 3.2 22.2 - - + -
609C ALA* 3.3 31.6 - - + -
637C PHE* 3.7 7.6 - - - +
638C GLN* 3.1 46.6 + - + +
640C ILE* 4.2 9.6 - - + -
1001C 4K7 4.3 19.1 - - + +
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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