Contacts of the strand formed by residues 584 - 591 (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 THR 584 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579C HIS* 3.3 4.3 - - - +
580C GLY* 2.9 35.0 + - - +
581C ALA 2.8 23.0 + - - -
582C GLU* 3.3 3.0 + - - +
583C GLY* 1.3 75.6 - - - +
585C ILE* 1.3 73.9 + - - +
586C VAL* 4.3 6.3 - - + -
599C LYS* 4.1 23.1 - - + -
600C ARG 3.5 15.7 - - - +
601C ILE* 4.0 19.8 - - + +
605C CYS* 5.2 0.5 - - - -
711C ASP* 4.6 4.0 - - - +
712C PHE* 5.6 0.2 - - + -
1001C 4K7 3.5 15.1 - - - +
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Residues in contact with ILE 585 (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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576C VAL* 4.1 20.2 - - + -
578C GLY 4.0 2.0 - - - +
579C HIS* 4.1 14.8 - - + -
583C GLY 3.5 8.3 + - - +
584C THR* 1.3 81.9 - - - +
586C VAL* 1.3 68.3 + - - +
587C TYR* 3.4 37.4 - - + +
598C VAL 3.6 0.7 - - - +
599C LYS* 3.7 0.3 - - - -
600C ARG* 2.8 54.3 + - - +
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Residues in contact with VAL 586 (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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576C VAL* 3.6 5.9 - - - +
577C LEU* 2.9 27.9 + - + -
578C GLY 3.0 23.3 + - - +
579C HIS* 4.4 1.3 - - - +
584C THR* 4.3 5.8 - - + -
585C ILE* 1.3 82.0 - - - +
587C TYR* 1.3 63.2 + - - +
597C ALA* 3.7 28.3 - - + -
598C VAL 3.3 10.3 - - - +
599C LYS* 4.2 11.7 - - + +
712C PHE* 3.7 48.0 - - + -
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Residues in contact with TYR 587 (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* 3.9 33.0 - + + -
572C CYS 3.6 13.2 - - - +
573C PRO* 3.7 32.3 - - + -
575C ASP 3.4 12.3 - - - +
576C VAL* 3.8 11.0 - - + -
577C LEU* 3.9 4.9 - - - +
585C ILE* 3.4 27.7 - - + +
586C VAL* 1.3 74.1 - - - +
588C ARG* 1.3 65.3 + - - +
597C ALA* 3.4 4.2 - - - -
598C VAL* 2.8 39.8 + - + +
600C ARG* 2.7 58.6 + - + -
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Residues in contact with ARG 588 (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* 3.2 3.9 - - - +
572C CYS* 3.1 34.1 + - - +
575C ASP* 3.1 39.9 + - + -
577C LEU* 3.4 43.7 - - + +
587C TYR* 1.3 72.4 - - - +
589C GLY* 1.3 64.6 + - - +
595C ASP* 5.5 7.9 - - + +
596C VAL 3.8 5.8 - - - +
644C LEU* 4.2 22.4 - - + +
698C MET* 6.1 0.8 - - - +
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Residues in contact with GLY 589 (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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570C SER* 3.0 15.3 - - - -
571C PHE* 3.7 5.2 - - - -
572C CYS* 5.6 1.6 - - - -
587C TYR 3.6 0.6 + - - -
588C ARG* 1.3 79.9 - - - +
590C MET* 1.3 69.1 + - - +
595C ASP* 3.5 5.7 - - - +
596C VAL* 2.8 34.2 + - - +
598C VAL* 4.0 4.9 - - - -
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Residues in contact with MET 590 (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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568C LYS 4.4 0.2 - - - +
569C ILE* 3.8 4.5 - - - +
570C SER* 2.8 46.9 + - - +
589C GLY* 1.3 78.3 - - - +
591C PHE* 1.3 62.1 + - - +
593C ASN* 4.4 26.5 - - - +
594C ARG 3.2 8.7 - - - +
595C ASP* 4.2 16.2 - - - +
596C VAL* 3.7 4.3 - - - +
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Residues in contact with PHE 591 (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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568C LYS* 3.2 41.3 - - + +
569C ILE* 4.2 5.6 - - + -
590C MET* 1.3 74.5 - - - +
592C ASP* 1.3 90.1 + - + +
593C ASN 3.2 2.0 - - - -
594C ARG* 2.8 31.1 + - - +
596C VAL* 3.7 15.3 - - + +
629C PHE* 4.0 35.9 - + + -
630C CYS* 3.2 37.2 - - + -
641C ALA* 4.2 9.6 - - + -
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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