Contacts of the strand formed by residues 584 - 591 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A HIS* 3.7 5.2 - - - +
580A GLY 3.1 35.5 + - - +
581A ALA 3.2 11.6 + - - -
582A GLU 3.1 3.8 + - - -
583A GLY* 1.3 78.5 - - - +
585A ILE* 1.3 68.0 + - - +
586A VAL* 4.5 4.9 - - + +
599A LYS* 4.0 31.9 - - + -
600A ARG 3.6 17.2 + - - +
601A ILE* 4.2 11.7 - - + +
602A LEU* 5.5 0.2 - - - -
605A CYS* 4.6 3.6 - - - +
711A ASP* 4.9 2.7 - - - +
712A PHE* 5.8 1.1 - - + -
1001A 4K7 3.3 18.7 - - - +
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Residues in contact with ILE 585 (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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576A VAL* 3.6 24.9 - - + -
578A GLY 3.7 4.3 - - - +
579A HIS* 4.1 13.0 - - + -
583A GLY 3.6 10.5 + - - +
584A THR* 1.3 80.9 - - - +
586A VAL* 1.3 65.9 + - - +
587A TYR* 3.6 30.1 - - + +
598A VAL 3.6 1.4 - - - +
599A LYS* 3.6 0.5 - - - -
600A ARG* 2.9 58.4 + - - +
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Residues in contact with VAL 586 (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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576A VAL* 3.4 6.4 - - - +
577A LEU* 2.6 33.3 + - + -
578A GLY 2.9 22.8 + - - +
584A THR* 4.5 4.7 - - + -
585A ILE* 1.3 78.7 - - - +
587A TYR* 1.3 59.3 + - - +
597A ALA* 3.6 30.7 - - + -
598A VAL 3.2 11.2 - - - +
599A LYS* 3.9 17.3 - - + -
712A PHE* 3.5 44.4 - - + -
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Residues in contact with TYR 587 (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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571A PHE* 3.6 33.2 - + + -
572A CYS 3.5 16.2 - - - +
573A PRO* 3.6 22.7 - - + -
575A ASP 3.3 18.4 - - - +
576A VAL* 4.2 9.4 - - + -
577A LEU* 4.1 5.2 - - - +
585A ILE* 3.6 40.5 - - + +
586A VAL* 1.3 75.1 - - - +
588A ARG* 1.3 61.4 - - - +
597A ALA* 3.4 3.8 - - - -
598A VAL* 2.7 46.2 + - + +
600A ARG* 3.6 40.8 + - + -
639A TYR* 6.3 0.2 - + - -
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Residues in contact with ARG 588 (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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571A PHE* 3.3 2.3 - - - +
572A CYS* 2.9 30.7 + - + +
575A ASP* 3.3 35.4 + - + +
577A LEU* 3.7 35.6 - - + +
587A TYR* 1.3 73.3 - - - +
589A GLY* 1.3 64.5 + - - +
595A ASP* 6.0 4.8 - - + +
596A VAL 3.9 7.4 - - - +
644A LEU* 3.7 26.8 - - + +
698A MET* 6.0 0.8 - - - +
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Residues in contact with GLY 589 (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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570A SER 3.1 13.0 - - - -
571A PHE* 3.6 6.5 - - - -
587A TYR 3.7 0.6 + - - -
588A ARG* 1.3 81.6 - - - +
590A MET* 1.3 70.6 + - - +
595A ASP* 3.7 3.5 - - - +
596A VAL* 2.9 31.4 + - - +
598A VAL* 4.1 4.0 - - - -
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Residues in contact with MET 590 (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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568A LYS 3.8 1.8 - - - +
569A ILE* 3.7 1.9 - - - +
570A SER* 2.8 43.3 + - - +
589A GLY* 1.3 79.0 - - - +
591A PHE* 1.3 62.0 + - - +
593A ASN* 4.9 19.3 - - - +
594A ARG 3.1 17.0 - - - +
595A ASP* 3.4 20.4 - - - +
596A VAL* 3.8 6.1 - - - +
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Residues in contact with PHE 591 (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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568A LYS* 3.7 37.7 - - + +
569A ILE* 4.0 13.2 - - + -
590A MET* 1.3 74.3 - - - +
592A ASP* 1.3 87.7 + - + +
593A ASN 3.2 1.8 - - - -
594A ARG* 2.9 32.1 + - + +
596A VAL* 3.8 6.3 - - + +
629A PHE* 4.0 26.2 - + + -
630A CYS* 3.5 33.9 - - + -
641A ALA* 4.1 20.2 - - + -
591B PHE* 3.9 16.8 - + - -
629B PHE 4.3 11.4 - - - -
630B CYS* 4.1 8.3 - - + -
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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