Contacts of the strand formed by residues 596 - 601 (chain A) in PDB entry 3RGZ
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 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A PHE* 6.5 0.7 - - - -
516A TRP* 4.4 4.0 - - - -
595A LYS* 1.3 74.5 - - - +
597A TYR* 1.3 67.0 + - - +
617A GLU* 3.9 6.8 - - - +
618A PHE* 3.0 44.4 + - + +
619A GLN* 4.0 22.0 + - + +
620A GLY 5.1 2.5 - - - +
621A ILE 5.7 1.1 - - - -
643A GLY* 4.9 1.0 - - - -
644A GLY* 3.1 28.8 + - - +
645A HIS* 3.0 40.9 + - + -
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Residues in contact with TYR 597 (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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516A TRP* 4.3 10.8 - - + -
595A LYS 3.6 2.5 - - - +
596A ARG* 1.3 79.2 + - - +
598A VAL* 1.3 75.8 + - - +
599A TYR* 4.3 3.4 - - + -
615A LEU* 3.6 24.9 - - + -
616A LEU 3.1 13.7 - - - +
618A PHE* 3.8 6.1 - - - +
642A TYR* 4.2 6.4 - - - +
643A GLY* 3.6 21.0 + - - -
644A GLY* 3.0 44.8 + - - -
645A HIS 3.4 23.4 + - - -
646A THR* 3.5 19.5 - - + -
800A BLD 3.4 49.9 + - + +
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Residues in contact with VAL 598 (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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597A TYR* 1.3 82.6 - - - +
599A TYR* 1.3 59.8 + - - +
600A ILE* 4.5 12.6 - - + -
614A ASN 3.4 1.4 - - - +
615A LEU* 3.5 2.3 - - - +
616A LEU* 2.8 49.4 + - + +
618A PHE* 3.4 50.3 - - + -
623A SER* 5.8 1.3 - - - -
626A LEU* 4.7 5.6 - - + -
641A VAL* 4.0 18.4 - - + -
642A TYR 3.2 11.2 - - - +
643A GLY* 4.6 4.3 - - - -
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Residues in contact with TYR 599 (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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564A TRP* 3.6 32.1 - + - -
597A TYR* 3.9 9.1 - - + -
598A VAL* 1.3 73.4 - - - +
600A ILE* 1.3 61.0 + - - +
601A LYS* 4.1 17.1 - - + +
612A ALA* 3.4 24.4 + - - +
613A GLY* 3.4 25.7 + - - -
614A ASN 3.3 9.2 - - - -
615A LEU* 3.9 5.4 - - + -
640A ARG 3.5 3.6 - - - +
641A VAL* 3.5 0.9 - - - -
642A TYR* 2.7 46.8 + + + +
658A PHE* 3.8 2.4 - + - -
682A ILE* 3.6 20.9 - - + +
706A ILE* 5.5 0.9 - - - +
800A BLD 3.3 52.2 + - + -
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Residues in contact with ILE 600 (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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598A VAL* 4.5 10.3 - - + -
599A TYR* 1.3 74.7 - - - +
601A LYS* 1.3 63.5 - - - +
613A GLY* 3.0 5.4 - - - -
614A ASN* 2.9 48.5 + - + +
616A LEU* 4.2 11.0 - - + -
626A LEU* 4.0 32.5 - - + -
629A LEU* 4.2 15.3 - - + -
633A ASN* 5.3 7.4 - - - +
635A CYS* 5.5 8.5 - - + -
637A ILE* 5.3 4.3 - - + +
639A SER* 3.7 20.9 - - - +
640A ARG 3.6 5.6 - - - +
641A VAL* 4.5 15.9 - - + -
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Residues in contact with LYS 601 (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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599A TYR* 3.7 10.6 + - + +
600A ILE* 1.3 73.8 - - - +
602A ASN* 1.3 80.8 + - - +
603A ASP* 3.5 8.2 + - - +
612A ALA 3.9 10.3 - - - +
635A CYS* 5.9 0.9 - - - +
639A SER* 3.3 25.5 + - - -
640A ARG* 3.0 25.7 + - + +
642A TYR* 4.0 23.8 - - + +
706A ILE* 5.1 2.2 - - + +
730A GLU* 2.9 32.0 + - - -
800A BLD 3.5 28.7 - - - +
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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