Contacts of the strand formed by residues 594 - 600 (chain V) in PDB entry 3RWR
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 594 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587V ASN 4.1 0.2 - - - +
588V PHE* 3.2 22.2 - - - -
589V SER* 3.6 6.5 + - - -
592V SER* 3.1 24.6 + - - +
593V CYS* 1.3 73.3 - - - +
595V PHE* 1.3 59.8 + - - +
596V PHE* 3.3 15.9 + - + -
610V SER* 4.2 20.4 - - - -
611V PHE 3.1 21.5 - - - -
612V ASN* 3.0 37.3 + - - -
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Residues in contact with PHE 595 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508V ILE* 5.6 2.0 - - + -
510V LEU* 6.0 1.8 - - + -
520V LEU* 3.7 28.0 - - + -
534V ILE* 4.4 9.2 - - + -
536V LEU* 4.1 28.7 - - + -
574V LEU* 5.6 2.5 - - + -
586V PHE* 3.8 33.0 - + + -
587V ASN 4.1 3.4 - - - -
588V PHE* 3.3 21.2 - + + -
593V CYS 3.9 0.6 + - - -
594V TYR* 1.3 68.4 - - - +
596V PHE* 1.3 60.3 + - - +
597V PHE* 4.6 13.4 - + + -
609V GLY 4.0 0.9 - - - +
610V SER* 3.6 1.2 - - - -
611V PHE* 2.6 44.3 + + + +
613V LEU* 3.6 42.2 - - + -
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Residues in contact with PHE 596 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587V ASN* 2.5 79.6 + - + +
588V PHE* 4.6 2.5 - - - -
594V TYR* 3.3 13.3 + - + +
595V PHE* 1.3 76.8 - - - +
597V PHE* 1.3 62.8 + - - +
598V GLU* 3.4 38.6 - - + -
607V ARG* 3.3 42.4 - - + -
609V GLY 3.6 7.2 - - - +
610V SER* 4.4 7.6 - - - -
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Residues in contact with PHE 597 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570V LEU* 3.7 19.7 - - + -
573V ALA* 4.1 15.5 - - + -
574V LEU* 3.4 31.9 - - + -
584V TYR* 4.7 4.3 - + + -
585V THR 5.0 0.7 - - - -
586V PHE* 3.3 40.8 - + + +
595V PHE* 4.6 10.5 - + + -
596V PHE* 1.3 79.0 - - - +
598V GLU* 1.3 60.1 + - - +
607V ARG* 4.6 2.4 - - - +
608V LEU* 3.0 53.3 + - + +
609V GLY* 3.0 32.5 + - - -
611V PHE* 5.5 7.0 - + - -
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Residues in contact with GLU 598 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584V TYR* 3.9 1.0 - - - -
585V THR* 3.3 37.0 + - + +
587V ASN* 5.5 1.3 - - - +
596V PHE* 3.4 30.3 - - + -
597V PHE* 1.3 74.6 - - - +
599V LYS* 1.3 62.3 + - - +
600V ASN* 3.3 13.2 + - - +
605V SER* 5.1 6.6 - - - -
606V PHE* 3.0 29.5 - - - +
607V ARG* 3.4 25.2 + - - +
608V LEU* 4.1 0.4 - - - -
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Residues in contact with LYS 599 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569V GLU* 2.8 17.3 + - - +
572V LYS* 5.2 1.0 - - - +
583V VAL* 3.5 22.2 - - + -
584V TYR* 2.7 48.2 + - + +
598V GLU* 1.3 70.0 - - - +
600V ASN* 1.3 65.4 + - - +
601V LEU* 3.8 13.7 + - + -
605V SER* 4.2 0.5 - - - -
606V PHE* 2.7 61.5 + - + +
608V LEU* 3.6 18.0 - - + +
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Residues in contact with ASN 600 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582V ASP 4.2 14.9 + - - +
583V VAL* 3.6 14.7 - - - +
584V TYR 4.0 5.0 - - - +
585V THR* 3.2 31.0 - - + +
598V GLU* 3.3 12.9 + - - +
599V LYS* 1.3 72.8 - - - +
601V LEU* 1.3 77.7 + - - +
604V VAL 5.0 3.8 + - - -
605V SER* 4.8 9.3 - - - +
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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