Contacts of the strand formed by residues 594 - 599 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587P ASN 3.7 1.7 - - - +
588P PHE* 2.9 7.3 - - - -
589P SER* 2.6 41.3 + - - +
592P SER* 3.1 16.6 - - - +
593P CYS* 1.3 75.0 - - - +
595P PHE* 1.3 73.2 + - - +
596P PHE* 4.5 11.1 - + + -
610P SER* 3.2 30.9 + - - -
611P PHE* 3.0 30.2 - - - -
612P ASN* 3.0 29.6 - - - +
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Residues in contact with PHE 595 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508P ILE* 4.9 2.5 - - + -
510P LEU* 3.5 28.7 - - + -
520P LEU* 3.5 31.9 - - + -
534P ILE* 4.1 19.7 - - + -
536P LEU* 4.6 13.9 - - + -
574P LEU* 5.7 2.0 - - + -
586P PHE* 3.6 36.1 - + + -
587P ASN 3.4 10.8 - - - -
588P PHE* 3.6 17.9 - + + -
594P TYR* 1.3 73.9 - - - +
596P PHE* 1.3 72.3 + - - +
597P PHE* 6.0 0.4 - + - -
610P SER* 3.1 1.4 - - - -
611P PHE* 2.7 46.8 + - + +
613P LEU* 3.7 9.9 - - + -
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Residues in contact with PHE 596 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586P PHE* 3.9 1.0 - - - -
587P ASN* 3.2 58.5 + - + -
589P SER* 4.6 14.4 - - - -
594P TYR* 4.5 16.6 - + + -
595P PHE* 1.3 82.2 - - - +
597P PHE* 1.3 63.6 + - - +
598P GLU* 3.9 20.4 - - - +
607P ARG* 4.1 27.1 - - + +
609P GLY 3.1 14.4 - - - +
610P SER* 3.3 14.4 - - - -
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Residues in contact with PHE 597 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570P LEU* 3.3 29.8 - - + -
573P ALA* 3.4 31.9 - - + -
574P LEU* 3.4 30.1 - - + -
584P TYR* 5.7 0.4 - - + -
585P THR 3.6 4.5 - - - +
586P PHE* 3.4 33.9 - + + -
595P PHE* 5.4 1.1 - + + -
596P PHE* 1.3 76.1 - - - +
598P GLU* 1.3 64.3 + - - +
607P ARG* 3.6 2.0 - - - -
608P LEU* 2.8 29.7 + - + +
609P GLY* 2.9 36.2 + - - -
611P PHE* 5.0 8.3 - + - -
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Residues in contact with GLU 598 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584P TYR* 3.5 5.7 - - - -
585P THR* 3.4 42.8 + - - +
586P PHE* 4.9 0.9 - - - -
587P ASN* 5.0 3.4 - - - +
596P PHE* 3.9 17.2 - - - +
597P PHE* 1.3 77.7 - - - +
599P LYS* 1.3 55.9 + - - +
600P ASN* 3.4 6.5 + - - +
605P SER* 2.9 24.0 - - - +
606P PHE 2.9 22.0 - - - +
607P ARG* 3.2 33.8 + - - +
608P LEU* 3.2 7.0 - - - -
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Residues in contact with LYS 599 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569P GLU* 3.6 24.9 + - - -
572P LYS* 5.8 2.9 - - - +
583P VAL* 3.2 24.7 - - + +
584P TYR* 3.5 24.0 - - + -
598P GLU* 1.3 69.0 - - - +
600P ASN* 1.3 69.3 + - - +
601P LEU* 3.3 29.5 - - + +
605P SER* 2.8 18.2 + - - -
606P PHE* 3.0 19.7 + - + +
608P LEU* 3.1 6.3 - - + +
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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