Contacts of the strand formed by residues 594 - 598 (chain A) in PDB entry 5G04
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 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 5.4 2.5 - - - -
18A GLN* 5.2 7.2 - - - +
88A ASP* 2.5 36.9 + - - +
89A TYR* 3.8 7.7 + - - +
90A ASP* 2.8 29.4 + - - -
482A VAL* 4.8 0.3 - - - +
590A PRO* 3.4 2.3 - - - +
591A VAL* 2.7 46.7 + - - +
592A HIS* 3.1 27.6 + - - +
593A ASN* 1.3 77.9 - - - +
595A VAL* 1.3 63.0 + - - +
606A ARG* 3.3 30.6 + - + +
607A ILE 3.4 3.6 - - - +
608A THR* 3.1 29.9 - - + +
533O THR* 3.8 24.1 - - - +
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Residues in contact with VAL 595 (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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480A ALA* 5.3 0.7 - - + -
481A PRO 3.9 11.7 - - - +
482A VAL* 4.2 12.8 - - + -
489A LEU* 3.8 22.2 - - + -
587A ILE* 3.5 30.3 - - + -
588A ARG 4.3 0.4 - - - +
589A ASP 4.2 3.8 - - - -
590A PRO* 3.8 21.8 - - + -
594A ARG* 1.3 81.5 - - - +
596A THR* 1.3 58.6 + - - +
597A LEU* 4.0 4.5 - - + -
606A ARG* 3.5 4.4 - - - -
607A ILE* 2.7 53.2 + - + +
609A ILE* 4.9 2.2 - - + -
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Residues in contact with THR 596 (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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20A PHE* 3.5 26.8 - - + -
587A ILE* 3.5 4.0 - - - +
588A ARG* 2.7 68.1 + - + +
589A ASP* 3.7 22.7 + - + +
595A VAL* 1.3 73.5 - - - +
597A LEU* 1.3 63.6 + - - +
604A MET* 4.0 14.7 - - - +
605A VAL 3.6 11.2 + - - -
606A ARG* 4.1 16.6 - - - +
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Residues in contact with LEU 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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497A LEU* 3.7 32.1 - - + -
511A ILE* 4.5 8.5 - - + -
584A ILE* 4.1 26.0 - - + +
586A SER 3.4 6.5 - - - +
587A ILE* 3.9 19.7 - - + -
595A VAL* 4.0 13.2 - - + -
596A THR* 1.3 83.6 + - - +
598A GLU* 1.3 60.4 + - - +
599A LEU* 3.7 4.1 + - + +
603A SER 3.9 0.5 - - - +
604A MET* 3.4 7.0 - - - -
605A VAL* 3.1 40.9 + - + +
607A ILE* 3.8 29.6 - - + -
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Residues in contact with GLU 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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584A ILE 2.3 23.6 - - - +
585A HIS* 2.9 44.9 + - - +
586A SER* 2.8 23.3 + - - +
588A ARG* 4.6 12.3 + - + +
596A THR 4.3 0.6 + - - -
597A LEU* 1.3 69.9 - - - +
599A LEU* 1.3 61.2 + - - +
602A GLY* 5.1 10.6 - - - +
604A MET* 3.6 39.4 - - + +
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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