Contacts of the strand formed by residues 597 - 601 (chain A) in PDB entry 6A69
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 597 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A SER* 5.4 7.8 + - - +
515A VAL* 5.0 14.4 - - + +
587A THR* 4.4 0.3 - - - +
589A LEU* 2.6 29.8 + - - +
590A LYS 2.5 42.1 + - - +
596A TYR* 1.3 72.8 - - - +
598A ILE* 1.3 61.2 + - - +
599A PHE* 3.6 36.9 + - + -
652A PHE* 5.5 8.5 - - + -
654A ASP 5.5 0.4 - - - -
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Residues in contact with ILE 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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586A SER* 5.8 2.9 - - - -
587A THR 3.3 15.3 - - - +
588A VAL* 3.7 38.4 - - + +
596A TYR* 3.2 17.9 + - + +
597A ARG* 1.3 71.3 - - - +
599A PHE* 1.3 70.8 + - - +
652A PHE* 4.4 2.2 - - - -
653A ARG* 3.2 54.2 + - + +
654A ASP* 4.7 13.2 + - + +
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Residues in contact with PHE 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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512A SER* 4.5 14.1 - - - -
515A VAL* 3.9 24.5 - - + -
516A THR* 3.6 37.9 - - + -
519A SER* 5.2 1.8 - - - -
586A SER* 3.3 2.8 - - - -
587A THR* 2.7 54.2 + - + +
589A LEU* 6.2 1.1 - - + -
597A ARG* 3.6 42.6 - - + -
598A ILE* 1.3 79.8 - - - +
600A SER* 1.3 62.4 + - - +
650A LEU 5.9 0.4 - - - -
651A ALA 3.4 13.7 - - - +
652A PHE* 3.4 33.2 - + + -
653A ARG* 4.9 1.6 - - - +
677A ILE* 5.1 3.4 - - + -
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Residues in contact with SER 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A SER* 4.8 2.9 - - - -
586A SER* 3.6 22.2 - - - +
587A THR* 4.5 1.3 - - - +
599A PHE* 1.3 81.4 - - - +
601A LYS* 1.3 65.3 + - - +
607A ILE* 4.0 10.3 - - - +
650A LEU* 4.2 2.7 - - - -
651A ALA* 2.5 55.5 + - - +
652A PHE 4.8 1.7 + - - -
653A ARG* 5.7 4.8 - - - +
674A LEU* 5.4 3.3 - - - +
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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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520A VAL* 3.4 29.0 + - + +
521A ASN* 4.0 0.2 + - - -
545A THR* 5.9 1.3 - - - +
546A GLU* 3.4 27.9 + - + +
549A LEU* 6.0 2.5 - - - -
584A SER* 3.3 12.9 - - - -
585A MET* 3.0 60.5 + - + +
600A SER* 1.3 76.7 - - - +
602A GLY* 1.3 62.8 + - - +
607A ILE* 3.3 12.4 - - - +
648A ILE* 4.4 13.9 - - + -
650A LEU* 3.7 27.9 - - + +
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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