Contacts of the strand formed by residues 537 - 541 (chain A) in PDB entry 5CH3
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 LYS 537 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A LEU* 3.8 7.4 + - - +
526A TRP* 5.3 0.5 + - - -
527A ASP* 4.9 13.1 - - + +
528A PRO 6.1 0.7 - - - +
529A ILE* 3.3 24.9 - - + +
533A ASP* 5.6 6.9 + - - +
535A VAL* 3.7 11.0 + - - +
536A TYR* 1.3 73.0 - - - +
538A CYS* 1.3 60.9 + - - +
547A MET* 4.2 18.8 - - + +
548A ILE 3.4 9.4 - - - +
549A ASP* 2.6 33.2 + - - +
550A VAL* 4.5 0.7 - - - -
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Residues in contact with CYS 538 (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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422A TRP* 6.0 0.4 - - + -
443A LEU* 3.2 24.7 - - + +
444A TYR 4.2 6.3 - - - +
445A ARG* 3.7 29.4 - - - -
537A LYS* 1.3 74.1 - - - +
539A LEU* 1.3 62.0 + - - +
540A ASN 3.4 0.2 + - - -
547A MET* 3.5 10.8 - - - -
548A ILE* 2.9 51.7 + - - -
550A VAL* 3.8 22.0 - - + -
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Residues in contact with LEU 539 (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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443A LEU 2.9 10.1 + - - -
444A TYR* 3.3 4.3 - - - +
445A ARG 2.9 23.9 + - - -
503A ILE* 4.1 8.1 - - + -
521A MET* 3.9 11.7 - - + -
524A VAL* 3.8 24.5 - - + -
526A TRP* 3.5 46.4 - - + +
538A CYS* 1.3 71.2 - - - +
540A ASN* 1.3 59.6 + - - +
541A ILE* 3.6 24.2 + - + +
545A LEU* 4.1 8.7 - - + -
546A LYS 3.7 25.4 - - - +
547A MET* 3.7 16.8 - - - +
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Residues in contact with ASN 540 (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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445A ARG* 3.0 43.9 + - + +
447A ASP* 3.0 26.9 + - - +
538A CYS 3.4 2.4 + - - -
539A LEU* 1.3 69.2 - - - +
541A ILE* 1.3 60.3 + - - +
542A SER* 4.2 8.5 - - - -
544A GLU 3.5 4.6 + - - +
545A LEU* 3.5 5.2 - - - -
546A LYS* 2.9 42.0 + - + +
548A ILE* 3.7 25.5 - - + +
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Residues in contact with ILE 541 (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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444A TYR* 4.1 26.7 - - + -
445A ARG 2.8 12.9 + - - +
446A PHE* 4.3 11.9 - - + -
447A ASP* 2.8 30.6 + - - -
448A PHE* 3.2 3.1 + - + +
496A THR* 5.1 6.5 - - + -
499A ARG* 5.5 4.7 - - + -
500A MET* 3.7 42.6 - - + -
503A ILE* 4.4 8.5 - - + -
504A TRP* 4.9 2.7 - - + -
526A TRP* 5.6 0.4 - - + -
539A LEU* 3.8 28.3 - - + +
540A ASN* 1.3 74.3 - - - +
542A SER* 1.3 61.5 + - - +
545A LEU* 3.7 20.2 - - + -
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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