Contacts of the strand formed by residues 524 - 527 (chain A) in PDB entry 1QWN
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 PHE 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A GLN* 4.8 2.6 - - - +
502A GLN* 3.2 45.0 + - + +
505A VAL* 3.7 20.2 - - + -
506A TYR* 3.7 25.4 - + + -
522A SER* 3.3 7.7 - - - -
523A TYR* 1.3 82.3 - - + +
525A THR* 1.3 66.6 + - - +
526A LEU 4.3 0.3 + - - -
554A HIS 5.2 0.4 - - - -
556A VAL* 3.9 20.2 - - + -
932A PHE* 3.7 29.2 - - + -
933A ILE 3.2 6.5 - - - +
934A PHE* 3.5 40.6 - + + -
935A ALA* 4.3 0.4 - - - +
939A TRP* 3.6 29.8 - + - -
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Residues in contact with THR 525 (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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498A GLN* 3.8 9.0 - - - +
522A SER* 5.1 8.3 - - - -
524A PHE* 1.3 80.3 - - - +
526A LEU* 1.3 68.7 + - - +
527A ASP 3.7 0.2 + - - -
541A THR* 4.2 22.3 + - + +
932A PHE* 3.4 3.6 - - - -
933A ILE* 2.9 44.7 + - - +
935A ALA* 4.9 12.1 - - + -
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Residues in contact with LEU 526 (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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435A TYR* 3.5 40.2 - - + +
498A GLN* 3.0 46.2 + - + +
501A MET* 4.2 12.1 - - + -
502A GLN* 6.1 0.2 - - - +
524A PHE 4.3 0.2 + - - -
525A THR* 1.3 79.8 + - - +
527A ASP* 1.3 61.3 + - - +
528A ASP 4.1 1.0 + - - +
540A ARG* 6.0 1.2 - - - -
541A THR* 5.6 4.3 + - - +
930A ASP* 4.5 3.6 - - + +
931A LYS 3.3 21.1 - - - +
932A PHE* 3.5 34.8 - - + -
933A ILE* 5.5 0.5 - - - +
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Residues in contact with ASP 527 (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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525A THR 3.7 0.2 + - - -
526A LEU* 1.3 76.3 - - - +
528A ASP* 1.3 59.3 + - - +
540A ARG* 2.8 57.0 + - - +
541A THR 4.4 8.1 + - - +
570A ASP 3.3 3.8 - - - +
571A PHE* 3.9 12.5 - - + -
572A TYR* 5.4 0.9 + - - -
931A LYS* 2.8 57.4 + - + +
933A ILE* 3.9 21.3 - - + +
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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