Contacts of the strand formed by residues 524 - 528 (chain A) in PDB entry 2MQ0
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 HIS 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A LEU 3.4 2.8 - - - +
489A ASP* 2.6 61.2 + - - +
490A GLY 4.5 0.7 + - - -
523A GLY* 1.3 73.1 - - - -
525A TYR* 1.3 63.4 + - - +
526A ALA* 3.6 3.3 + - + +
535A LEU* 4.6 19.3 - - + -
536A ALA 3.5 6.1 - - - +
537A GLU* 2.6 46.2 + - + -
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Residues in contact with TYR 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.8 7.7 - - + +
473A PHE* 3.6 26.9 - + + -
486A TRP* 5.1 11.0 - + + -
487A LEU 3.3 12.1 - - - +
488A LYS* 3.5 23.3 - - + -
493A LEU* 4.6 15.9 - - + -
501A TYR* 5.3 1.9 - - - -
512A LEU* 4.9 7.2 - - + -
514A ILE* 3.2 26.2 - - + +
517A ALA* 5.8 0.3 - - - +
521A ASP* 2.8 20.7 + - - +
522A ALA* 3.1 22.8 + - - -
524A HIS* 1.3 70.8 - - - +
526A ALA* 1.3 60.2 + - - +
535A LEU* 3.4 5.9 - - - +
536A ALA* 2.8 51.0 + - + +
538A LEU* 3.5 26.5 - - + +
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Residues in contact with ALA 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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460A LEU* 4.7 0.4 - - - -
485A LYS 3.3 3.6 - - - +
486A TRP* 5.1 2.9 - - - -
487A LEU* 3.0 40.1 + - + +
524A HIS 3.6 2.7 + - - +
525A TYR* 1.3 77.0 - - - +
527A LEU* 1.3 61.5 + - - +
528A CYS* 3.5 10.2 + - - -
533A GLN* 3.9 17.3 - - - +
534A ALA 3.7 4.9 - - - -
535A LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 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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456A ILE* 3.6 30.8 - - + +
460A LEU* 4.1 14.9 - - + +
475A CYS* 4.0 30.7 - - + -
477A VAL* 4.8 4.5 - - + -
484A VAL* 3.7 26.9 - - + -
485A LYS 3.5 13.7 - - - +
486A TRP* 3.6 31.9 - - + +
510A HIS* 5.5 1.6 - - + -
526A ALA* 1.3 70.0 - - - +
528A CYS* 1.3 59.4 + - - +
529A THR* 4.0 12.6 - - + -
532A GLY 3.5 17.2 - - - +
533A GLN* 3.7 8.2 + - - -
534A ALA 3.5 7.0 + - - +
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Residues in contact with CYS 528 (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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484A VAL* 3.5 2.1 - - - -
485A LYS* 2.8 52.3 + - + +
487A LEU* 3.5 32.8 - - - -
526A ALA* 4.0 11.7 - - - -
527A LEU* 1.3 73.0 - - - +
529A THR* 1.3 63.2 - - - +
532A GLY 4.8 0.4 - - - -
533A GLN* 4.9 10.8 - - - +
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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