Contacts of the strand formed by residues 501 - 506 (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 TYR 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A LYS* 4.9 1.0 + - - -
493A LEU* 4.6 26.6 - - + +
494A THR 5.3 8.7 - - - -
498A THR* 3.1 19.9 + - + +
499A PHE 4.5 0.2 - - - +
500A LYS* 1.3 108.6 + - + +
502A ARG* 1.3 81.8 + - - +
503A PHE* 4.1 11.8 + + + -
512A LEU* 3.7 19.5 - - + -
513A ILE 3.7 2.5 - - - -
514A ILE* 3.6 49.4 - - + -
516A GLU 5.2 3.4 + - - -
521A ASP* 2.9 36.6 + - + +
525A TYR* 5.3 2.5 - + - -
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Residues in contact with ARG 502 (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 THR* 2.7 41.4 + - - -
499A PHE* 3.5 24.3 + - - +
501A TYR* 1.3 88.8 + - - +
503A PHE* 1.3 63.2 + - - +
504A LYS* 3.7 13.3 - - + +
511A HIS 3.1 6.4 - - - +
512A LEU* 3.3 3.1 - - - +
513A ILE* 3.0 50.4 + - + -
515A ASN* 3.6 20.2 - - - +
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Residues in contact with PHE 503 (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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486A TRP* 3.6 43.7 - + + -
493A LEU* 4.0 25.8 - - + -
494A THR 4.4 2.2 - - - -
495A ARG* 3.9 32.5 - - + -
498A THR* 4.0 20.1 + - + -
501A TYR* 4.1 7.4 - - + -
502A ARG* 1.3 73.8 - - - +
504A LYS* 1.3 63.5 + - - +
505A LYS 4.2 0.5 + - - -
511A HIS 3.5 3.1 - - - -
512A LEU* 3.5 28.0 - - + -
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Residues in contact with LYS 504 (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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472A GLU* 5.3 3.2 + - - -
502A ARG* 3.7 19.1 - - + +
503A PHE* 1.3 78.4 - - - +
505A LYS* 1.3 60.4 + - - +
506A ASP* 4.0 15.7 + - - +
510A HIS* 3.3 7.8 + - - +
511A HIS* 2.8 61.5 + - + +
513A ILE* 3.5 28.7 - - - +
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Residues in contact with LYS 505 (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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481A GLY* 3.9 27.1 + - - -
482A ALA 5.7 0.7 - - - -
503A PHE 4.2 0.6 + - - -
504A LYS* 1.3 73.5 - - - +
506A ASP* 1.3 66.2 + - - +
507A GLY* 3.9 13.9 + - - +
509A ARG 3.8 3.1 - - - +
510A HIS* 3.8 27.8 - - + +
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Residues in contact with ASP 506 (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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504A LYS* 4.0 17.3 - - - +
505A LYS* 1.3 78.8 - - - +
507A GLY* 1.3 57.9 + - - +
508A GLN 3.0 8.8 + - - -
509A ARG* 2.8 68.3 + - - +
511A HIS* 4.8 2.8 - - - -
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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