Contacts of the strand formed by residues 502 - 505 (chain B) in PDB entry 5SUY
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 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A ARG* 4.1 17.5 + - - -
442A ARG 3.8 11.4 + - - -
443A MET* 3.5 44.5 - - + -
444A TRP* 3.7 47.8 - - + +
452B ALA* 4.7 4.0 - - + -
453B PHE 3.4 18.6 - - - +
454B LEU* 3.6 30.5 - - + +
490B HIS* 4.1 4.2 + - - -
491B THR* 3.1 27.3 + - + +
500B GLN 4.5 4.5 - - - -
501B CYS* 1.3 74.9 - - - +
503B TYR* 1.3 67.3 + - - +
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Residues in contact with TYR 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B ALA* 3.4 8.1 - - - +
453B PHE* 2.8 52.4 + + + +
454B LEU 4.3 0.2 - - - -
455B GLY* 3.6 19.7 - - - -
458B VAL* 5.6 0.2 - - + -
483B LEU* 4.0 8.1 - - + -
488B ILE* 4.3 12.6 - - + -
489B ARG 3.3 22.9 - - - +
490B HIS* 3.2 43.2 + + - -
491B THR* 4.4 2.9 - - - -
497B PHE* 3.4 19.0 - + - -
498B SER 2.9 40.5 + - - -
501B CYS* 3.2 28.0 - - + +
502B TYR* 1.3 71.4 - - - +
504B VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ILE* 3.9 27.6 - - + -
450B PRO 5.0 2.2 - - - +
451B ASN 4.4 4.9 - - - +
452B ALA* 4.2 8.7 - - - -
453B PHE* 3.6 11.0 - - - -
488B ILE* 3.5 4.5 - - - +
489B ARG* 2.9 58.3 + - + +
490B HIS 5.1 2.0 - - - +
491B THR* 4.0 14.1 - - + +
503B TYR* 1.3 77.8 - - - +
505B PHE* 1.3 69.6 + - - +
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A THR* 3.8 22.7 - - + -
430A MET* 3.5 32.1 - - + -
431A ALA* 3.5 46.0 - - + -
437A LEU* 3.8 16.8 - - + -
451B ASN* 5.1 7.8 + - + -
453B PHE* 3.5 27.3 - + - -
487B LEU 3.9 4.9 - - - -
488B ILE* 4.1 2.2 - - + -
489B ARG* 3.0 22.8 + - - -
504B VAL* 1.3 78.9 - - - +
506B GLY* 1.3 67.6 + - - +
508B LEU* 4.3 8.3 - - + -
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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