Contacts of the strand formed by residues 512 - 516 (chain F) in PDB entry 4RYD
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 ARG 512 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422F HIS* 3.8 14.4 - - - -
504F HIS* 3.5 35.1 + - + +
505F LEU 3.5 3.4 - - - -
506F VAL* 3.9 18.7 - - + +
510F GLY 3.4 6.4 + - - +
511F THR* 1.3 74.4 - - - +
513F SER* 1.3 60.6 + - - +
514F THR* 4.9 2.2 + - - +
537F HIS* 4.7 2.6 + - - -
550F GLU* 2.6 46.1 + - - -
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Residues in contact with SER 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F SER* 4.1 4.7 - - - -
422F HIS* 3.9 4.7 - - - -
504F HIS* 3.3 1.5 - - - -
505F LEU* 2.7 44.8 + - - +
511F THR* 3.6 5.0 + - - +
512F ARG* 1.3 73.9 - - - +
514F THR* 1.3 59.5 + - - +
515F LEU* 3.3 8.8 + - - -
535F THR* 2.7 42.8 + - - +
537F HIS* 3.5 14.5 - - - +
538F SER* 4.9 3.1 + - - -
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Residues in contact with THR 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F CYS* 4.6 2.8 - - - -
334F SER* 3.6 11.2 + - - -
422F HIS* 2.8 39.7 + - + -
503F ILE 3.6 7.4 - - - +
504F HIS* 2.8 27.5 + - + +
512F ARG* 3.9 4.6 + - - +
513F SER* 1.3 70.8 - - - +
515F LEU* 1.3 61.0 + - - +
516F LEU 3.7 26.2 - - - +
517F ALA* 3.9 12.8 - - + +
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Residues in contact with LEU 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F SER* 4.3 0.7 + - - -
304F ASN* 3.0 32.8 + - - +
333F CYS* 5.5 0.4 - - - +
334F SER* 3.7 15.0 - - - +
489F ALA* 3.6 29.8 - - + -
491F LEU* 5.0 0.4 - - + -
503F ILE* 2.8 29.2 + - + +
505F LEU* 3.8 24.5 - - + +
513F SER* 4.0 18.4 - - - +
514F THR* 1.3 73.1 - - - +
516F LEU* 1.3 60.8 + - - +
533F PHE* 3.4 31.8 - - + +
534F MET 4.7 3.1 - - - +
535F THR* 4.4 9.2 - - + -
549F LEU* 4.2 4.3 - - + -
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Residues in contact with LEU 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F SER* 4.2 12.6 - - - +
305F CYS* 3.8 28.3 - - - -
498F ARG* 4.8 4.7 - - + +
499F GLY* 6.3 0.4 - - - -
501F LEU* 4.0 20.0 - - + +
502F ALA* 3.0 5.2 - - - +
503F ILE* 2.7 50.7 + - + +
514F THR* 3.3 7.8 - - - +
515F LEU* 1.3 82.0 - - - +
517F ALA* 1.3 74.4 + - - +
519F ARG* 4.6 7.2 - - + +
528F PHE* 3.8 31.4 - - + -
533F PHE* 4.0 9.9 - - + -
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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