Contacts of the strand formed by residues 508 - 512 (chain F) in PDB entry 4R8A
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 LEU 508 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F GLU 4.2 11.2 - - - +
371F VAL* 4.0 16.8 - - + -
372F ARG* 4.1 21.1 - - + +
375F LEU* 5.0 5.2 - - + -
382F VAL* 4.2 12.1 - - + -
383F HIS 3.2 18.4 - - - +
384F TYR* 3.7 25.1 - - + -
506F PRO* 4.5 1.0 - - - +
507F ASP* 1.3 88.9 - - + +
509F ILE* 1.3 63.8 + - - +
520F MET* 3.4 5.4 - - - +
521F VAL* 2.7 48.6 + - + +
523F VAL* 3.8 23.1 - - + -
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Residues in contact with ILE 509 (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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381F ALA 4.3 0.2 - - - +
382F VAL* 3.6 1.8 - - - +
383F HIS* 2.9 33.6 + - + +
385F VAL* 3.4 28.0 - - + +
389F LEU* 3.8 14.8 - - + -
390F ILE* 5.8 3.6 - - + -
482F LEU* 5.2 1.6 - - + -
505F LEU* 6.2 0.7 - - + -
506F PRO* 4.7 9.0 - - + +
508F LEU* 1.3 78.3 - - - +
510F GLN* 1.3 64.1 + - - +
511F PHE* 3.7 36.1 - - + -
518F TYR* 4.5 10.3 - - + -
519F ARG 4.4 1.3 - - - +
520F MET* 3.4 47.1 - - + -
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Residues in contact with GLN 510 (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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375F LEU* 3.2 34.1 - - - +
380F CYS* 3.6 8.4 - - - -
381F ALA 3.4 5.2 - - - +
382F VAL* 3.6 29.2 - - + +
509F ILE* 1.3 74.9 - - - +
511F PHE* 1.3 63.6 + - - +
512F TRP* 3.8 30.5 + - - +
518F TYR* 3.4 2.6 - - - +
519F ARG* 2.9 63.6 + - - +
521F VAL* 4.3 11.5 - - + +
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Residues in contact with PHE 511 (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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380F CYS* 3.6 3.8 - - - -
381F ALA 2.9 31.6 + - - +
383F HIS* 3.9 12.1 - + - -
389F LEU* 3.9 17.5 - - + -
474F LEU* 3.9 22.4 - - + -
477F GLN* 3.8 31.2 - - + +
478F ALA* 3.9 21.1 - - + -
481F CYS* 3.6 33.4 - - + -
482F LEU* 4.2 14.8 - - + -
509F ILE* 3.7 29.4 - - + -
510F GLN* 1.3 75.2 - - - +
512F TRP* 1.3 60.6 + - - +
513F PRO* 3.2 8.8 - - + +
517F ARG 3.7 2.7 - - - -
518F TYR* 3.8 8.5 - - + -
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Residues in contact with TRP 512 (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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377F GLU* 3.9 17.3 - - - -
379F GLY* 3.7 9.2 - - - +
380F CYS* 3.5 38.1 - - + -
510F GLN* 3.8 34.7 + - - +
511F PHE* 1.3 75.0 - - - +
513F PRO* 1.3 61.2 - - - +
514F ALA* 3.2 2.5 - - - -
515F GLN* 3.0 35.2 + - + +
516F ARG 2.9 21.7 + - - -
517F ARG 2.8 37.5 + - - +
518F TYR* 4.3 0.2 - - - -
519F ARG* 3.2 46.5 - - - +
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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