Contacts of the strand formed by residues 508 - 512 (chain A) in PDB entry 5Y7G
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A GLU 4.4 4.0 - - - +
371A VAL* 4.2 9.0 - - + +
372A ARG* 4.1 31.2 - - + +
375A LEU* 5.0 1.8 - - + -
382A VAL* 4.2 16.4 - - + -
383A HIS 3.1 18.2 - - - +
384A TYR* 3.5 22.0 - - + -
385A VAL* 4.5 4.9 - - - -
506A PRO* 3.3 3.7 - - - +
507A ASP* 1.3 91.6 - - + +
509A ILE* 1.3 61.4 + - - +
520A MET* 3.3 10.2 - - - +
521A VAL* 2.9 42.5 + - + +
523A VAL* 3.9 21.8 - - + -
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Residues in contact with ILE 509 (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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382A VAL* 4.6 2.2 - - - -
383A HIS* 2.9 39.0 + - + +
385A VAL* 3.5 21.3 - - + -
389A LEU* 3.8 22.0 - - + -
390A ILE* 5.7 0.9 - - + -
474A LEU* 4.6 0.4 - - + -
482A LEU* 4.4 8.3 - - + -
490A TRP* 6.1 0.4 - - + -
508A LEU* 1.3 74.7 - - - +
510A GLN* 1.3 67.2 + - - +
511A PHE* 3.6 37.2 - - + -
518A TYR* 4.1 17.9 - - + -
519A ARG 3.5 10.1 - - - +
520A MET* 4.1 22.9 - - + -
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Residues in contact with GLN 510 (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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375A LEU* 3.8 23.8 + - - +
380A CYS* 3.7 8.4 - - - -
381A ALA 3.2 11.9 - - - +
382A VAL* 3.7 25.9 - - + +
509A ILE* 1.3 72.9 - - - +
511A PHE* 1.3 62.4 + - - +
512A TRP* 3.2 29.5 - - + -
518A TYR* 2.9 8.7 - - - +
519A ARG* 2.9 77.8 + - + +
521A VAL* 4.4 6.0 - - + +
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Residues in contact with PHE 511 (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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380A CYS* 3.7 3.5 - - - -
381A ALA* 2.8 34.4 + - + +
383A HIS* 4.2 7.0 - + - -
389A LEU* 4.2 0.9 - - + -
474A LEU* 4.0 20.9 - - + -
477A GLN* 3.1 30.7 - - + +
478A ALA* 3.5 33.9 - - + -
481A CYS* 3.3 36.1 - - + -
482A LEU* 4.2 5.8 - - + -
509A ILE* 3.6 28.7 - - + -
510A GLN* 1.3 73.6 - - - +
512A TRP* 1.3 62.8 + - - +
513A PRO* 3.4 9.7 - - + +
517A ARG 3.4 1.6 - - - +
518A TYR* 3.4 24.0 - - + -
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Residues in contact with TRP 512 (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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377A GLU* 5.5 1.7 - - + +
379A GLY 3.9 19.1 - - - +
380A CYS* 3.3 24.0 - - + +
481A CYS* 4.3 0.2 - - - -
510A GLN* 3.2 33.0 - - + -
511A PHE* 1.3 72.8 - - - +
513A PRO* 1.3 63.0 - - - +
514A ALA* 3.3 2.9 - - + -
515A GLN* 3.3 34.2 + - + +
516A ARG 2.8 22.0 + - - -
517A ARG* 2.9 48.1 + - + -
518A TYR* 3.8 24.9 - - - -
519A ARG* 3.9 16.2 - - + -
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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