Contacts of the strand formed by residues 508 - 512 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 4.4 3.4 - - + +
371B VAL* 4.3 13.0 - - + +
372B ARG* 4.2 19.5 - - + +
375B LEU* 5.4 2.0 - - + -
382B VAL* 4.3 17.5 - - + -
383B HIS 3.1 14.8 - - - +
384B TYR* 3.5 24.2 - - + -
506B PRO* 3.4 3.3 - - - +
507B ASP* 1.3 91.2 - - + +
509B ILE* 1.3 71.6 + - - +
520B MET* 3.5 4.9 - - - +
521B VAL* 2.8 47.8 + - + +
523B VAL* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 3.4 3.3 - - - -
383B HIS* 2.9 36.3 + - + +
385B VAL* 3.8 30.1 - - + +
389B LEU* 3.4 30.5 - - + -
390B ILE* 4.2 12.8 - - + -
482B LEU* 5.8 1.6 - - + -
506B PRO 5.7 0.4 - - - +
508B LEU* 1.3 80.8 - - - +
510B GLN* 1.3 64.2 + - - +
511B PHE* 3.6 34.5 - - + -
518B TYR* 4.9 4.5 - - + -
519B ARG 3.7 11.2 - - - +
520B MET* 4.4 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 3.4 36.1 - - - +
380B CYS* 3.7 12.5 - - - -
381B ALA 2.8 13.5 - - - +
382B VAL* 3.7 10.7 - - + +
509B ILE* 1.3 75.2 - - - +
511B PHE* 1.3 60.6 - - - +
512B TRP* 3.8 21.9 - - + -
518B TYR* 3.1 8.0 - - - +
519B ARG* 2.5 86.8 + - + +
521B VAL* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B CYS* 3.3 4.4 - - - -
381B ALA* 2.8 35.7 + - + -
383B HIS* 4.2 10.8 - + - -
389B LEU* 4.1 7.0 - - + -
474B LEU* 3.9 21.1 - - + -
477B GLN* 3.1 44.6 - - + +
478B ALA* 3.9 23.1 - - + -
481B CYS* 3.6 32.8 - - + -
482B LEU* 4.5 7.6 - - + -
509B ILE* 3.6 26.5 - - + -
510B GLN* 1.3 74.5 - - - +
512B TRP* 1.3 62.4 + - - +
513B PRO* 3.4 6.8 - - + +
517B ARG 3.6 1.3 - - - -
518B TYR* 3.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLY 3.5 5.4 - - - +
380B CYS* 2.7 45.6 - - + +
510B GLN* 3.8 16.8 - - + -
511B PHE* 1.3 72.8 - - - +
513B PRO* 1.3 62.6 - - - +
514B ALA 3.3 2.7 - - - -
515B GLN* 3.4 27.7 + - + +
516B ARG 3.0 20.8 + - - -
517B ARG* 2.9 68.8 + - + +
518B TYR* 3.3 29.4 - - - -
519B ARG* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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