Contacts of the strand formed by residues 536 - 540 (chain D) in PDB entry 4YFF
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 ALA 536 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D LEU* 5.1 4.0 - - + -
463D ILE* 4.5 11.4 - - + -
465D PHE* 5.6 0.4 - - + -
489D ILE* 4.2 14.4 - - + -
490D LYS 3.3 12.8 - - - +
491D ARG* 4.7 8.5 - - + +
506D PHE* 3.9 3.3 - - - -
527D ALA* 3.1 8.5 - - - +
528D CYS* 2.8 38.1 + - + +
534D GLN 3.3 7.7 + - - +
535D PHE* 1.3 78.3 - - - +
537D ILE* 1.3 63.2 + - - +
538D VAL* 4.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D ILE* 3.3 4.3 - - - +
490D LYS* 2.8 45.2 + - + +
506D PHE* 3.6 27.1 - - + -
509D GLU* 3.5 38.8 - - + +
510D VAL* 4.2 12.6 - - + -
513D LEU* 3.5 25.8 - - + -
524D PHE* 4.2 6.1 - - + -
526D GLY 3.9 2.7 - - - -
527D ALA* 4.3 3.1 - - + -
536D ALA* 1.3 75.7 - - - +
538D VAL* 1.3 67.5 + - - +
539D THR* 4.2 4.5 - - + -
801D 4CV 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D LEU* 3.6 24.7 - - + -
463D ILE* 4.0 21.5 - - + -
482D CYS* 4.2 6.3 - - + -
487D VAL* 3.7 37.7 - - + -
488D ALA 3.5 3.1 - - - +
489D ILE* 4.2 10.1 - - + -
524D PHE* 3.6 2.8 - - - -
525D VAL* 3.0 35.4 + - + -
526D GLY 3.0 15.0 + - - +
536D ALA 4.9 1.3 - - - -
537D ILE* 1.3 82.2 - - - +
539D THR* 1.3 68.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D VAL* 3.1 22.9 - - - +
488D ALA* 2.9 14.1 + - - +
513D LEU* 4.8 4.5 - - + -
522D ILE* 3.7 20.6 - - + +
523D GLN 3.3 14.6 - - - +
524D PHE* 4.6 7.2 - - + -
525D VAL* 3.7 7.6 - - - -
537D ILE* 4.2 8.7 - - + -
538D VAL* 1.3 79.2 - - - +
540D GLN* 1.3 72.4 + - - +
801D 4CV 2.8 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D LYS* 6.5 0.2 - - - -
486D ILE 4.3 5.2 - - - +
487D VAL* 4.9 0.7 - - - -
488D ALA 4.0 0.6 + - - -
521D VAL 4.0 4.0 - - - +
522D ILE* 3.5 20.9 - - + +
523D GLN* 3.1 60.8 + - + +
525D VAL* 3.9 5.4 - - + +
539D THR* 1.3 88.5 + - - +
541D TYR* 1.3 61.6 + - - +
542D ILE* 3.8 17.1 - - + +
597D TYR* 2.9 35.5 + - - -
603D VAL* 4.9 1.0 - - - +
801D 4CV 3.5 10.7 - - - -
----------------------------------------------------------
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