Contacts of the strand formed by residues 528 - 535 (chain E) in PDB entry 4OMC
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 PHE 528 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E VAL* 3.8 23.8 - - + -
305E CYS* 4.6 4.3 - - - -
491E LEU 3.9 13.2 - - - +
492E THR* 3.1 5.5 - - - +
493E LEU* 2.9 56.7 + - + +
498E ARG* 3.6 28.0 - - + -
501E LEU* 4.4 6.5 - - + -
503E ILE* 4.7 1.1 - - + -
516E LEU* 3.7 35.0 - - + -
519E ARG* 5.6 0.4 - - - -
522E ASP* 5.3 0.7 - - - -
526E ASP 4.8 2.0 - - - -
527E GLY* 1.3 76.6 - - - -
529E ASN* 1.3 60.9 + - - +
530E ASP 3.8 0.4 - - - -
531E TRP* 3.9 19.3 - + + -
533E PHE* 3.8 28.7 - + + -
602E FMT 3.6 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 529 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492E THR* 4.3 11.7 + - - +
526E ASP 5.7 2.0 - - - +
528E PHE* 1.3 70.0 - - - +
530E ASP* 1.3 75.6 + - - +
531E TRP* 3.2 3.5 + - - -
602E FMT 3.0 23.5 + - - +
268F ARG* 4.7 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 530 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490E ARG* 3.1 47.8 + - - +
491E LEU 3.1 6.4 + - - -
492E THR* 2.8 23.8 + - - +
529E ASN* 1.3 77.6 + - - +
531E TRP* 1.3 63.5 + - - +
532E ALA 3.6 0.5 + - - -
565E LYS* 2.9 26.0 + - - +
233F ASP* 4.5 8.0 - - - +
267F ALA* 5.3 2.3 - - - +
268F ARG* 3.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 531 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E VAL* 3.7 28.7 - - + +
264E ASP* 3.6 25.1 - - - -
265E GLY* 4.5 2.2 - - - -
304E ASN 2.8 28.3 + - - -
305E CYS* 3.9 5.8 - - - +
307E GLY* 3.9 24.0 - - - -
310E ASN* 4.4 8.7 - - - +
489E ALA 3.3 0.9 - - - +
490E ARG* 4.2 0.4 - - - -
491E LEU 3.0 25.9 + - - -
528E PHE* 3.9 28.7 - + + -
529E ASN 3.2 2.4 - - - -
530E ASP* 1.3 77.7 - - - +
532E ALA* 1.3 62.4 + - - +
533E PHE* 3.3 42.9 + + + -
602E FMT 4.0 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ASN* 2.5 30.3 + - - +
488E GLN* 3.8 19.7 + - - +
489E ALA 3.9 3.8 - - - -
490E ARG* 3.5 39.3 - - + +
530E ASP 3.6 2.4 + - - -
531E TRP* 1.3 73.4 - - - +
533E PHE* 1.3 61.7 + - - +
534E MET* 3.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 533 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E ASN* 4.2 9.2 - - + +
305E CYS* 5.1 1.6 - - - -
310E ASN* 4.0 5.4 - - - +
488E GLN* 3.1 4.2 - - - -
489E ALA* 2.9 44.4 + - - +
491E LEU* 3.8 29.8 - - + -
503E ILE* 4.3 7.0 - - + -
515E LEU* 3.3 52.5 - - + +
516E LEU* 4.0 15.5 - - + -
528E PHE* 3.8 33.0 - + - -
531E TRP* 3.5 38.1 - + + -
532E ALA* 1.3 69.9 - - - +
534E MET* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 534 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E ASN* 3.6 2.3 + - - +
310E ASN* 3.0 48.2 + - - +
311E SER 3.7 17.5 - - - +
312E ILE* 4.0 16.6 - - + -
314E THR 5.5 0.4 - - - +
334E SER* 2.7 22.7 + - - -
335E SER* 3.4 37.8 + - - +
486E HIS* 4.1 18.8 - - + -
487E ALA 3.4 11.2 - - - +
488E GLN* 4.2 7.4 - - + +
515E LEU* 4.8 1.6 - - - -
532E ALA 4.1 2.7 - - - +
533E PHE* 1.3 75.9 - - - +
535E THR* 1.3 85.7 + - - +
536E THR* 3.6 13.2 - - + -
608E NA 4.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 535 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E SER* 3.4 17.8 - - - -
485E GLU 4.4 1.2 - - - +
486E HIS* 3.9 2.4 - - - -
487E ALA* 3.0 42.9 + - + +
505E LEU* 4.7 13.9 - - + -
513E SER* 2.6 34.2 + - - +
515E LEU* 4.6 3.4 - - + -
533E PHE 5.9 0.2 - - - +
534E MET* 1.3 83.2 - - - +
536E THR* 1.3 60.8 + - - +
537E HIS* 3.1 13.0 + - - +
538E SER* 5.1 8.6 + - - +
547E TRP* 5.7 2.0 - - + -
----------------------------------------------------------
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