Contacts of the strand formed by residues 732 - 734 (chain B) in PDB entry 1OFD
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 732 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B PHE* 4.1 20.6 - - + -
496B LYS 3.1 20.4 - - - +
497B GLN* 3.8 23.8 - - + -
498B ARG* 3.6 16.9 - - - +
651B HIS* 3.9 4.7 - + - -
654B ALA* 3.8 11.0 - - + -
655B CYS* 3.6 36.6 - - - -
658B GLY* 4.3 6.3 - - - -
659B TYR* 3.7 32.1 - + - +
726B TYR* 3.0 29.6 - + - -
730B GLN 2.7 12.1 + - - +
731B ILE* 1.3 95.4 - - - +
733B GLU* 1.3 59.5 + - - +
734B ALA 4.3 0.2 - - - -
749B THR* 3.9 10.9 - - - +
750B THR* 5.0 2.9 + - - +
1039B ILE* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR 3.9 0.2 - - - +
495B PHE* 3.6 0.7 - - - -
496B LYS* 2.8 37.1 + - + +
498B ARG* 4.0 4.5 - - + +
732B PHE* 1.3 75.6 - - - +
734B ALA* 1.3 71.8 + - - +
735B ILE* 4.3 6.9 - - + +
749B THR* 4.3 1.1 - - - -
750B THR* 3.9 12.5 + - - +
752B ARG* 2.8 36.9 + - - +
1038B GLU* 3.5 2.1 - - + +
1039B ILE* 2.9 39.7 + - + +
1078B SER* 2.7 31.6 + - - +
1082B LEU* 4.2 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR 3.3 7.2 - - - +
495B PHE* 4.3 8.3 - - + +
733B GLU* 1.3 76.9 - - - +
735B ILE* 1.3 65.6 + - - +
737B LEU* 3.9 26.0 - - + -
742B VAL* 5.0 2.5 - - + -
749B THR* 3.7 13.4 - - + +
750B THR 3.0 19.2 + - - +
751B SER* 3.4 28.9 - - - +
752B ARG 4.3 2.6 + - - -
----------------------------------------------------------
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