Contacts of the strand formed by residues 324 - 327 (chain A) in PDB entry 1OHV
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 VAL 324 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A MET* 4.1 3.6 - - - -
143A ALA* 4.0 20.2 - - + -
146A THR* 5.3 3.1 - - + -
147A ILE* 4.2 23.3 - - + -
295A PHE 3.2 4.1 + - - +
296A LEU* 3.3 13.9 - - + -
297A VAL 2.9 24.6 + - - -
322A ALA* 3.8 2.9 - - - +
323A ASP* 1.3 93.0 - - + +
325A MET* 1.3 63.4 + - - +
336A PHE* 3.7 25.8 - - + -
337A PHE 3.4 12.6 - - - +
338A HIS* 3.9 8.5 - - + -
342A PHE* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 3.8 4.7 - - + -
127A MET* 4.0 19.5 - - + -
297A VAL* 3.2 20.6 - - + +
299A GLU* 3.6 18.8 - - + -
311A TRP* 3.4 48.0 - - + -
313A HIS* 3.4 32.5 - - + +
322A ALA* 5.2 0.2 - - + -
324A VAL* 1.3 75.1 - - - +
326A THR* 1.3 68.7 + - - +
327A PHE* 4.1 2.3 - - + -
336A PHE* 3.1 3.2 - - - -
337A PHE* 3.0 47.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 3.7 24.9 - - - +
140A ASN* 2.6 30.3 + - - +
143A ALA* 3.8 11.9 - - + -
296A LEU* 3.9 6.8 - - + +
297A VAL 3.0 4.7 + - - -
298A ASP* 3.4 18.5 + - - -
299A GLU* 2.9 29.7 + - - +
300A VAL* 4.2 3.8 - - - +
324A VAL* 4.7 0.2 - - + -
325A MET* 1.3 75.2 - - - +
327A PHE* 1.3 63.6 + - - +
335A GLY 3.4 5.4 - - - -
336A PHE* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.5 34.5 - - + -
130A LEU* 3.9 6.1 - - + -
131A ILE 4.9 0.2 - - - -
139A SER* 3.5 5.7 + - - -
299A GLU 4.5 0.9 - - - +
300A VAL* 3.8 12.3 - - - +
311A TRP* 3.7 24.9 - + + -
325A MET* 4.1 4.0 - - + -
326A THR* 1.3 80.0 - - - +
328A SER* 1.3 69.7 + - - +
331A MET* 3.7 12.1 - - + -
333A THR 3.7 12.1 - - - -
334A GLY* 3.2 35.0 - - - -
335A GLY* 3.2 33.2 + - - -
336A PHE* 3.6 4.0 - - - -
337A PHE* 3.4 34.8 - + - -
----------------------------------------------------------
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