Contacts of the helix formed by residues 328 - 332 (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 SER 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS* 3.4 10.8 - - - -
136A GLY* 3.2 33.2 + - - -
299A GLU 4.8 0.5 + - - +
300A VAL* 3.6 17.2 - - - +
303A GLY 5.3 0.9 - - - +
327A PHE* 1.3 80.6 - - - +
329A LYS* 1.3 78.3 + - - +
330A LYS* 2.9 5.2 + - - +
331A MET* 3.0 15.6 + - - +
333A THR 3.4 13.7 - - - -
334A GLY* 3.7 4.9 - - - -
600A PLP 4.4 0.7 + - - -
354B TRP* 3.6 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.4 32.5 - - - +
73A SER 3.7 11.0 - - - +
74A SER* 3.2 23.1 - - - +
300A VAL* 3.4 24.7 - - + +
301A GLN* 3.6 11.2 - - + +
328A SER* 1.3 79.4 + - - +
330A LYS* 1.3 65.8 + - - +
332A MET* 3.0 13.5 + - - -
500A ACT 4.4 1.4 - - - +
600A PLP 1.4 81.1 + - - +
353B THR* 3.1 23.6 - - + +
354B TRP* 3.5 21.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 5.1 1.4 + - - +
73A SER* 3.3 41.9 + - - +
74A SER* 3.6 9.8 - - - +
75A ILE 4.3 5.1 + - - +
76A PRO* 3.6 49.4 - - + +
300A VAL 5.7 0.2 - - - +
301A GLN 4.7 1.4 + - - -
303A GLY 3.8 25.6 + - - +
304A GLY* 4.2 23.8 - - - +
306A SER* 3.9 21.0 + - - -
328A SER 2.9 3.9 + - - +
329A LYS* 1.3 77.0 - - - +
331A MET* 1.3 59.2 - - - +
332A MET* 3.1 9.2 + - - +
364A LEU* 4.5 2.9 - - - +
367A VAL* 4.9 0.2 - - - +
447A ARG* 5.5 1.8 + - - +
448A PRO 4.2 12.0 + - - -
449A THR* 5.5 0.2 - - - +
450A LEU* 4.5 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.6 26.2 - - + -
122A VAL* 4.2 5.4 - - + -
299A GLU 6.0 0.2 - - - +
303A GLY 5.2 1.3 - - - -
304A GLY* 4.4 10.1 - - - +
310A PHE* 3.5 42.0 - - + -
311A TRP* 3.8 18.6 - - + -
327A PHE* 3.7 20.4 - - + -
328A SER 3.0 14.7 + - - +
330A LYS* 1.3 77.9 - - + +
332A MET* 1.3 59.1 + - - +
333A THR* 2.8 27.0 + - - +
364A LEU* 3.2 35.5 - - + +
368A ILE* 4.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER 4.8 1.8 - - - +
76A PRO* 3.8 23.8 - - + -
84A LEU* 4.8 8.7 - - + -
134A ALA 4.8 0.3 - - - +
329A LYS 3.0 15.6 + - - +
330A LYS 3.1 12.5 - - - +
331A MET* 1.3 77.5 - - - +
333A THR* 1.3 58.1 + - - +
360A LYS* 3.8 36.5 - - + +
363A LEU* 3.8 32.8 - - + -
364A LEU* 4.0 21.1 - - + +
367A VAL* 4.5 10.5 - - + -
98B ILE 5.0 8.1 - - - +
100B ARG* 4.0 7.8 + - + -
354B TRP* 3.4 23.3 - - - -
----------------------------------------------------------
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