Contacts of the helix formed by residues 274 - 280 (chain A) in PDB entry 1O5T
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 CYS 274 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 4.4 15.3 - - - -
272A SER 3.8 2.0 + - - -
273A ASP* 1.3 78.2 - - - +
275A ILE* 1.3 64.6 + - + +
276A GLY* 2.9 9.5 + - - +
277A LYS* 3.4 47.9 + - - +
278A ILE* 3.5 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASP 3.6 1.5 + - - +
274A CYS* 1.3 73.0 - - + +
276A GLY* 1.3 66.1 + - - +
278A ILE* 3.5 17.3 + - + +
279A SER* 3.2 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.5 27.6 - - - +
274A CYS* 2.9 8.0 - - - +
275A ILE* 1.3 82.6 - - - +
277A LYS* 1.3 62.5 + - - -
279A SER* 2.9 21.9 + - - -
280A PHE* 3.0 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.5 27.1 - - + +
203A TRP* 3.6 65.3 + - + +
269A PHE* 3.7 13.1 - - + -
273A ASP* 3.9 31.2 + - + +
274A CYS* 3.4 25.2 + - - +
276A GLY* 1.3 72.2 - - - +
278A ILE* 1.3 64.4 + - - +
280A PHE* 3.0 14.6 + - - +
281A PRO* 3.3 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.8 46.9 - - + -
263A VAL* 4.5 10.3 - - + +
269A PHE* 4.1 17.9 - - + -
270A THR 4.7 5.2 - - - +
271A ASP* 5.9 2.0 - - - -
273A ASP* 4.3 18.6 - - + +
274A CYS 3.5 13.9 + - - +
275A ILE* 3.5 18.3 + - + +
276A GLY 3.3 0.8 - - - -
277A LYS* 1.3 75.0 - - - +
279A SER* 1.3 60.6 + - - +
281A PRO* 3.4 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 4.0 23.2 + - - +
275A ILE 3.2 9.9 + - - -
276A GLY* 2.9 17.4 + - - -
278A ILE* 1.3 76.9 - - - +
280A PHE* 1.3 66.5 + - - +
281A PRO* 3.0 6.4 - - - +
282A ALA* 3.0 21.8 + - - +
283A ILE* 4.2 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 3.5 19.7 - - + -
198A ASP* 3.5 23.6 - - - -
199A GLU* 3.3 40.2 - - + -
202A LEU* 4.6 6.5 - - + -
203A TRP* 3.9 25.4 - + + -
237A ASP* 4.1 0.2 - - - -
276A GLY 3.0 11.3 + - - +
277A LYS* 3.0 16.4 + - - +
279A SER* 1.3 77.0 + - - +
281A PRO* 1.3 64.4 - - + +
283A ILE* 2.7 47.7 + - + -
284A GLN* 3.3 32.4 + - + -
----------------------------------------------------------
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