Contacts of the helix formed by residues 272 - 278 (chain A) in PDB entry 1ORZ
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 GLU 272 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 2.7 40.3 + - + +
144A GLY* 2.8 32.4 - - - +
259A HIS* 4.0 8.0 + - + -
261A SER* 4.7 4.3 - - - -
270A ILE 3.6 1.6 + - - -
271A THR* 1.4 68.1 + - - +
273A GLY* 1.3 64.5 + - - +
274A ALA 2.9 3.1 - - - -
275A ARG* 2.9 44.0 + - + +
276A GLY* 3.1 6.8 + - - -
299A ASP 4.5 2.1 - - - +
301A ALA 4.1 7.4 - - - +
303A ARG* 2.7 42.0 + - - +
418A GLY* 4.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 5.5 1.8 - - - -
141A LYS* 5.6 8.1 - - - -
142A GLU 4.3 4.9 - - - +
143A TYR* 3.6 14.8 - - - -
271A THR* 2.9 17.8 + - - -
272A GLU* 1.3 79.7 - - - +
274A ALA* 1.3 50.4 + - - +
276A GLY* 2.7 3.6 + - - -
277A GLU* 2.6 45.0 + - - +
343A LEU* 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 5.4 0.9 - - + -
271A THR* 3.3 20.7 + - + +
272A GLU 2.9 1.2 - - - -
273A GLY* 1.3 76.5 - - - +
275A ARG* 1.3 53.4 + - + +
277A GLU* 3.0 12.5 + - - +
278A GLY 2.9 7.3 + - - -
279A GLY* 2.6 26.2 + - - -
329A LEU* 4.2 17.9 - - + -
331A LEU* 3.2 30.7 - - + +
343A LEU* 4.5 7.9 - - + -
346A ILE* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 3.0 28.1 - - - +
261A SER* 2.8 30.4 + - - +
272A GLU* 2.9 27.8 + - + +
274A ALA* 1.3 78.5 - - + +
276A GLY* 1.3 58.6 + - - +
278A GLY* 2.8 19.6 + - - -
279A GLY* 3.4 13.3 + - - +
281A LEU* 3.2 46.9 - - + +
299A ASP* 3.6 31.3 + - + +
300A LEU* 4.7 11.3 - - + +
303A ARG* 2.8 27.3 - - - +
306A VAL* 4.0 12.3 - - - +
329A LEU* 5.5 4.6 - - + +
365A ILE* 5.2 1.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
142A GLU* 2.8 62.0 - - - +
143A TYR* 4.5 3.3 - - - -
272A GLU 3.1 6.8 + - - -
273A GLY 2.7 8.3 + - - -
275A ARG* 1.3 79.3 - - - +
277A GLU* 1.3 60.1 + - - +
278A GLY* 3.3 0.9 + - - -
300A LEU* 5.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 2.8 41.8 - - - +
273A GLY 2.6 21.9 + - - +
274A ALA* 3.3 12.8 - - - +
276A GLY* 1.3 72.2 - - - +
278A GLY* 1.4 56.7 + - - +
334A LEU* 3.8 30.7 - - + +
338A VAL* 3.9 10.8 - - + +
342A ARG* 3.6 23.4 - - + +
343A LEU* 4.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG 2.8 11.4 + - - -
276A GLY 3.1 0.9 - - - -
277A GLU* 1.4 81.2 - - - +
279A GLY* 1.4 62.7 + - - +
280A PHE* 3.9 9.7 - - - -
333A HIS* 2.6 33.0 + - - -
334A LEU* 4.7 1.3 - - - -
----------------------------------------------------------
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