Contacts of the helix formed by residues 274 - 281 (chain A) in PDB entry 1ORB
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 274 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ILE* 5.8 0.2 - - - -
246A THR* 3.3 11.8 - - - +
247A CYS 3.1 19.0 + - - -
248A ARG 3.1 23.1 - - - -
249A LYS* 3.8 0.2 - - - -
250A GLY* 3.0 21.2 + - - -
271A TYR* 3.0 33.1 + - - -
272A ASP 3.2 0.4 - - - -
273A GLY* 1.3 85.5 - - - +
275A TRP* 1.3 65.3 + - - +
278A TRP* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 3.8 30.6 - - - +
193A GLU* 4.1 14.3 - - + +
199A LEU* 4.0 11.5 - - + +
200A ASP 2.9 29.3 + - - -
201A SER* 3.9 14.8 - - - +
202A GLY 3.8 14.6 - - - -
203A HIS* 3.7 21.8 - - - -
204A ILE* 3.8 13.7 - - + -
246A THR* 4.1 2.5 - - - +
247A CYS 3.2 17.5 + - - +
248A ARG* 4.0 7.0 - - + -
274A SER* 1.3 75.0 - - - +
276A PHE* 1.3 62.3 + - - +
278A TRP* 4.0 13.5 - + - -
279A PHE* 2.8 45.7 + + + +
287A TRP* 3.6 39.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO 3.8 22.4 - - - -
70A TYR* 3.8 16.2 - + + -
71A GLU* 2.9 52.0 - - + +
195A ASP 5.6 0.7 - - - -
196A ALA* 4.6 12.6 - - + -
199A LEU* 4.1 12.3 - - + -
248A ARG* 3.0 32.1 + - - +
249A LYS* 5.1 0.9 - - - -
273A GLY 4.2 2.9 - - - +
275A TRP* 1.3 85.3 - - - +
277A GLU* 1.3 62.6 + - - +
279A PHE* 3.6 0.5 + - - +
280A HIS* 2.8 45.7 + + - -
----------------------------------------------------------
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
----------------------------------------------------------
70A TYR* 3.6 36.4 - - + +
73A MET* 4.5 6.5 - - - +
164A TYR* 3.6 15.0 + - + +
271A TYR* 2.4 36.0 + - - +
273A GLY* 3.3 24.3 + - - +
276A PHE* 1.3 77.2 - - - +
278A TRP* 1.3 61.1 + - - +
280A HIS* 3.1 2.3 + - - -
281A ARG* 2.8 63.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.5 46.4 - + - -
167A VAL* 4.0 12.1 - - + -
168A LEU* 3.8 21.8 - - + -
171A LEU* 3.6 28.3 - - + -
204A ILE* 3.5 42.2 - - + +
271A TYR* 3.7 12.1 + + - +
274A SER 3.1 18.2 + - - +
275A TRP* 3.7 20.2 - + - +
277A GLU* 1.3 76.3 - - - +
279A PHE* 1.3 62.8 + - - +
281A ARG 2.8 0.9 + - - -
282A ALA* 2.7 45.4 + - + +
286A THR* 3.1 29.7 + - + -
287A TRP* 4.1 8.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY 3.6 20.4 - - - -
199A LEU* 3.5 26.7 - - + -
200A ASP* 3.6 27.6 - - + -
275A TRP* 2.8 38.4 + + + +
276A PHE 3.8 1.6 - - - +
278A TRP* 1.3 77.6 - - - +
280A HIS* 1.3 77.3 + + - +
281A ARG 3.7 0.2 + - - -
282A ALA 4.5 7.1 - - - +
287A TRP* 3.5 41.4 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.0 17.6 + + + +
197A VAL 5.2 5.7 + - - -
198A GLY 5.6 0.4 + - - -
199A LEU* 4.1 16.0 - - + +
276A PHE* 2.8 50.9 + + - +
277A GLU 3.1 6.1 + - - +
278A TRP 3.1 0.6 - - - -
279A PHE* 1.3 101.7 - + - +
281A ARG* 1.3 60.9 + - - +
282A ALA 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.4 26.0 - - - +
164A TYR* 3.4 52.6 + - + +
165A GLU* 3.8 16.2 + - - -
277A GLU* 2.8 53.9 + - - +
278A TRP 2.8 2.2 + - - -
280A HIS* 1.3 77.6 - - - +
282A ALA* 1.3 63.1 + - - +
283A PRO* 3.9 2.9 - - - +
----------------------------------------------------------
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