Contacts of the helix formed by residues 246 - 252 (chain B) in PDB entry 4O0Z
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 246 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.8 4.9 + - + -
19A LYS* 2.8 27.5 + - - -
22A HIS* 3.1 31.1 + - + +
26A TYR* 3.8 0.2 + - - -
146A ASN* 2.8 24.6 + - - +
149A GLU* 3.9 3.7 - - - +
245B ALA* 1.3 75.7 - - - +
247B HIS* 1.3 66.9 + - - +
248B SER* 2.4 34.5 + - - +
249B THR* 2.9 21.0 + - + +
250B ILE* 3.5 10.4 + - - +
277B VAL* 3.6 7.9 - - - -
603B PO4 3.4 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 4.8 7.7 - - + -
415A LYS* 3.4 39.2 + - + +
246B GLU* 1.3 75.3 - - - +
248B SER* 1.3 52.7 + - - +
250B ILE 3.3 0.7 + - - +
251B THR* 2.7 45.0 + - + +
277B VAL* 3.3 16.9 - - + +
279B ASP* 2.6 27.1 + - - -
280B SER* 3.0 32.3 + - - +
313B ASP* 3.3 26.5 - - - -
603B PO4 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 2.7 27.8 + - - -
146A ASN* 3.7 11.2 - - - -
401A CYS* 3.8 21.7 - - - -
246B GLU* 2.4 33.1 + - - +
247B HIS* 1.3 79.1 - - - +
249B THR* 1.3 56.3 + - - +
251B THR* 3.6 7.4 + - - -
252B ALA* 3.1 30.0 + - - +
603B PO4 4.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 3.8 29.4 - - + -
25A GLN* 3.7 33.3 - - + +
26A TYR* 4.0 21.1 - - + -
245B ALA* 3.2 14.4 - - - +
246B GLU* 2.9 30.3 + - + -
248B SER* 1.3 77.2 - - - +
250B ILE* 1.3 62.6 + - - +
253B TRP* 3.0 27.6 + - - -
265B ILE* 3.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ALA* 4.1 1.8 - - + -
246B GLU 3.6 12.8 - - - +
247B HIS 3.3 5.0 + - - +
249B THR* 1.3 78.4 - - - +
251B THR* 1.3 66.2 + - - +
252B ALA 3.2 1.3 - - - -
253B TRP* 3.2 21.8 + - - +
254B GLY 4.4 1.9 + - - +
257B HIS 5.1 0.3 - - - +
258B GLU* 3.6 33.7 - - + +
261B ALA* 4.0 9.0 - - + +
262B PHE* 3.8 24.7 - - + -
265B ILE* 3.6 28.7 - - + -
276B VAL* 4.1 7.6 - - + -
277B VAL* 4.0 20.4 - - + +
280B SER* 3.9 15.7 - - - +
281B TYR* 4.7 2.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A CYS* 4.9 6.1 + - - +
413A VAL* 3.2 19.1 - - - +
414A PHE 3.2 39.5 + - - +
415A LYS* 4.1 7.0 - - + +
247B HIS* 2.7 31.4 + - + +
248B SER* 3.6 8.5 - - - -
250B ILE* 1.3 70.1 - - - +
252B ALA* 1.3 61.3 + - - +
254B GLY* 2.9 19.9 + - - -
280B SER* 3.8 20.9 - - - +
281B TYR* 3.5 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.9 10.1 - - + -
27A PRO* 3.7 27.1 - - + +
30A THR* 5.7 0.4 - - + +
401A CYS* 5.2 0.4 - - - -
404A VAL* 3.6 28.0 - - + +
406A THR* 4.7 1.6 + - - -
411A ILE* 3.4 15.9 - - - +
413A VAL* 4.1 9.9 - - - -
248B SER 3.1 18.9 + - - +
250B ILE 3.2 1.0 - - - -
251B THR* 1.3 81.1 + - - +
253B TRP* 1.3 60.9 + - + +
254B GLY 3.3 0.5 + - - -
----------------------------------------------------------
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