Contacts of the helix formed by residues 267 - 271 (chain B) in PDB entry 4LXZ
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 GLY 267 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE 3.7 0.2 - - - +
181B ASP* 3.4 30.9 - - - +
265B GLN* 2.8 17.8 + - - -
266B CYS* 1.3 66.5 - - - +
268B ALA* 1.3 52.1 + - - -
269B ASP* 3.3 8.5 + - - -
270B SER* 3.1 11.1 + - - -
286B HIS* 2.8 23.4 + - - -
304B GLY 3.7 0.4 + - - -
305B GLY* 4.0 5.2 - - - -
306B GLY 3.6 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B CYS 3.1 1.8 + - - -
267B GLY* 1.3 69.0 - - - -
269B ASP* 1.3 55.6 + - - +
270B SER 3.1 6.1 - - - -
271B LEU* 3.2 42.6 + - + +
274B ASP* 4.0 4.5 - - - +
286B HIS* 3.9 8.1 - - - -
306B GLY 2.9 12.1 + - - +
307B GLY* 3.8 4.4 - - - -
313B VAL* 4.0 24.2 - - + +
316B CYS* 4.2 6.7 - - + -
317B TRP* 4.1 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 3.0 11.5 - - - +
182B ILE* 3.0 42.8 + - + +
183B HIS* 3.1 3.5 + - + -
267B GLY 3.8 0.2 - - - -
268B ALA* 1.3 70.4 - - - +
270B SER* 1.3 57.1 + - - +
271B LEU 3.2 5.3 + - - +
274B ASP* 3.4 37.2 - - - +
277B GLY* 3.7 7.8 - - - +
279B PHE* 5.1 0.2 - - - +
306B GLY* 3.4 3.8 - - - -
307B GLY* 3.5 15.5 - - - +
308B TYR* 3.5 4.1 - - + -
401B ZN 1.9 34.2 - - - -
408B SHH 3.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE 2.8 28.1 + - - -
182B ILE* 3.9 13.2 - - - -
242B TYR* 5.5 0.2 - - - -
267B GLY 3.1 11.3 + - - -
268B ALA 3.1 0.2 - - - -
269B ASP* 1.3 78.1 + - - +
271B LEU* 1.4 59.8 + - - +
279B PHE* 3.2 38.6 - - - +
281B LEU* 3.4 24.6 - - - +
286B HIS* 3.2 14.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ALA* 3.2 21.3 - - + +
269B ASP 3.2 2.3 - - - +
270B SER* 1.4 80.3 - - - +
272B SER* 1.3 72.4 + - - +
273B GLY 3.4 0.2 + - - -
274B ASP* 3.3 20.2 + - + +
277B GLY 5.6 0.2 - - - -
279B PHE 3.8 7.0 + - - +
281B LEU* 3.5 3.6 - - + +
282B THR 3.5 33.2 - - - +
283B VAL* 4.0 9.9 - - + +
286B HIS* 3.7 22.2 - - + -
312B ASN* 3.5 39.3 - - + +
313B VAL 4.6 0.2 - - - +
316B CYS* 3.7 16.8 - - + -
350B ILE* 4.3 4.3 - - + -
----------------------------------------------------------
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