Contacts of the helix formed by residues 225 - 235 (chain E) in PDB entry 1LVO
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 225 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E MET* 1.3 79.5 - - - +
226E LEU* 1.3 65.9 + - - +
227E GLU* 3.7 5.6 + - - +
228E SER* 3.0 30.9 + - - -
229E TYR* 2.9 21.8 + - - +
259E GLU* 4.2 7.6 - - - -
262E LEU* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E MET 3.8 0.4 + - - -
225E SER* 1.3 74.2 - - - +
227E GLU* 1.3 68.6 + - + +
229E TYR* 3.3 0.9 + - - +
230E ASN* 2.9 53.7 + - - +
241E LEU* 3.7 37.7 - - + +
242E SER 5.7 0.4 - - - +
243E SER* 4.9 6.1 - - - -
244E THR* 4.1 28.5 - - + +
259E GLU* 4.5 6.5 + - - +
262E LEU* 3.9 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E SER* 3.3 5.4 + - - +
226E LEU* 1.3 88.4 - - + +
228E SER* 1.3 63.9 + - - +
230E ASN* 3.4 12.8 + - - +
231E THR* 3.2 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E MET* 3.5 29.4 - - - +
225E SER* 3.0 23.2 + - - -
227E GLU* 1.3 74.4 - - - +
229E TYR* 1.3 67.4 + - - +
231E THR* 3.4 7.4 + - - -
232E TRP 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E SER* 2.8 38.5 + - - -
224E MET* 3.8 16.5 - - - +
225E SER 2.9 19.1 + - - +
226E LEU 3.7 2.9 - - - +
228E SER* 1.3 77.2 - - - +
230E ASN* 1.3 64.8 + - - +
232E TRP* 3.1 29.1 + + - +
233E ALA* 2.7 42.0 + - + -
238E PHE* 3.5 16.5 - - - -
239E THR 4.2 1.3 - - - -
241E LEU* 4.6 4.7 - - + -
262E LEU* 3.7 56.5 - - + -
265E ILE* 3.7 20.9 - - + +
266E VAL* 4.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 2.9 40.5 + - - +
227E GLU* 3.9 14.5 + - - +
228E SER 3.2 0.2 - - - -
229E TYR* 1.3 83.6 - - - +
231E THR* 1.3 62.1 - - - +
233E ALA* 3.3 3.8 + - - +
234E LYS* 3.1 31.7 + - - +
240E GLU* 3.3 32.9 + - + +
241E LEU 2.9 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E GLU 3.2 13.6 + - - -
228E SER* 3.7 9.8 - - - -
229E TYR 3.2 0.2 - - - -
230E ASN* 1.3 79.0 - - - +
232E TRP* 1.3 61.4 + - - +
234E LYS* 3.5 15.9 + - - +
235E THR* 2.9 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E MET* 3.8 14.8 - - + -
228E SER 3.1 14.4 + - - +
229E TYR* 3.4 37.2 - + - +
231E THR* 1.3 78.9 - - - +
233E ALA* 1.3 83.9 + - - +
235E THR* 3.0 14.8 + - - -
236E ASN* 3.1 49.1 + - + +
238E PHE* 3.7 38.8 - + - -
265E ILE* 4.0 9.0 - - + -
266E VAL* 3.6 40.2 - - + +
269E ASN* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E TYR* 2.7 31.9 + - + +
230E ASN* 3.3 7.8 + - - +
232E TRP* 1.3 83.3 - - - +
234E LYS* 1.3 57.8 + - - +
236E ASN 3.1 12.6 + - - -
237E SER 3.3 0.2 + - - -
238E PHE* 3.0 38.7 + - + +
239E THR 3.4 27.1 - - - +
240E GLU 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ASN* 3.1 22.9 + - - +
231E THR* 3.9 14.4 + - - +
232E TRP 3.3 0.2 - - - -
233E ALA* 1.3 74.4 - - - +
235E THR* 1.3 63.3 + - + +
236E ASN 3.5 0.2 - - - -
237E SER* 4.7 2.5 + - - -
238E PHE 4.1 6.1 - - - +
240E GLU* 3.6 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E THR* 2.9 25.5 + - + +
232E TRP* 3.0 7.2 + - - -
234E LYS* 1.3 81.1 - - + +
236E ASN* 1.3 73.5 + - - +
237E SER 3.8 1.6 - - - -
----------------------------------------------------------
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