Contacts of the helix formed by residues 257 - 269 (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 257 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E TYR* 3.2 2.1 + - - -
223E SER* 4.5 2.1 + - - -
251E ALA* 4.5 5.2 - - - -
255E GLY 4.2 1.2 + - - -
256E GLN* 1.3 75.5 - - - +
258E VAL* 1.3 66.2 + - - +
259E GLU* 3.4 19.8 + - - +
260E LYS* 2.9 43.5 + - - +
261E LEU* 3.5 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL* 4.5 10.8 - - + -
208E TYR* 3.0 18.7 + - + +
241E LEU* 3.8 29.2 - - + -
244E THR* 3.7 30.5 - - + +
247E PHE* 3.7 24.7 - - + -
251E ALA* 4.6 8.2 - - + +
257E SER* 1.3 73.5 - - - +
259E GLU* 1.3 62.9 + - - +
261E LEU* 2.9 7.5 + - - +
262E LEU* 2.8 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E SER* 3.4 12.5 - - - -
224E MET 2.9 45.6 + - - +
225E SER* 4.2 11.4 - - - -
226E LEU* 4.5 4.8 + - - +
244E THR* 3.9 21.9 + - - +
257E SER* 3.1 19.9 - - - +
258E VAL* 1.3 83.7 + - - +
260E LYS* 1.3 61.0 + - - +
262E LEU* 4.2 4.5 - - + -
263E ASP 3.3 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ARG* 4.5 11.7 - - - +
219E VAL* 4.1 12.2 - - + +
220E THR 3.4 25.2 + - - +
221E ASN* 4.2 15.2 - - - +
222E THR 3.4 18.5 - - - +
223E SER* 3.5 14.8 + - - +
256E GLN* 4.0 23.1 + - - +
257E SER* 2.9 31.6 + - - +
259E GLU* 1.3 77.7 - - - +
261E LEU* 1.3 65.1 + - + +
263E ASP* 3.4 5.4 + - - +
264E SER* 3.1 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL* 3.9 12.1 - - + +
207E LEU* 3.7 29.2 - - + -
208E TYR* 3.6 44.0 - - + +
211E LEU* 4.1 18.2 - - + -
218E PHE* 4.5 7.2 - - + -
219E VAL* 4.3 16.2 - - + -
256E GLN* 4.7 2.0 - - + -
257E SER 3.5 11.6 + - - +
258E VAL 2.9 7.0 + - - +
260E LYS* 1.3 81.0 - - + +
262E LEU* 1.3 66.0 + - - +
264E SER* 3.3 10.3 - - - +
265E ILE* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL* 3.7 26.2 - - + -
224E MET* 3.8 19.5 - - + +
226E LEU* 3.9 18.4 - - + +
229E TYR* 3.7 52.9 - - + -
241E LEU* 4.1 16.8 - - + -
244E THR* 5.2 0.4 - - + -
258E VAL* 2.8 33.8 + - + +
259E GLU* 3.9 8.1 - - + +
261E LEU* 1.3 71.4 - - - +
263E ASP* 1.3 63.2 - - - +
265E ILE* 3.2 13.7 + - + +
266E VAL* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E THR* 4.0 0.7 + - - -
222E THR* 2.7 48.3 + - - +
223E SER* 3.7 22.3 - - - +
224E MET* 4.0 11.5 - - - +
259E GLU 3.3 3.6 + - - -
260E LYS 3.6 4.0 - - - +
261E LEU 3.1 0.8 - - - -
262E LEU* 1.3 80.5 - - - +
264E SER* 1.3 61.8 + - - +
266E VAL* 3.2 10.1 + - - +
267E ARG* 3.1 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E LEU* 4.2 12.6 - - - -
218E PHE* 2.8 36.3 + - - -
219E VAL* 4.2 4.2 - - - -
220E THR 5.1 0.3 + - - -
260E LYS 3.1 15.4 + - - -
261E LEU* 3.1 15.6 + - - +
263E ASP* 1.3 76.7 + - - +
265E ILE* 1.3 59.1 + - - +
267E ARG* 3.2 13.3 + - - +
268E LEU* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E SER 4.3 1.8 - - - +
203E VAL* 3.5 32.3 - - + -
204E VAL* 3.6 29.2 - - + +
207E LEU* 3.8 9.9 - - + -
229E TYR* 3.7 31.6 - - + +
232E TRP* 4.0 10.5 - - + -
238E PHE* 3.8 22.0 - - + -
261E LEU 2.9 15.9 + - - +
262E LEU* 3.2 9.3 + - + +
264E SER* 1.3 75.6 - - - +
266E VAL* 1.3 59.0 + - - +
268E LEU* 4.7 1.3 - - - -
269E ASN* 2.8 30.7 + - - +
283E LEU* 4.0 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E MET* 3.6 30.3 - - + -
229E TYR* 4.3 0.9 - - + -
232E TRP* 3.6 52.5 - - + +
262E LEU 3.3 6.3 + - - +
263E ASP* 3.2 12.0 + - - +
264E SER 3.2 0.2 - - - -
265E ILE* 1.3 79.7 - - - +
267E ARG* 1.3 65.5 - - + +
269E ASN* 3.8 9.4 + - - +
270E LYS* 4.3 9.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS 5.6 6.0 + - - -
273A GLY* 6.1 3.4 - - - -
217E TRP* 5.5 3.8 + - - -
218E PHE* 2.4 40.6 + - - +
220E THR* 3.5 30.3 + - - +
222E THR* 4.5 2.7 - - - -
263E ASP* 3.1 34.0 + - - +
264E SER* 3.6 16.6 + - - +
266E VAL* 1.3 86.9 - - + +
268E LEU* 1.3 64.8 + - - +
270E LYS* 2.8 45.0 + - - +
271E GLY 4.2 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E LEU* 4.0 8.7 - - + -
217E TRP* 3.4 38.1 - - + -
218E PHE* 3.7 18.2 - - + -
264E SER* 2.7 29.3 + - - +
265E ILE 4.1 0.4 - - - +
267E ARG* 1.3 78.2 - - - +
269E ASN* 1.3 65.3 + - - +
270E LYS 3.1 2.5 - - - -
271E GLY* 3.1 22.6 + - - +
272E PHE* 3.9 20.8 - - + -
277E ILE* 3.4 26.5 - - + -
283E LEU* 3.9 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E MET* 5.8 0.5 - - - +
232E TRP* 3.8 21.6 - - + -
236E ASN* 4.9 8.9 + - - +
238E PHE* 3.4 27.7 - - - -
265E ILE 2.8 18.7 + - - +
266E VAL 3.9 7.2 + - - +
267E ARG 3.3 0.4 - - - -
268E LEU* 1.3 78.6 - - - +
270E LYS* 1.3 59.5 + - - +
271E GLY 3.2 3.9 + - - -
283E LEU* 3.9 11.0 - - + +
----------------------------------------------------------
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