Contacts of the helix formed by residues 257 - 271 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C TYR* 3.2 2.8 + - - -
223C SER* 4.5 4.3 + - - -
251C ALA* 4.3 7.9 - - - -
255C GLY 4.2 2.0 + - - -
256C GLN* 1.3 75.8 + - - +
258C VAL* 1.3 65.4 + - - +
259C GLU* 3.8 15.3 + - - +
260C LYS* 2.9 38.3 + - - +
261C LEU* 3.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C VAL* 4.8 4.9 - - + -
208C TYR* 3.0 13.3 + - + +
241C LEU* 4.6 9.4 - - + -
244C THR* 3.7 39.5 - - + +
247C PHE* 3.4 40.8 - - + -
251C ALA* 4.6 4.8 - - + +
257C SER* 1.3 72.2 - - - +
259C GLU* 1.3 57.8 + - - +
261C LEU* 2.7 27.9 + - - +
262C LEU* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C SER* 3.6 11.1 - - - +
224C MET 3.0 49.5 + - - +
225C SER* 4.1 4.0 - - - -
226C LEU* 4.1 17.2 + - - +
244C THR* 3.6 25.6 + - + +
257C SER* 3.4 14.1 + - - +
258C VAL* 1.3 78.0 + - - +
260C LYS* 1.3 60.4 + - - +
262C LEU* 3.7 9.9 - - + -
263C ASP 3.2 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ARG* 5.7 0.4 - - - +
219C VAL* 3.6 12.4 - - + +
220C THR* 3.0 27.1 + - - +
221C ASN* 3.9 26.5 - - - +
222C THR 3.7 8.7 - - - +
223C SER* 3.5 18.5 + - - +
256C GLN* 2.6 45.7 + - + +
257C SER* 2.9 26.7 + - - +
259C GLU* 1.3 79.8 - - - +
261C LEU* 1.3 59.9 + - + +
263C ASP* 3.4 5.9 + - - +
264C SER* 3.0 23.1 + - - -
267C ARG* 5.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C VAL* 3.7 20.9 - - + +
207C LEU* 3.7 28.7 - - + +
208C TYR* 3.1 55.4 - - + +
211C LEU* 3.9 17.5 - - + -
218C PHE* 4.0 4.3 - - + -
219C VAL* 3.9 20.0 - - + -
256C GLN* 5.2 2.5 - - + -
257C SER 4.2 4.3 - - - +
258C VAL 2.7 13.3 + - - +
260C LYS* 1.3 73.7 - - - +
262C LEU* 1.3 65.4 + - - +
264C SER* 3.1 6.1 + - - +
265C ILE* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C SER* 5.9 0.2 - - - -
204C VAL* 3.9 25.1 - - + -
224C MET* 4.0 11.2 - - + +
226C LEU* 3.9 27.1 - - + -
229C TYR* 3.7 47.2 - - + -
241C LEU* 4.1 14.8 - - + -
258C VAL* 2.9 24.6 + - + +
259C GLU* 3.8 18.6 - - + +
260C LYS 3.3 0.2 - - - -
261C LEU* 1.3 75.2 - - - +
263C ASP* 1.3 62.9 - - - +
265C ILE* 3.3 14.7 + - + +
266C VAL* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C THR* 3.5 12.3 - - - +
222C THR* 3.5 37.6 - - - +
223C SER 4.1 0.9 - - - +
224C MET* 3.9 24.3 - - - +
259C GLU 3.2 8.7 + - - +
260C LYS 3.7 4.0 - - - +
261C LEU 3.2 0.6 - - - -
262C LEU* 1.3 80.9 - - - +
264C SER* 1.3 62.3 + - - +
266C VAL* 3.3 6.2 + - - +
267C ARG* 3.1 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.5 3.1 - - - -
218C PHE* 3.1 30.9 + - - -
219C VAL* 4.0 9.2 - - - +
260C LYS 3.0 14.9 + - - -
261C LEU* 3.1 11.2 + - - -
263C ASP* 1.3 78.7 - - - +
265C ILE* 1.4 57.5 + - - +
267C ARG* 3.5 16.6 + - - +
268C LEU* 2.8 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C SER* 4.3 3.4 - - - +
203C VAL* 3.5 36.3 - - + -
204C VAL* 3.9 22.7 - - + -
207C LEU* 4.0 8.5 - - + -
229C TYR* 3.8 34.1 - - + +
232C TRP* 4.4 4.7 - - + -
238C PHE* 4.0 20.9 - - + -
261C LEU 2.9 17.6 + - - +
262C LEU* 3.6 8.7 - - + +
263C ASP 3.2 0.2 - - - -
264C SER* 1.4 75.5 - - - +
266C VAL* 1.3 58.4 + - - +
268C LEU* 4.0 5.1 - - - +
269C ASN* 2.8 32.9 + - - +
283C LEU* 4.0 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C MET* 3.7 28.0 - - + -
229C TYR* 4.1 3.4 - - + -
232C TRP* 3.8 53.5 - - + +
262C LEU 3.6 13.5 - - - +
263C ASP* 3.3 8.6 + - - +
264C SER 3.3 0.4 - - - -
265C ILE* 1.3 78.2 - - - +
267C ARG* 1.3 64.0 + - + +
269C ASN* 3.6 3.6 + - - +
270C LYS* 3.6 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TRP* 5.4 1.6 + - - -
218C PHE* 2.9 34.4 + - - +
220C THR* 3.1 36.2 - - - +
263C ASP* 3.1 25.4 + - - +
264C SER* 3.5 19.7 + - - +
265C ILE 3.3 0.2 - - - -
266C VAL* 1.3 78.5 - - + +
268C LEU* 1.3 64.3 + - + +
270C LYS* 3.0 29.0 + - - +
271C GLY 3.4 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.2 7.2 - - + -
217C TRP* 3.4 37.9 - - + -
218C PHE* 3.7 17.5 - - + -
264C SER* 2.8 36.2 + - - +
265C ILE 4.0 0.4 - - - +
267C ARG* 1.3 73.7 - - - +
269C ASN* 1.3 61.4 + - - +
270C LYS 2.9 5.4 - - - -
271C GLY* 2.9 19.1 + - - +
272C PHE* 3.5 33.1 - - + -
277C ILE* 3.4 26.5 - - + -
283C LEU* 3.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TRP* 3.6 30.5 - - + -
236C ASN* 4.3 11.8 + - - +
238C PHE* 3.5 20.4 - - + -
265C ILE 2.8 18.2 + - - +
266C VAL 3.7 6.0 + - - +
268C LEU* 1.3 76.8 - - - +
270C LYS* 1.3 61.8 + - - +
271C GLY 3.5 0.3 + - - -
283C LEU* 3.9 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C VAL* 3.6 7.3 + - + +
267C ARG* 3.0 19.0 + - - +
268C LEU 2.9 0.4 - - - -
269C ASN* 1.3 83.4 - - - +
271C GLY* 1.3 54.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ARG 3.4 10.8 + - - +
268C LEU* 2.9 13.1 + - - +
269C ASN 3.3 0.6 - - - -
270C LYS* 1.3 79.9 - - - +
272C PHE* 1.3 64.6 + - - -
273C GLY 3.3 6.5 + - - -
----------------------------------------------------------
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