Contacts of the helix formed by residues 270 - 282 (chain C) in PDB entry 5LSW
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 THR 270 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASP* 2.8 24.2 + - - +
269A ASP* 3.9 10.1 + - - +
267C LYS 5.1 0.5 + - - -
269C ASP* 1.3 72.1 + - - +
271C THR* 1.3 63.9 + - - +
272C THR 3.3 0.4 - - - -
273C LYS* 3.3 26.7 + - - +
274C ARG* 3.2 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS* 3.5 36.8 - - + +
269A ASP* 3.3 23.6 - - - +
271A THR* 3.0 15.5 + - - +
810B ASP* 6.2 2.7 - - - -
230C LYS* 4.2 8.1 - - - -
269C ASP* 2.6 21.2 + - - +
270C THR* 1.3 77.8 - - - +
272C THR* 1.3 63.1 + - - +
274C ARG* 3.6 10.3 + - - +
275C TRP* 3.4 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU 4.7 0.4 - - - +
230C LYS* 3.4 40.7 - - + +
233C VAL* 4.4 20.6 - - + -
266C LEU* 3.7 28.9 - - + -
269C ASP* 2.5 27.1 + - - -
270C THR 3.3 0.4 - - - -
271C THR* 1.3 76.3 + - - +
273C LYS* 1.3 66.3 + - - +
275C TRP* 3.3 8.9 + - + +
276C LEU* 2.9 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ALA 5.6 0.4 - - - +
266C LEU* 3.3 49.6 + - + +
267C LYS* 4.4 16.0 + - + +
269C ASP 3.6 1.1 + - - +
270C THR* 3.3 35.9 + - + +
272C THR* 1.3 78.4 - - - +
274C ARG* 1.3 52.0 + - + +
276C LEU* 3.2 6.7 + - - +
277C ALA* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 5.5 5.7 - - - +
227A ARG* 4.3 25.0 - - - +
806B VAL* 4.6 16.9 - - + +
810B ASP* 2.6 43.0 + - + -
270C THR* 3.2 38.8 + - + +
271C THR* 3.9 9.7 - - - +
273C LYS* 1.3 76.4 - - + +
275C TRP* 1.3 56.8 + - + +
277C ALA* 3.6 6.9 - - - +
278C GLN* 2.7 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS* 5.8 4.3 - - - -
810B ASP* 3.7 35.6 + - + +
187C GLN* 5.7 2.7 - - - -
230C LYS* 3.6 55.9 - - + -
231C HIS* 6.0 1.3 - + - -
233C VAL* 3.9 11.9 - - + -
234C ARG* 3.5 41.8 - - + +
237C LEU* 3.9 26.9 - - + +
271C THR* 3.4 22.8 + - - +
272C THR* 3.3 11.1 + - - +
273C LYS 3.2 0.4 - - - -
274C ARG* 1.3 81.5 - - + +
276C LEU* 1.3 52.5 + - - +
278C GLN* 3.1 7.7 + - - +
279C LEU* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 3.7 17.2 - - + +
257C LEU* 3.5 54.3 - - + +
259C ASP 6.1 0.9 - - - +
262C PHE* 5.7 2.5 - - + -
266C LEU* 3.8 25.8 - - + -
272C THR 2.9 16.5 + - - +
273C LYS* 3.7 5.2 - - - +
275C TRP* 1.3 76.4 - - - +
277C ALA* 1.3 61.2 + - - +
279C LEU* 4.1 17.7 - - + -
280C VAL* 3.2 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LYS 2.7 22.4 + - - +
274C ARG* 3.6 8.1 - - - +
276C LEU* 1.3 71.5 - - - +
278C GLN* 1.3 62.6 + - - +
280C VAL* 3.3 8.9 - - + +
281C LYS* 3.1 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B ASP* 3.1 51.7 + - - +
810B ASP 4.9 4.9 - - - +
237C LEU* 4.0 24.8 - - + +
274C ARG 2.7 21.8 + - - +
275C TRP* 3.7 7.3 - - - +
277C ALA* 1.3 74.0 - - - +
279C LEU* 1.3 57.7 + - - +
281C LYS* 3.5 9.8 + - + +
282C ASN* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 4.8 4.9 - - + +
236C TYR* 3.5 48.9 - - + +
237C LEU* 3.8 12.5 - - + +
240C SER* 3.9 15.3 - - - -
249C LEU* 4.8 3.6 - - + -
253C LEU* 4.2 18.8 - - + -
257C LEU* 4.9 2.2 - - + -
275C TRP 2.7 19.8 + - - +
276C LEU* 3.6 25.4 - - + +
277C ALA 3.2 0.4 - - - -
278C GLN* 1.3 71.7 - - - +
280C VAL* 1.3 66.9 + - + +
282C ASN* 3.1 13.2 + - - +
283C LEU* 3.2 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 4.7 13.7 - - + -
257C LEU 4.2 18.4 - - - +
258C LYS* 5.2 6.7 - - + -
276C LEU* 3.2 19.3 + - + +
277C ALA* 3.3 18.4 - - - +
279C LEU* 1.3 76.0 - - + +
281C LYS* 1.3 67.9 + - + +
283C LEU* 3.4 13.7 + - - +
284C GLN* 3.3 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B LYS* 4.5 28.5 - - - +
277C ALA* 3.1 29.8 + - - +
278C GLN* 3.8 10.1 - - + +
279C LEU 3.1 0.8 - - - -
280C VAL* 1.3 80.7 - - + +
282C ASN* 1.3 61.4 + - - +
283C LEU 3.1 2.8 + - - -
284C GLN* 3.4 23.5 + - - +
285C GLU* 3.9 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU* 4.8 2.2 - - - +
240C SER* 4.0 28.4 + - - +
241C ASP* 4.7 7.2 + - - -
246C ARG* 3.2 35.7 - - - +
278C GLN* 2.9 40.6 + - - +
279C LEU 3.1 6.2 + - - +
281C LYS* 1.3 76.7 - - - +
283C LEU* 1.3 52.3 + - - +
284C GLN 3.4 1.8 - - - -
285C GLU* 2.8 22.4 - - - +
----------------------------------------------------------
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