Contacts of the helix formed by residues 263 - 279 (chain T) in PDB entry 5L4K
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 LEU 263 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200T LEU* 3.9 28.5 - - + +
201T SER* 4.1 16.2 - - - +
203T ASN* 5.1 2.5 - - - +
232T LEU* 5.4 4.0 - - + -
236T LEU* 3.8 31.0 - - + -
243T LYS* 4.8 9.9 - - + -
260T ILE* 2.9 38.1 + - + +
262T ILE* 1.3 79.0 - - - +
264T LEU* 1.3 56.2 + - + +
265T ASP 3.1 0.7 - - - -
266T THR* 2.9 34.9 + - + +
267T ILE* 3.1 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244T VAL* 3.9 38.1 - - + +
247T ALA* 4.0 19.5 - - + -
248T LYS* 3.6 31.4 - - - +
260T ILE* 4.2 6.7 - - + +
261T ASP* 3.4 24.2 - - + +
262T ILE 3.1 1.6 + - - -
263T LEU* 1.3 76.7 - - + +
265T ASP* 1.3 59.0 + - - +
266T THR 3.5 0.2 - - - -
267T ILE* 4.0 15.4 - - + +
268T ARG* 2.9 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261T ASP 4.7 5.0 - - - +
262T ILE* 3.4 10.9 + - - +
263T LEU 3.0 1.2 + - - -
264T LEU* 1.3 78.4 - - - +
266T THR* 1.3 63.5 + - - +
267T ILE 3.5 0.2 - - - -
268T ARG* 4.3 13.5 + - - +
269T ASP* 2.8 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201T SER* 5.3 1.4 + - - -
203T ASN* 3.9 33.8 + - - +
236T LEU* 6.4 0.9 - - + -
262T ILE 4.5 1.9 + - - -
263T LEU* 2.9 20.2 + - + +
265T ASP* 1.3 77.3 - - - +
267T ILE* 1.3 65.7 + - - +
269T ASP* 3.0 18.9 + - + +
270T GLU* 3.0 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236T LEU* 5.9 0.4 - - + -
241T TYR* 4.0 12.8 - - + -
243T LYS* 3.7 36.8 - - + +
244T VAL* 3.5 25.4 - - + +
247T ALA* 6.2 0.2 - - + -
263T LEU* 3.1 35.0 + - + +
264T LEU* 4.0 26.7 - - + +
265T ASP 3.5 0.2 - - - -
266T THR* 1.3 75.9 - - - +
268T ARG* 1.3 63.7 + - + +
270T GLU* 3.0 15.2 - - - +
271T ILE* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244T VAL* 5.2 8.1 - - + +
264T LEU* 2.9 43.2 + - - +
265T ASP* 4.5 14.1 + - - +
266T THR 3.3 0.4 - - - -
267T ILE* 1.3 82.1 - - + +
269T ASP* 1.3 58.0 + - - +
271T ILE* 3.4 7.8 + - + +
272T ALA* 3.0 31.0 + - - +
291T LEU* 3.2 31.8 + - + +
292T PHE* 3.2 31.3 + - + +
293T PHE* 3.4 31.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443S ARG* 4.8 1.3 + - - -
265T ASP 2.8 18.5 - - - +
266T THR* 3.0 14.5 + - + +
268T ARG* 1.3 77.0 - - - +
270T GLU* 1.3 61.2 + - - +
272T ALA* 3.5 4.1 + - - +
273T GLY* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440S LYS* 4.6 10.1 + - - +
443S ARG* 3.3 29.8 + - - +
236T LEU* 4.2 19.6 - - - +
239T GLY* 4.8 0.5 - - - -
241T TYR* 2.6 35.4 + - + +
243T LYS* 3.9 11.1 + - - -
266T THR* 3.0 19.2 + - + +
267T ILE* 3.0 31.9 + - - +
269T ASP* 1.3 75.4 - - - +
271T ILE* 1.3 62.9 + - - +
273T GLY 3.0 8.8 + - - -
274T CYS* 3.0 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436S PHE* 5.5 6.1 - - + -
241T TYR* 3.6 50.9 - - + -
267T ILE* 3.0 32.2 + - + +
268T ARG* 3.7 7.4 - - + +
270T GLU* 1.3 77.2 - - - +
272T ALA* 1.3 59.3 + - - +
274T CYS* 3.2 5.3 + - - +
275T ILE* 2.9 48.9 + - + +
290T ILE* 4.2 11.7 - - + +
291T LEU* 3.6 15.7 - - + -
292T PHE* 4.6 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268T ARG 3.0 17.2 + - - +
269T ASP* 4.1 3.8 - - - +
271T ILE* 1.3 78.2 - - - +
273T GLY* 1.3 58.8 + - - +
275T ILE* 4.3 7.9 - - - -
276T GLU* 2.9 35.0 + - + +
291T LEU* 4.4 13.2 - - + -
306T ARG* 4.6 21.5 - - + +
308T TRP* 5.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443S ARG* 4.0 23.5 - - - +
269T ASP 2.9 15.4 + - - -
270T GLU 3.0 5.5 + - - -
272T ALA* 1.3 79.2 - - - +
274T CYS* 1.3 62.2 + - - +
276T GLU* 3.7 13.4 - - - +
277T LYS* 4.0 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 274 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439S ALA* 3.9 20.4 - - + +
440S LYS* 4.0 24.5 - - - -
442S ILE* 5.5 0.7 - - - +
443S ARG* 3.1 54.2 - - + +
241T TYR* 5.3 4.3 - - - -
270T GLU 3.0 12.0 + - - -
271T ILE* 3.8 6.3 - - - +
273T GLY* 1.3 72.5 - - - +
275T ILE* 1.3 60.4 + - + +
276T GLU 3.1 1.8 - - - -
277T LYS* 2.8 22.9 + - - +
278T ALA* 2.9 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436S PHE* 5.5 4.5 - - + -
439S ALA* 5.4 4.3 - - + -
271T ILE* 2.9 40.8 + - + +
272T ALA* 4.1 6.5 - - - +
274T CYS* 1.3 77.6 - - + +
276T GLU* 1.3 62.0 + - - +
277T LYS 3.0 1.7 + - - -
278T ALA* 3.4 13.2 + - + +
279T TYR* 3.7 23.9 + - + +
282T ILE* 5.3 4.9 - - + -
290T ILE* 3.6 26.5 - - + -
291T LEU* 5.0 3.1 - - + -
306T ARG* 5.4 3.8 - - - +
308T TRP* 4.1 9.6 - - + -
316T TYR* 3.2 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272T ALA* 2.9 20.7 + - + +
273T GLY* 3.7 10.8 - - - +
274T CYS 3.1 0.2 - - - -
275T ILE* 1.3 77.6 - - - +
277T LYS* 1.3 61.9 + - + +
279T TYR 4.8 1.2 - - - +
280T GLU* 5.3 1.7 - - - +
306T ARG* 4.1 18.2 - - + +
308T TRP* 2.5 45.3 + - + -
316T TYR* 4.5 6.7 - - - +
317T SER* 3.8 27.1 + - - +
319T ALA* 5.1 12.2 + - + +
320T SER 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442S ILE* 4.4 15.8 - - + +
443S ARG* 4.0 38.8 - - + +
449S ALA 5.3 3.6 - - - +
450S SER* 5.1 4.3 + - - -
273T GLY 4.0 9.4 - - - +
274T CYS 2.8 7.8 + - - +
276T GLU* 1.3 84.5 - - + +
278T ALA* 1.3 61.6 + - - +
279T TYR 3.4 7.1 + - - +
280T GLU* 5.4 0.5 - - - +
318T PHE* 6.2 0.7 - - - -
319T ALA* 4.1 17.5 + - - +
320T SER* 4.2 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439S ALA* 4.1 20.4 - - + +
442S ILE* 4.1 16.2 - - + -
450S SER* 3.8 3.4 + - - -
451S ILE* 2.9 39.8 + - + +
274T CYS 2.9 13.7 + - - +
275T ILE* 3.4 1.7 + - - -
277T LYS* 1.3 78.6 - - - +
279T TYR* 1.3 82.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 279 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435S GLU* 3.2 36.6 + - - +
436S PHE* 5.2 1.9 - - - -
439S ALA* 4.4 3.6 - - + +
450S SER* 5.0 4.2 + - - -
451S ILE* 3.2 53.1 - - + +
453S HIS* 3.7 30.7 - - + +
275T ILE* 3.7 37.2 + - + +
276T GLU 4.8 1.0 - - - +
277T LYS 4.1 7.6 - - - +
278T ALA* 1.3 95.3 - - + +
280T GLU* 1.3 76.3 + - - +
281T LYS 4.6 1.1 - - - +
282T ILE* 4.4 9.2 - - + -
290T ILE* 5.7 3.8 - - + -
316T TYR* 3.5 27.0 - - + +
----------------------------------------------------------
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