Contacts of the helix formed by residues 270 - 289 (chain B) in PDB entry 3KXK
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 270 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 1.3 76.3 - - - +
271B GLU* 1.3 60.2 + - - +
272B ASN* 3.8 7.5 + - - +
273B LEU* 3.4 28.8 + - - +
274B LEU* 2.8 30.0 + - - +
312B LYS* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER* 1.3 72.3 - - - +
272B ASN* 1.3 74.0 + - - +
274B LEU* 3.2 10.0 + - + +
275B ILE* 2.9 38.7 + - + +
311B LYS* 3.0 40.1 + - - +
312B LYS* 5.7 9.6 - - + -
315B LEU* 5.4 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER* 3.4 7.7 + - - +
271B GLU* 1.3 82.8 + - - +
273B LEU* 1.3 65.0 - - + +
275B ILE* 3.9 11.4 + - - +
276B GLU* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 3.7 30.1 - - + -
270B SER* 3.4 24.8 + - - +
271B GLU 3.1 0.8 - - - -
272B ASN* 1.3 81.9 - - + +
274B LEU* 1.3 59.5 + - - +
275B ILE 3.3 0.2 - - - -
276B GLU* 3.2 20.9 + - - +
277B THR* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 3.8 19.5 - - + -
266B ASP 3.3 26.9 - - - +
267B SER* 4.4 5.4 - - - +
269B PHE* 3.8 12.6 - - + +
270B SER 2.8 24.0 + - - +
271B GLU* 3.6 8.5 - - + +
273B LEU* 1.3 73.6 - - - +
275B ILE* 1.3 60.6 + - - +
277B THR* 3.3 3.6 + - - -
278B LEU* 2.9 37.7 + - - +
299B LEU* 4.6 5.4 - - + -
312B LYS* 3.8 42.4 - - + -
315B LEU* 4.6 12.1 - - + -
316B VAL* 4.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLU* 2.9 29.7 + - + +
272B ASN* 4.0 12.3 - - - +
274B LEU* 1.3 75.5 - - - +
276B GLU* 1.3 58.3 + - - +
278B LEU* 3.8 0.9 - - - +
279B GLN* 3.0 61.9 + - - +
315B LEU* 4.2 20.0 - - + -
319B LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 3.0 34.2 + - - +
272B ASN 3.4 11.4 + - - +
273B LEU* 3.2 26.8 + - - +
274B LEU 3.2 0.4 - - - -
275B ILE* 1.3 76.6 - - - +
277B THR* 1.3 62.5 + - - +
279B GLN* 3.3 9.9 + - - +
280B SER* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 4.0 24.6 - - + -
238B ARG* 4.8 10.2 + - - +
265B ILE* 3.8 29.8 - - + -
266B ASP 5.4 0.2 - - - +
269B PHE* 3.6 28.0 - - + -
273B LEU* 2.8 27.6 + - - +
274B LEU* 3.8 4.7 - - - -
276B GLU* 1.3 75.5 - - - +
278B LEU* 1.3 54.8 + - - +
280B SER* 3.4 5.3 + - - -
281B SER* 2.7 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.7 3.1 - - + -
265B ILE* 3.9 29.6 - - + -
274B LEU 2.9 20.2 + - - +
275B ILE 3.8 3.6 - - - +
277B THR* 1.3 77.1 - - - +
279B GLN* 1.3 62.6 + - - +
281B SER* 3.2 4.4 + - - -
282B PHE* 3.0 45.1 + - + -
297B VAL* 4.9 0.7 - - + -
315B LEU* 4.5 4.3 - - + -
316B VAL* 3.8 44.2 - - + +
319B LEU* 3.6 30.3 - - + -
320B SER* 3.9 16.4 - - - +
323B LEU* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 3.0 44.6 + - + +
276B GLU* 3.8 6.1 - - - +
278B LEU* 1.3 77.4 - - - +
280B SER* 1.3 57.7 + - - +
282B PHE* 4.0 0.6 - - - -
283B GLU* 3.0 31.0 + - - +
286B ARG* 4.2 6.1 + - - +
319B LEU* 4.5 10.4 - - + +
323B LEU* 3.7 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.1 25.4 - - - -
238B ARG* 3.7 14.9 + - - -
276B GLU* 2.8 27.4 + - - +
277B THR 3.7 2.9 - - - -
279B GLN* 1.3 75.5 - - - +
281B SER* 1.3 65.7 + - - +
283B GLU* 3.2 12.2 + - - +
284B ILE* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.5 18.9 + - - -
236B PHE* 3.9 16.6 - - - -
263B LEU* 3.8 28.9 - - - +
265B ILE* 3.8 12.9 - - - +
277B THR 2.7 27.0 + - - -
278B LEU 3.7 3.6 - - - -
280B SER* 1.3 73.2 - - - +
282B PHE* 1.3 61.4 + - - +
284B ILE* 3.4 4.4 + - - +
285B LEU* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.6 28.0 - - + -
278B LEU* 3.0 39.1 + - + +
279B GLN 4.3 0.4 - - - +
281B SER* 1.3 74.9 - - - +
283B GLU* 1.3 66.3 + - - +
285B LEU* 3.1 17.1 + - + +
286B ARG* 3.0 44.3 + - + +
295B ILE* 4.4 8.1 - - + -
297B VAL* 4.5 2.5 - - + -
320B SER* 3.6 41.5 - - - -
323B LEU* 4.1 16.8 - - + +
324B TYR* 3.5 37.5 - + + -
327B ILE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLN 3.0 21.1 + - - +
280B SER* 3.2 13.0 + - - +
282B PHE* 1.3 76.5 - - - +
284B ILE* 1.3 57.8 + - + +
286B ARG* 3.1 28.5 + - - +
287B GLU* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.6 25.4 - - + +
236B PHE* 3.7 36.1 - - + -
237B ILE 5.3 3.8 - - - +
248B PHE* 5.1 4.7 - - + -
249B PHE* 5.0 5.4 - - + -
252B LEU* 3.6 28.9 - - + -
280B SER* 2.9 18.7 + - - +
281B SER 3.6 5.2 - - - +
283B GLU* 1.3 76.4 - - + +
285B LEU* 1.3 61.5 + - - +
287B GLU* 3.1 26.9 + - - +
288B ILE* 3.1 15.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL* 4.5 12.3 - - + -
236B PHE* 4.0 21.5 - - + -
261B LEU* 4.3 13.5 - - + -
263B LEU* 5.0 7.9 - - + -
281B SER 3.2 15.7 + - - +
282B PHE* 3.1 24.5 + - + +
284B ILE* 1.3 77.6 - - - +
286B ARG* 1.3 58.0 + - + +
288B ILE* 3.1 26.5 - - + +
290B VAL* 2.8 42.4 + - + +
295B ILE* 3.7 29.4 - - + -
324B TYR* 5.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLN* 4.2 6.5 + - - +
282B PHE* 3.0 24.1 + - + +
283B GLU* 3.2 46.5 - - - +
285B LEU* 1.3 75.5 - - + +
287B GLU* 1.3 59.6 + - - +
289B GLY* 2.9 19.3 + - - +
290B VAL 4.5 9.6 - - - +
323B LEU* 4.2 35.8 + - - +
324B TYR* 6.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PHE* 3.1 40.8 - - + -
283B GLU* 2.9 16.0 + - + +
284B ILE* 3.1 25.4 + - - +
286B ARG* 1.3 79.2 - - - +
288B ILE* 1.3 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PHE* 3.8 21.8 - - + -
252B LEU* 3.8 45.3 - - + +
253B SER* 4.1 22.1 + - - +
255B ALA* 4.6 7.9 - - + -
256B LYS* 3.0 29.0 + - + +
284B ILE 3.1 10.3 + - - +
285B LEU* 3.1 29.8 - - + +
287B GLU* 1.3 76.1 - - - +
289B GLY* 1.3 56.6 + - - +
290B VAL* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS* 3.4 23.3 + - - -
285B LEU 3.1 0.4 + - - -
286B ARG 2.9 14.5 + - - -
287B GLU 3.3 0.2 - - - -
288B ILE* 1.3 80.8 - - - +
290B VAL* 1.3 64.1 + - - +
291B SER* 3.6 6.1 + - - -
293B LYS* 4.3 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