Contacts of the helix formed by residues 247 - 261 (chain B) in PDB entry 3KTC
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 HIS 247 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 4.8 3.4 - - + -
206B LEU* 3.4 21.6 - - + +
232B ASP* 2.8 35.8 + - - +
233B ASN 2.8 21.8 + - - -
234B LEU* 4.3 9.9 - - - -
235B ARG* 3.4 33.1 + - + +
244B GLY* 5.2 0.4 - - - -
246B VAL* 1.3 86.7 - - + +
248B MSE 1.3 63.8 + - - +
249B THR* 3.3 3.5 + - - -
250B GLU* 3.4 18.0 + - + +
251B ILE* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLY* 3.2 28.3 - - - +
245B THR 5.4 0.4 - - - -
246B VAL 3.7 4.0 + - - -
247B HIS* 1.3 74.6 - - - +
249B THR* 1.3 63.4 + - - +
251B ILE* 3.2 11.0 - - - +
252B PHE* 2.9 25.1 + - - +
288B PHE* 3.8 24.2 - - + -
291B HIS* 6.2 1.1 - - + +
292B ILE* 4.6 0.3 - - - +
324B LEU* 3.8 26.8 - - + +
325B LEU* 5.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 4.1 10.8 - - + -
136A PHE* 3.5 19.8 - - + -
247B HIS 3.3 1.0 - - - -
248B MSE 1.3 75.6 - - - +
250B GLU* 1.3 60.6 + - - +
252B PHE* 3.2 5.6 + - - +
253B GLU 2.9 22.3 + - - -
317B GLN* 3.9 30.0 + - - +
320B VAL* 4.5 6.2 - - + +
321B GLN* 6.2 0.3 - - - +
324B LEU* 3.8 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TRP* 5.3 6.9 - - - -
135A PRO* 3.7 33.0 - - + +
202B PHE* 3.5 20.5 - - + -
206B LEU* 3.9 8.7 - - + +
210B GLU 5.6 0.5 - - - +
211B SER* 5.8 1.4 - - - -
212B PRO* 5.0 8.7 - - + +
213B ALA* 5.5 0.9 + - - +
235B ARG* 2.8 44.6 + - - -
247B HIS* 3.4 20.2 + - + +
248B MSE 3.4 0.4 - - - -
249B THR* 1.3 75.9 - - - +
251B ILE* 1.3 64.6 + - - +
253B GLU* 3.3 11.9 + - - +
254B PHE* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 3.5 44.3 - - + -
230B VAL* 3.8 22.4 - - + -
232B ASP* 6.0 0.9 - - - +
243B VAL* 3.7 19.3 - - + -
244B GLY* 4.7 2.7 - - - +
247B HIS 3.1 16.2 + - - +
248B MSE 3.2 16.6 - - - +
250B GLU* 1.3 73.0 - - - +
252B PHE* 1.3 65.7 + - - +
254B PHE* 3.1 3.9 + - + +
255B PHE* 3.1 46.8 + - + -
288B PHE* 3.7 26.7 - - + -
292B ILE* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.7 18.2 - + - -
248B MSE 2.9 18.4 + - - +
249B THR 3.4 4.0 - - - +
251B ILE* 1.3 78.4 - - - +
253B GLU* 1.3 56.9 + - - +
255B PHE* 3.3 1.2 + - - -
256B TYR* 2.9 28.9 + - - +
292B ILE* 3.8 28.9 - - + -
295B ALA* 3.6 38.1 - - + -
296B LEU* 3.5 25.6 - - + -
299B LEU* 4.1 21.5 - - + -
320B VAL* 3.8 33.0 - - + -
323B ALA* 4.0 5.8 - - + -
324B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 3.8 15.4 - - - +
136A PHE* 3.0 61.7 + - + -
138A VAL 4.6 1.2 - - - +
140A HIS* 2.9 26.8 + - - -
211B SER* 4.3 4.2 + - - -
212B PRO* 6.0 0.9 - - - +
213B ALA* 3.6 20.8 - - + +
249B THR 2.9 9.1 + - - +
250B GLU* 3.5 14.8 - - - +
251B ILE 3.2 0.2 - - - -
252B PHE* 1.3 76.6 - - - +
254B PHE* 1.3 56.9 + - - +
256B TYR* 3.3 5.8 + - + +
257B VAL* 2.9 30.5 + - + +
308B GLN* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.8 39.7 - - + -
202B PHE* 3.8 22.0 - + + -
212B PRO* 3.6 32.1 - - + -
213B ALA* 4.2 7.7 - - - +
216B ALA* 4.1 8.5 - - + +
225B LEU* 6.1 0.7 - - + -
228B MSE 4.2 18.6 - - + -
230B VAL* 4.0 20.9 - - + -
250B GLU 3.1 12.4 + - - +
251B ILE* 3.1 16.1 + - + +
253B GLU* 1.3 76.7 - - - +
255B PHE* 1.3 68.5 + + - +
257B VAL* 3.2 4.9 + - - +
258B LEU* 3.1 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B MSE 3.9 15.3 - - + -
230B VAL* 3.8 18.2 - - + -
251B ILE* 3.1 50.3 + - + +
252B PHE 4.0 1.3 - - - +
254B PHE* 1.3 78.7 - + - +
256B TYR* 1.3 57.8 + - - +
258B LEU* 3.3 14.3 + - + +
259B LYS* 2.9 29.1 + - - +
267B TRP* 3.4 47.4 - + + -
289B LEU* 3.7 26.5 - - + -
292B ILE* 3.8 29.2 - - + -
296B LEU* 3.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.8 22.0 - + + -
139A SER* 6.5 0.2 - - - -
252B PHE 2.9 18.1 + - - +
253B GLU* 3.4 9.4 - - + +
255B PHE* 1.3 75.8 - - - +
257B VAL* 1.3 72.3 + - + +
259B LYS* 3.2 4.4 + - + +
260B ILE* 3.0 56.9 + - + +
296B LEU* 3.8 15.8 - - + +
299B LEU* 3.7 17.9 - - + -
301B ILE* 4.0 17.5 - - + -
304B LEU* 3.7 20.7 - - + +
305B GLN* 3.0 33.8 + - - +
308B GLN* 3.8 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 4.6 10.8 - - + +
213B ALA* 3.6 37.7 - - + +
216B ALA* 4.0 7.6 - - + -
217B GLN* 3.7 21.8 - - + +
220B ILE* 4.8 0.9 - - + -
253B GLU* 2.9 20.8 + - + +
254B PHE 3.8 4.7 - - - +
256B TYR* 1.3 88.2 - - + +
258B LEU* 1.3 64.9 + - - +
260B ILE* 3.4 9.4 + - + +
261B ASN* 2.8 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 4.1 12.1 - - + -
220B ILE* 3.9 12.1 - - + -
225B LEU* 3.7 30.1 - - + -
228B MSE 3.8 30.5 - - + -
254B PHE* 3.1 32.2 + - + +
255B PHE* 3.3 20.2 + - + +
257B VAL* 1.3 76.9 - - - +
259B LYS* 1.3 62.2 + - - +
261B ASN* 3.3 0.7 + - - -
262B ASN 3.2 2.9 + - - -
263B TRP* 3.0 50.7 + - + +
267B TRP* 5.2 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE 2.9 13.4 + - - +
256B TYR* 3.2 9.6 + - - +
258B LEU* 1.3 77.4 - - - +
260B ILE* 1.3 59.4 + - + +
262B ASN* 2.9 22.0 + - - +
263B TRP 5.3 1.1 - - - -
264B GLN* 6.0 2.0 - - - +
296B LEU* 4.0 43.0 + - + +
297B ASP* 5.4 4.4 + - - +
301B ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 6.0 1.8 - - - +
217B GLN* 4.6 2.5 - - - +
256B TYR* 3.0 60.3 + - + +
257B VAL* 3.5 17.9 - - + +
259B LYS* 1.3 74.5 - - + +
261B ASN* 1.3 67.1 + - - +
262B ASN* 3.3 1.0 + - - +
301B ILE* 4.4 12.8 - - + -
305B GLN* 3.8 15.7 - - - +
339B EDO 3.5 38.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 5.1 0.3 - - - +
217B GLN* 2.9 43.3 + - - -
220B ILE* 3.7 32.1 - - + +
221B ASP* 4.6 0.9 - - - +
257B VAL* 2.8 33.6 + - - +
258B LEU 3.8 3.4 - - - +
259B LYS 3.1 0.8 - - - -
260B ILE* 1.3 81.7 - - - +
262B ASN* 1.3 68.8 + - - +
263B TRP* 3.3 2.3 + - + +
339B EDO 3.6 12.5 + - - -
----------------------------------------------------------
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