Contacts of the helix formed by residues 229 - 248 (chain M) in PDB entry 6LTJ
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 ASN 229 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196M ASP* 5.1 4.9 - - - +
198M GLN* 4.1 13.8 - - - +
228M LEU* 1.3 76.8 - - - +
230M PRO* 1.3 72.2 - - - +
231M LEU* 3.8 22.5 - - - +
232M THR* 2.6 42.8 + - - -
233M PHE* 3.0 20.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 230 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220M GLU* 3.9 16.4 - - - +
223M CYS* 3.6 30.5 - - + +
224M ASP* 6.3 0.9 - - - -
228M LEU 3.1 14.1 - - - +
229M ASN* 1.3 85.6 - - - +
231M LEU* 1.3 64.4 + - + +
234M VAL* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229M ASN* 3.8 18.4 - - - +
230M PRO* 1.3 80.3 - - + +
232M THR* 1.3 76.0 + - - +
234M VAL* 5.4 0.2 - - - -
235M PRO* 3.4 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LYS* 2.3 47.6 + - - +
195M ILE* 3.5 14.6 - - + -
196M ASP* 4.4 4.4 + - - +
229M ASN* 2.6 40.2 + - - -
231M LEU* 1.3 81.5 - - - +
233M PHE* 1.3 70.0 + - + +
235M PRO* 3.4 9.9 - - - +
236M ALA* 4.0 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 233 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193M MET* 4.5 10.1 - - + -
195M ILE* 3.9 26.9 - - + -
196M ASP* 4.5 1.6 - - - -
198M GLN* 3.2 56.3 - - + -
200M LEU* 4.1 18.2 - - + -
223M CYS* 4.6 3.8 - - + -
228M LEU* 3.8 28.5 - - + -
229M ASN* 3.0 33.0 + - + +
232M THR* 1.3 78.7 - - + +
234M VAL* 1.3 56.8 + - - +
236M ALA* 2.7 31.2 + - - +
237M ILE* 2.8 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216M GLU* 4.1 17.3 - - + +
219M SER* 3.2 31.7 + - - +
220M GLU* 3.2 28.3 - - - +
223M CYS* 3.5 23.6 - - - -
230M PRO 2.9 26.1 + - - +
231M LEU* 5.4 0.2 - - - -
233M PHE* 1.3 70.7 - - - +
235M PRO* 1.3 65.6 - - + +
237M ILE* 4.5 0.6 - - - +
238M ALA* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 235 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216M GLU* 6.3 0.2 - - + -
230M PRO 3.7 0.2 - - - +
231M LEU* 3.4 19.5 - - - +
232M THR 3.4 15.5 - - - +
234M VAL* 1.3 96.4 - - + +
236M ALA* 1.3 55.9 + - - +
238M ALA* 3.9 4.5 - - + +
239M SER* 2.9 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ARG* 5.9 6.9 + - - -
74G LYS* 6.1 1.1 - - - +
193M MET* 3.7 22.6 - - + +
195M ILE* 5.8 8.1 - - + -
232M THR 4.0 8.7 + - - +
233M PHE* 2.7 15.2 + - - +
235M PRO* 1.3 76.0 - - - +
237M ILE* 1.3 56.7 + - - +
239M SER* 2.7 22.1 + - - -
240M ALA* 2.9 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191M LEU* 3.8 21.3 - - + -
193M MET* 3.7 26.0 - - + -
200M LEU* 3.6 20.4 - - + -
218M PHE* 4.8 0.2 - - + -
219M SER* 3.6 32.1 - - - +
222M LEU* 3.9 15.9 - - + -
223M CYS* 5.1 1.1 - - + -
228M LEU* 4.9 3.6 - - + -
233M PHE* 2.8 39.6 + - + +
234M VAL 4.5 0.4 - - - +
236M ALA* 1.3 71.9 - - - +
238M ALA* 1.3 57.7 + - - +
240M ALA* 3.3 1.6 + - - +
241M ILE* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215M PRO* 4.0 21.0 - - - +
216M GLU* 3.5 36.1 - - + +
219M SER* 4.2 0.6 - - - +
234M VAL 2.9 18.1 + - - +
235M PRO* 3.9 4.7 - - + +
237M ILE* 1.3 76.9 - - - +
239M SER* 1.3 58.1 + - - +
241M ILE* 3.4 1.6 + - - +
242M ARG* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ARG* 6.0 0.5 + - - -
235M PRO 2.9 15.8 + - - -
236M ALA* 2.7 25.5 + - - -
238M ALA* 1.3 77.9 - - - +
240M ALA* 1.3 59.4 + - - +
242M ARG* 3.3 5.5 + - - +
243M GLN* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ARG* 5.1 9.4 - - - +
190M ARG 5.3 0.4 - - - +
191M LEU* 3.9 20.0 - - + -
193M MET* 4.5 7.0 - - + -
236M ALA 2.9 13.1 + - - +
237M ILE 3.7 4.0 - - - +
239M SER* 1.3 81.6 + - - +
241M ILE* 1.3 64.0 + - - +
243M GLN* 3.2 18.6 - - - +
244M GLN* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M ILE* 4.0 25.9 - - + +
191M LEU* 4.6 2.9 - - + -
204M PHE* 4.0 7.0 - - + -
206M TRP* 4.5 14.4 - - + -
215M PRO* 3.8 32.8 - - + +
218M PHE* 3.6 36.8 - - + -
237M ILE* 2.9 30.4 + - + +
238M ALA 3.7 3.8 - - - +
240M ALA* 1.3 77.2 - - - +
242M ARG* 1.3 57.4 + - - +
244M GLN* 3.3 1.9 + - - +
245M ILE* 2.9 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M THR* 4.4 3.8 - - - -
215M PRO* 3.7 30.1 - - + +
216M GLU* 2.3 50.1 + - - -
238M ALA* 2.9 26.6 + - - +
239M SER* 3.9 5.3 - - - +
241M ILE* 1.3 76.5 - - - +
243M GLN* 1.3 55.2 + - - +
245M ILE* 3.1 8.2 + - + +
246M GLU* 2.7 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ARG* 4.4 16.4 - - - +
47H PRO* 5.5 7.2 - - - +
48H ASP* 4.7 9.9 - - - +
239M SER* 2.9 21.2 + - - +
240M ALA* 3.2 25.7 + - - +
242M ARG* 1.3 76.5 - - - +
244M GLN* 1.3 63.1 + - + +
246M GLU* 3.6 7.9 + - - +
247M SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M VAL* 5.0 1.7 - - - +
188M PRO 3.8 11.7 - - - +
189M ILE* 3.7 27.1 - - + +
190M ARG* 2.6 51.3 + - - +
191M LEU* 4.3 3.8 - - - +
240M ALA* 2.9 25.2 + - - +
243M GLN* 1.3 81.0 - - + +
245M ILE* 1.3 64.0 - - - +
247M SER* 3.6 8.8 + - - -
248M TYR* 3.3 19.4 + - - +
376M ARG* 4.7 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M VAL* 4.2 22.2 - - + +
189M ILE* 4.3 1.8 - - + -
206M TRP* 3.4 33.7 - - + +
208M MET* 3.8 32.9 - - + +
215M PRO* 4.9 5.2 - - + -
241M ILE* 2.9 32.4 + - + +
242M ARG* 3.1 11.9 + - + +
244M GLN* 1.3 77.7 - - - +
246M GLU* 1.3 72.4 + - + +
248M TYR* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M ARG* 2.7 47.9 + - - +
243M GLN* 4.0 6.1 + - - +
245M ILE* 1.3 83.8 - - + +
247M SER* 1.3 66.3 + - - +
248M TYR 3.2 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M GLN 2.9 20.2 + - - -
244M GLN* 3.7 10.5 - - - -
245M ILE 3.3 0.4 - - - -
246M GLU* 1.3 76.4 - - - +
248M TYR* 1.3 61.9 + - - +
249M PRO* 3.6 4.0 - - - +
324M LYS* 5.2 3.1 - - - -
380M ASN* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M VAL* 4.3 12.2 - - + +
186M LEU 3.7 14.3 + - - -
187M VAL* 3.5 30.3 - - + -
188M PRO* 3.9 22.7 - - + -
208M MET* 3.6 17.7 - - + -
244M GLN 3.3 9.5 + - - +
245M ILE 3.2 17.0 + - - +
246M GLU 3.1 10.7 - - - +
247M SER* 1.3 80.5 - - - +
249M PRO* 1.3 99.2 - - + +
320M SER* 4.0 19.3 - - - -
323M GLN* 6.2 0.2 - - - +
----------------------------------------------------------
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