Contacts of the helix formed by residues 195 - 214 (chain B) in PDB entry 1L8A
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 GLY 195 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ARG* 3.8 1.8 - - - -
194B MET* 1.3 72.5 - - - +
196B LEU* 1.3 58.1 + - - +
198B PRO* 3.3 11.1 - - - +
199B ILE* 3.0 23.0 - - - +
232B GLU* 2.9 15.4 + - - +
235B GLU* 3.8 11.4 - - - -
237B GLU* 3.2 11.7 - - - +
238B SER* 3.4 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ARG* 3.7 28.0 - - - +
639A GLN* 4.4 1.6 - - - +
190B PRO 5.0 8.5 - - - +
193B SER* 3.3 22.4 - - - +
194B MET 3.2 3.6 + - - -
195B GLY* 1.3 77.4 - - - +
197B GLY* 1.3 58.9 + - - +
199B ILE* 3.4 17.6 - - + +
200B GLY* 2.9 28.6 + - - -
237B GLU* 4.7 4.3 - - + -
572B LEU* 5.3 2.5 - - + -
576B CYS* 5.2 0.2 - - - -
609B ASP* 3.7 43.7 - - + +
610B LEU* 4.2 22.6 - - + +
613B ALA* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.9 20.7 - - - -
190B PRO 5.1 1.3 - - - -
191B THR* 4.3 20.3 + - - +
193B SER 4.4 3.0 + - - -
195B GLY 4.4 0.6 - - - +
196B LEU* 1.3 77.9 - - - +
198B PRO* 1.3 63.0 - - - +
200B GLY 3.7 0.2 - - - -
201B ALA* 2.8 32.3 + - - +
226B ALA* 5.1 1.1 - - - -
228B LEU* 4.6 4.0 - - - -
232B GLU* 4.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLY* 3.3 21.3 - - - +
197B GLY* 1.3 89.1 - - - +
199B ILE* 1.3 59.3 + - - +
201B ALA* 3.3 1.9 + - + +
202B ILE* 3.1 19.8 + - - +
228B LEU* 3.5 24.4 - - + -
232B GLU* 3.5 14.6 - - - +
237B GLU 4.9 0.2 - - - -
238B SER* 3.6 35.4 - - - +
255B PHE* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PRO* 4.9 5.6 - - + -
195B GLY 3.0 22.0 - - - +
196B LEU* 3.4 26.9 - - + +
198B PRO* 1.3 72.0 - - - +
200B GLY* 1.3 66.1 + - - +
202B ILE* 3.3 7.2 + - - +
203B TYR* 3.1 40.2 + - + -
237B GLU* 3.3 22.5 + - + +
241B ALA* 3.9 25.1 - - + -
572B LEU* 3.4 37.2 - - + -
573B GLY* 5.1 2.2 - - - -
576B CYS* 3.9 15.7 - - - -
610B LEU* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.6 12.5 + - - -
196B LEU 2.9 17.6 + - - -
197B GLY 3.7 0.7 - - - -
199B ILE* 1.3 80.2 - - - +
201B ALA* 1.3 55.7 + - - +
203B TYR* 3.4 2.4 + - - +
204B GLN* 2.9 28.1 + - - +
576B CYS* 3.9 18.0 - - - +
579B LEU* 6.0 4.7 - - - -
580B ALA* 5.7 0.2 - - - +
610B LEU* 6.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.8 19.3 - - + -
197B GLY 2.8 18.4 + - - +
198B PRO 3.7 2.7 - - - +
199B ILE 3.2 0.4 - - - -
200B GLY* 1.3 73.3 - - - +
202B ILE* 1.3 66.3 + - - +
204B GLN* 3.1 2.1 + - - +
205B ALA* 2.9 24.8 + - - +
224B VAL* 3.7 16.9 - - + +
226B ALA* 3.6 26.2 - - + -
253B LEU* 4.0 6.1 - - + -
255B PHE* 4.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO 3.1 16.0 + - - +
199B ILE* 3.3 9.8 + - - +
201B ALA* 1.3 76.0 - - - +
203B TYR* 1.3 76.5 + - + +
205B ALA* 3.4 3.8 + - - +
206B LYS* 3.1 22.2 + - + +
237B GLU 5.9 0.4 - - - +
238B SER 5.1 2.0 - - - +
241B ALA* 3.8 38.4 - - + +
242B ILE* 4.0 13.0 - - + +
244B ILE* 4.9 4.7 - - + -
245B ALA* 4.7 6.5 - - + +
250B LEU* 3.6 19.4 - - + +
253B LEU* 3.7 19.3 - - + +
255B PHE* 3.7 25.4 - - + -
287B TRP* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 3.1 36.7 + - + +
200B GLY 4.0 0.7 - - - +
202B ILE* 1.3 88.8 - - + +
204B GLN* 1.3 60.2 + - - +
206B LYS* 3.8 18.5 - - + +
207B PHE* 3.0 27.2 + - - +
241B ALA* 4.2 5.9 - - + +
244B ILE* 3.9 19.9 - - + +
567B GLU* 3.5 23.0 + - - -
570B ASN* 2.8 24.6 + - - -
573B GLY* 3.4 27.1 - - - -
576B CYS* 3.5 32.5 - - + +
577B SER* 3.1 22.8 + - - +
580B ALA* 4.0 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.4 33.1 - - + +
138B TYR* 3.1 32.0 + - + +
189B PHE* 3.7 15.1 - - - -
200B GLY 2.9 10.8 + - - +
201B ALA* 3.1 6.5 + - - +
203B TYR* 1.3 74.4 - - - +
205B ALA* 1.3 66.7 + - - +
207B PHE* 3.2 8.3 + - - +
208B LEU* 3.0 30.5 + - - +
224B VAL* 4.0 7.0 - - + -
580B ALA* 4.0 29.0 + - + +
583B THR* 5.0 2.8 + - - -
587B THR* 4.6 9.1 + - - +
588B ASN* 4.9 2.6 - - - +
617B GLN* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ALA 2.9 12.1 + - - +
202B ILE 3.6 8.1 - - - +
204B GLN* 1.3 78.8 - - - +
206B LYS* 1.3 62.0 + - - +
208B LEU* 3.2 1.8 + - - -
209B LYS* 3.1 15.2 + - - +
224B VAL* 3.8 16.3 - - + +
250B LEU* 3.9 4.0 - - + -
252B ASN* 3.1 41.2 - - - +
253B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.1 16.1 + - + +
203B TYR* 3.8 22.0 - - + +
204B GLN 3.3 0.2 - - - -
205B ALA* 1.3 78.3 - - - +
207B PHE* 1.3 56.4 + - - +
209B LYS* 3.3 5.2 + - + +
210B TYR* 3.0 24.9 + - - +
244B ILE* 4.3 9.0 - - + -
248B GLU* 3.3 45.6 + - + +
250B LEU* 3.9 14.5 - - + +
538B TYR* 4.4 9.2 + - + -
565B LEU* 3.9 20.4 - - - +
566B GLN 5.6 1.0 + - - +
567B GLU* 2.9 41.1 + - - -
577B SER* 3.9 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR 3.0 19.0 + - - +
204B GLN* 3.6 11.4 - - - +
205B ALA 3.2 0.4 - - - -
206B LYS* 1.3 75.4 - - - +
208B LEU* 1.3 59.8 + - + +
210B TYR* 3.2 29.7 - + - +
211B LEU* 3.0 55.0 + - + +
516B VAL* 4.3 6.5 - - + -
565B LEU* 4.5 10.8 - - + -
577B SER* 4.5 7.9 - - - +
580B ALA* 3.7 20.6 - - + -
581B ALA* 3.5 39.7 - - + -
584B SER* 3.9 12.6 - - - -
588B ASN* 5.0 1.6 - - - -
592B MET* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.9 9.9 - - + -
204B GLN* 3.0 26.9 + - - +
205B ALA 3.2 7.6 + - - +
207B PHE* 1.3 73.8 - - + +
209B LYS* 1.3 66.1 + - - +
211B LEU* 3.3 5.5 + - + +
212B GLU 3.2 11.3 + - - -
219B THR* 2.5 35.0 + - + +
222B GLN* 3.8 37.2 - - + +
224B VAL* 3.8 26.5 - - + -
252B ASN* 3.8 10.3 - - - +
588B ASN* 3.7 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA 3.1 15.6 + - - +
206B LYS* 3.4 10.1 - - + +
207B PHE 3.2 0.2 - - - -
208B LEU* 1.3 73.9 - - - +
210B TYR* 1.3 54.1 + - - +
212B GLU* 3.0 19.5 + - - +
213B HIS* 2.8 50.1 + - + +
219B THR* 4.6 0.4 - - - -
248B GLU 5.0 2.7 - - - +
249B LYS 3.9 14.9 + - - -
250B LEU* 3.9 14.6 - - + +
251B ASP* 2.8 28.5 + - - -
252B ASN* 3.6 27.9 - - - +
538B TYR* 3.6 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LYS* 3.0 14.4 + - - +
207B PHE* 3.2 41.1 - + + +
209B LYS* 1.3 77.2 - - - +
211B LEU* 1.3 59.3 + - + +
214B ARG* 2.8 78.7 + - + +
515B LEU 4.0 3.1 + - - -
516B VAL* 3.9 13.6 - - + +
538B TYR* 3.3 36.7 + + + -
562B GLY 3.8 5.8 - - - -
563B GLN* 2.7 32.1 + - - +
565B LEU* 3.7 17.5 - - + -
592B MET* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 3.0 39.6 + - + +
208B LEU* 3.7 9.4 - - + +
209B LYS 3.3 0.2 - - - -
210B TYR* 1.3 78.9 - - + +
212B GLU* 1.3 59.6 + - - +
214B ARG* 3.6 0.6 + - - -
215B GLY 3.3 1.7 + - - -
216B LEU* 2.8 49.8 + - + +
217B LYS* 3.1 10.7 + - + +
219B THR* 4.1 19.5 - - + -
584B SER* 4.0 0.9 - - - +
588B ASN* 3.8 22.7 - - - +
590B LEU* 3.6 30.7 - - + -
592B MET* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU 3.2 8.3 + - - +
209B LYS* 3.0 24.3 + - - +
211B LEU* 1.3 77.6 - - - +
213B HIS* 1.3 74.1 + - + +
215B GLY* 3.0 14.2 + - - -
217B LYS 3.1 17.2 + - - +
218B ASP* 3.8 8.1 - - - +
219B THR* 3.8 6.5 + - - +
220B SER* 3.3 35.0 + - - -
561B LYS* 5.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 2.8 32.9 + - + +
210B TYR 3.8 0.2 - - - +
212B GLU* 1.3 81.8 + - + +
214B ARG* 1.3 56.2 + - - +
215B GLY 3.1 0.2 - - - -
538B TYR* 2.7 27.8 + - + -
540B PRO* 3.4 23.5 - - + +
560B GLU* 3.1 48.2 + - + +
561B LYS* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B TYR* 2.8 60.9 + - + +
211B LEU 4.1 0.2 - - - +
213B HIS* 1.3 75.1 - - - +
215B GLY* 1.3 61.7 + - - +
216B LEU* 3.4 22.9 + - + +
513B ASP* 3.3 50.1 + - - +
560B GLU 4.3 2.5 - - - +
561B LYS* 3.1 35.9 + - - +
562B GLY 3.1 25.5 + - - -
563B GLN* 3.7 20.8 + - - +
592B MET* 4.7 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