Contacts of the helix formed by residues 198 - 216 (chain P) in PDB entry 5LN3
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 ASP 198 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193P CYS* 3.9 10.1 + - + +
196P VAL* 3.5 16.4 - - + -
197P LYS* 1.4 76.5 - - - +
199P TYR* 1.3 66.0 + - - +
200P ILE* 3.5 30.8 - - - +
201P ARG* 3.3 36.2 + - - +
202P THR* 3.3 17.8 + - - -
233P LEU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197P LYS* 3.4 48.0 + - + +
198P ASP* 1.3 75.8 + - - +
200P ILE* 1.4 69.4 + - + +
202P THR* 3.5 14.0 + - - -
203P GLN* 3.0 24.7 + - - +
233P LEU* 4.3 24.9 - - + +
236P HIS* 3.8 35.9 + + + -
237P GLU* 5.3 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198P ASP* 3.5 25.6 - - - +
199P TYR* 1.4 75.2 - - + +
201P ARG* 1.4 64.9 + - + +
203P GLN* 3.2 29.5 + - - +
204P ILE* 3.7 10.7 + - - +
274Q LYS* 6.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P ALA* 4.3 16.0 + - - +
164P SER* 5.3 3.2 + - - +
167P GLN* 5.0 16.7 - - - +
189P GLN* 4.3 16.9 - - - +
193P CYS* 4.3 21.0 - - - -
196P VAL* 3.8 30.1 - - - +
198P ASP* 3.3 27.0 + - - +
199P TYR 3.5 0.6 - - - -
200P ILE* 1.4 78.7 - - + +
202P THR* 1.4 62.5 + - - +
204P ILE* 3.3 28.2 - - + +
205P ILE* 3.4 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P MET* 4.3 33.0 - - + +
193P CYS* 3.8 15.9 + - + +
194P LEU* 5.8 0.4 - - - +
198P ASP 3.3 18.2 + - - -
199P TYR 3.7 6.7 + - - -
200P ILE 3.4 0.8 - - - -
201P ARG* 1.4 73.4 - - - +
203P GLN* 1.4 64.0 + - - +
205P ILE* 3.3 9.0 - - - +
206P SER* 3.1 30.6 + - - -
229P LEU* 5.1 9.9 - - + -
233P LEU* 3.9 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199P TYR* 3.0 30.9 + - - +
200P ILE* 3.2 19.1 + - - +
202P THR* 1.4 58.1 - - - +
204P ILE* 1.4 64.6 + - + +
206P SER* 2.8 21.6 + - - -
207P LYS* 3.1 25.3 + - - +
233P LEU* 4.9 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200P ILE 3.7 6.9 + - - +
201P ARG* 3.3 27.8 - - + +
203P GLN* 1.4 81.7 - - + +
205P ILE* 1.4 69.1 + - + +
206P SER 3.4 0.2 + - - -
207P LYS* 3.5 22.1 + - - +
208P LYS* 3.9 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P GLN* 4.8 17.3 - - - +
170P GLN* 4.4 17.0 - - - +
186P ILE* 4.6 8.6 - - + +
189P GLN* 4.0 25.4 - - + -
190P MET* 3.9 29.4 - - + +
193P CYS* 5.0 2.2 - - - -
201P ARG 3.4 13.7 - - - +
202P THR* 3.3 17.3 - - - +
204P ILE* 1.4 82.3 - - + +
206P SER* 1.4 64.8 - - - +
207P LYS 3.3 0.2 - - - -
208P LYS* 3.3 20.8 + - - +
209P ILE* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P MET* 4.8 15.5 - - - -
202P THR* 3.1 20.4 + - - -
203P GLN* 2.8 23.6 + - - -
205P ILE* 1.4 77.9 - - - +
207P LYS* 1.4 67.7 + - - +
209P ILE* 3.1 23.0 - - - +
210P ASN* 3.2 17.7 + - - -
230P MET* 5.2 13.2 - - - +
233P LEU* 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203P GLN* 3.1 31.1 + - - +
204P ILE* 3.5 22.9 + - - +
205P ILE 3.3 0.6 - - - -
206P SER* 1.4 85.3 + - - +
208P LYS* 1.3 64.1 + - - +
210P ASN* 3.5 11.8 + - - +
211P THR* 3.6 17.8 + - - +
230P MET* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170P GLN* 3.8 28.0 + - - +
179P LYS* 5.9 0.6 - - - +
182P ARG* 5.1 8.4 - - - +
186P ILE* 3.3 31.5 - - - +
204P ILE 3.9 5.7 + - - +
205P ILE* 3.4 27.6 + - - +
206P SER 3.3 0.2 - - - -
207P LYS* 1.3 79.3 - - - +
209P ILE* 1.4 65.1 + - - +
211P THR* 3.3 18.0 + - - -
212P LYS* 3.4 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P LYS* 4.4 15.7 + - - +
183P VAL* 3.9 18.4 - - + -
186P ILE* 3.6 42.6 - - + -
187P LEU* 4.2 6.5 - - + -
190P MET* 4.5 8.3 - - + -
205P ILE 3.1 11.3 + - - +
206P SER* 3.1 25.6 - - - +
208P LYS* 1.4 81.4 - - - +
210P ASN* 1.3 67.4 + - - +
211P THR 3.4 0.2 + - - -
212P LYS* 3.5 2.6 + - - +
213P PHE* 3.3 18.9 + - - +
226P TYR* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 210 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P MET* 5.6 1.2 - - - +
206P SER* 3.2 19.1 + - - +
207P LYS* 3.8 9.4 - - - +
208P LYS 3.5 0.4 - - - -
209P ILE* 1.3 77.4 - - - +
211P THR* 1.3 66.7 + - + +
213P PHE* 3.5 1.9 + - - +
214P PHE* 3.1 24.1 + - - +
223P LYS* 4.1 7.1 + - - -
226P TYR* 3.6 35.8 - - - +
230P MET* 3.3 30.3 - - - +
250P ILE* 5.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207P LYS 3.6 12.5 + - - +
208P LYS* 3.3 13.7 + - - -
210P ASN* 1.3 74.4 - - + +
212P LYS* 1.4 75.9 + - - +
214P PHE* 3.4 4.7 + - - +
215P GLN* 3.0 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175P GLY 4.4 8.3 - - - -
176P SER* 3.4 25.8 - - - +
179P LYS* 3.6 26.7 - - + +
182P ARG* 5.5 2.5 - - - +
208P LYS* 3.4 43.1 + - + +
209P ILE 3.5 2.2 + - - +
210P ASN 3.4 0.4 - - - -
211P THR* 1.4 80.5 + - - +
213P PHE* 1.3 61.8 + - - +
215P GLN* 3.7 8.0 + - - +
216P GLU* 2.7 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P LYS* 4.6 12.7 - - + +
180P LYS* 6.4 1.6 - - + -
183P VAL* 4.9 10.5 - - + -
209P ILE* 3.3 12.6 + - + +
210P ASN 3.8 3.8 - - - +
211P THR 3.2 0.4 - - - -
212P LYS* 1.3 80.8 - - - +
214P PHE* 1.4 55.4 + - - +
216P GLU* 2.9 30.6 + - + +
217P GLU* 3.3 24.8 - - - +
218P ASN* 3.0 17.5 - - - +
219P THR* 3.5 17.0 - - - -
222P LEU* 3.6 31.2 - - + -
223P LYS* 3.6 33.4 - - + -
226P TYR* 2.9 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210P ASN 3.1 14.3 + - - +
211P THR* 3.4 6.5 + - - +
213P PHE* 1.4 73.1 - - - +
215P GLN* 1.3 68.7 + - + +
216P GLU 3.2 7.4 - - - +
218P ASN* 3.4 25.0 + - - +
223P LYS* 3.6 25.9 - - - +
249P ALA* 4.3 21.3 - - + -
252P ASP* 3.6 29.8 - - + -
253P THR* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211P THR* 3.0 34.5 + - - +
212P LYS* 3.9 8.9 - - - +
214P PHE* 1.3 81.6 - - + +
216P GLU* 1.3 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P LYS* 3.2 39.7 - - - +
180P LYS* 6.0 0.2 - - - +
212P LYS* 2.7 37.8 + - - +
213P PHE* 2.9 19.4 + - + +
214P PHE 3.2 6.4 - - - +
215P GLN* 1.3 85.5 - - + +
217P GLU* 1.4 66.5 + - - +
218P ASN* 3.6 5.2 + - - +
----------------------------------------------------------
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