Contacts of the helix formed by residues 177 - 195 (chain A) in PDB entry 1L9W
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 177 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.5 8.2 - - - +
176A GLN* 1.3 77.8 - - - +
178A LYS* 1.3 62.7 + - - +
179A HIS* 3.3 10.8 + - - +
180A ASP* 3.1 34.7 + - - +
181A VAL* 3.7 3.5 + - - +
208A GLU* 3.6 13.2 + - - -
193B GLN* 5.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 1.3 70.8 - - - +
179A HIS* 1.3 66.0 + - - +
181A VAL* 3.1 23.6 + - - +
182A LEU* 3.5 4.3 + - - +
208A GLU* 3.8 18.3 + - + +
189B LEU* 3.8 32.1 - - + +
192B GLN* 4.5 11.0 - - - +
193B GLN* 4.3 13.4 - - - +
217B GLU 4.8 2.6 + - - -
218B VAL* 3.2 42.3 + - + +
219B PHE* 4.1 12.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 3.3 10.5 + - - +
178A LYS* 1.3 76.9 - - - +
180A ASP* 1.3 66.0 + - - +
182A LEU* 3.2 16.1 + - + +
183A THR* 2.9 38.9 + - - -
186B THR* 5.0 12.6 - - + +
189B LEU* 3.6 21.3 - - + +
193B GLN* 5.4 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 3.6 29.6 - - - +
175A PRO* 3.7 7.9 - - + -
176A GLN* 2.5 50.2 + - - +
177A SER* 3.1 20.7 + - - +
178A LYS 3.1 0.8 - - - -
179A HIS* 1.3 82.1 + - - +
181A VAL* 1.3 61.4 + - - +
183A THR* 3.1 11.5 + - - -
184A LEU* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.9 15.7 - - + -
177A SER 3.8 10.8 - - - +
178A LYS* 3.1 15.2 + - + +
180A ASP* 1.3 76.0 - - - +
182A LEU* 1.3 63.1 + - - +
184A LEU* 3.2 6.4 + - - +
185A LEU* 3.0 25.6 + - + +
204A SER* 3.9 16.2 - - - +
208A GLU* 3.7 22.7 - - + +
209A GLY* 4.1 11.4 - - - +
211A ILE* 3.7 30.3 - - + -
212A SER* 4.7 2.2 - - - -
218B VAL* 5.7 1.1 - - + -
219B PHE* 4.5 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS 3.5 1.1 + - - +
179A HIS* 3.2 21.7 + - + +
181A VAL* 1.3 76.4 - - - +
183A THR* 1.4 61.4 + - - +
185A LEU* 3.3 7.7 + - + +
186A THR* 2.8 35.7 + - - +
182B LEU* 4.3 19.7 - - + +
185B LEU* 4.0 26.9 - - + +
186B THR* 3.8 33.9 - - - +
189B LEU* 3.8 27.8 - - + -
219B PHE* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 4.5 4.9 - - + -
149A PRO 4.0 4.9 - - - +
150A SER* 4.5 2.0 - - - -
151A ALA* 3.6 35.2 - - + +
154A MET* 3.9 8.5 - - + +
179A HIS* 2.9 33.6 + - - -
180A ASP* 3.1 12.9 + - - -
182A LEU* 1.4 77.3 - - - +
184A LEU* 1.3 61.4 + - - +
186A THR* 3.3 6.1 + - - -
187A ALA* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 4.0 18.0 - - - +
171A ILE* 4.6 7.9 - - + -
173A VAL* 4.0 23.3 - - + -
180A ASP 3.1 12.0 + - - +
181A VAL 3.2 8.0 + - - +
183A THR* 1.3 76.6 - - - +
185A LEU* 1.4 67.9 + - + +
187A ALA* 3.2 5.0 + - + +
188A THR* 2.8 28.0 + - - +
202A THR* 3.9 31.4 - - + +
203A MET 3.9 15.0 - - - +
204A SER* 3.9 24.2 - - - +
212A SER* 4.0 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 3.0 25.3 + - + +
182A LEU* 3.7 14.8 - - + +
184A LEU* 1.4 80.2 - - + +
186A THR* 1.4 62.1 + - - +
188A THR* 3.3 6.8 + - + +
189A LEU* 3.0 25.5 + - - +
202A THR* 5.8 0.2 - - - +
211A ILE* 4.8 13.7 - - + -
212A SER* 4.1 28.3 - - - +
215A ALA* 5.0 2.9 - - + -
219A PHE* 3.7 41.3 - - + +
182B LEU* 3.8 21.2 - - + +
185B LEU* 5.4 2.0 - - + -
219B PHE* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA* 4.9 11.2 - - + -
182A LEU* 2.8 26.5 + - - +
183A THR* 3.7 7.3 - - - -
185A LEU* 1.4 74.6 - - - +
187A ALA* 1.4 58.9 + - - +
189A LEU* 3.4 1.0 + - - +
190A GLU* 2.9 39.4 + - + +
179B HIS* 4.5 20.2 - - + +
182B LEU* 3.8 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA* 4.1 14.0 - - - +
154A MET* 4.0 33.2 - - + -
155A VAL* 4.1 14.5 - - + +
158A LEU* 5.5 5.4 - - + -
171A ILE* 6.5 0.2 - - + -
183A THR 3.0 13.4 + - - +
184A LEU* 3.2 9.4 + - + +
186A THR* 1.4 76.2 - - - +
188A THR* 1.3 64.5 + - - +
189A LEU 3.3 0.2 + - - -
190A GLU* 3.3 2.2 + - - +
191A MET* 2.9 26.0 + - - +
202A THR* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.5 0.4 - - - -
184A LEU* 2.8 19.4 + - - +
185A LEU* 3.6 11.2 - - + +
187A ALA* 1.3 78.6 - - - +
189A LEU* 1.4 58.3 + - - +
191A MET* 3.5 5.8 + - - +
192A GLN* 3.0 30.1 + - - +
200A VAL* 5.7 2.0 - - + -
202A THR* 2.9 44.9 + - + +
219A PHE* 3.5 20.2 - - + +
220A GLY 3.8 20.4 - - - +
221A SER* 4.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU 3.0 17.6 + - - +
186A THR 4.1 1.8 - - - +
188A THR* 1.4 75.2 - - - +
190A GLU* 1.3 66.6 + - - +
192A GLN* 3.3 11.1 + - + +
193A GLN* 2.8 48.8 + - + +
218A VAL 4.0 6.1 - - - +
219A PHE* 3.3 29.6 + - + +
178B LYS* 3.7 41.7 - - + -
179B HIS* 4.9 17.7 - - + +
182B LEU* 4.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA* 5.2 7.1 - - - +
155A VAL* 4.4 18.8 - - + +
186A THR* 2.9 27.4 + - + +
187A ALA 3.8 3.1 - - - +
189A LEU* 1.3 80.0 - - - +
191A MET* 1.3 60.1 + - - +
193A GLN* 4.7 0.9 - - - +
194A HIS* 3.1 55.4 + - + +
195A TYR* 3.8 18.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 4.3 11.3 - - + +
158A LEU* 3.6 48.7 - - + +
159A ARG* 4.0 20.9 - - + -
162A GLN* 3.9 17.3 - - - +
169A PRO* 5.6 0.2 - - + -
187A ALA 2.9 17.5 + - - +
188A THR* 3.6 4.9 - - - +
190A GLU* 1.3 73.9 - - - +
192A GLN* 1.3 63.7 + - - +
195A TYR* 2.9 22.8 + - + +
196A ALA* 2.8 51.1 + - + +
200A VAL* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 30.9 - - + +
188A THR 3.0 14.1 + - - +
189A LEU* 3.4 23.1 - - + +
191A MET* 1.3 78.0 - - - +
193A GLN* 1.3 71.1 + - + +
196A ALA* 4.2 11.9 + - - +
200A VAL* 6.2 1.8 - - + -
217A GLU 5.9 0.4 + - - -
218A VAL 4.5 0.4 + - - -
219A PHE 3.7 9.9 - - - +
220A GLY* 3.9 28.8 - - - +
178B LYS* 4.4 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 2.8 42.8 + - + +
190A GLU* 4.4 0.9 - - - +
192A GLN* 1.3 90.2 - - + +
194A HIS* 1.3 79.4 + - + +
177B SER* 6.0 2.7 - - - -
178B LYS* 4.3 20.1 - - - +
179B HIS* 5.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLU* 3.1 43.0 + - + +
193A GLN* 1.3 95.3 + - + +
195A TYR* 1.4 87.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.9 28.5 - - + -
159A ARG* 3.5 45.7 + - + +
162A GLN* 3.0 14.5 - - - +
190A GLU* 3.9 23.8 + - + -
191A MET* 2.9 30.2 + - + -
194A HIS* 1.4 99.9 - + + +
196A ALA* 1.3 64.6 + - - +
197A ASP* 3.5 2.8 + - - +
----------------------------------------------------------
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