Contacts of the helix formed by residues 173 - 192 (chain A) in PDB entry 4WMI
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 VAL 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 4.3 16.4 - - + -
141A VAL* 4.0 15.7 - - + -
142A SER 3.4 4.3 + - - -
143A GLU* 3.6 36.3 - - + +
171A HIS 3.3 5.7 + - - -
172A ASP* 1.3 74.9 + - - +
174A ALA* 1.3 56.6 + - + +
176A LEU* 3.9 2.5 - - - +
177A THR* 2.8 42.6 + - - +
203A ILE* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.0 17.3 + - - +
173A VAL* 1.3 78.5 - - + +
175A VAL* 1.3 65.9 + - + +
177A THR* 3.5 7.9 + - - -
178A ASP* 3.2 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.1 32.9 + - + +
174A ALA* 1.3 76.8 - - + +
176A LEU* 1.3 73.9 + - + +
178A ASP* 3.2 8.4 + - - +
179A LYS* 3.1 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 3.8 32.8 - - + -
171A HIS* 3.8 28.3 - - + +
172A ASP 3.0 17.7 + - - +
173A VAL 4.0 0.7 - - - +
175A VAL* 1.3 88.1 - - + +
177A THR* 1.3 53.5 + - - +
179A LYS* 3.2 11.3 + - + +
180A LEU* 2.8 41.6 + - - +
203A ILE* 3.9 12.8 - - + -
206A LEU* 4.0 19.3 - - + -
213A ILE* 3.9 26.2 - - + -
214A MET* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 2.8 34.0 + - - +
174A ALA* 3.6 8.4 - - - +
175A VAL 3.3 0.2 - - - -
176A LEU* 1.3 77.4 - - - +
178A ASP* 1.3 60.9 + - - +
180A LEU* 3.3 9.3 + - - +
181A PHE* 3.0 28.8 + - - +
199A TYR* 3.7 43.2 + - + +
202A SER* 4.0 10.0 - - - -
203A ILE* 4.2 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 3.2 15.2 + - - +
175A VAL* 3.2 8.8 + - - +
177A THR* 1.3 81.3 - - - +
179A LYS* 1.3 64.7 + - + +
181A PHE* 3.7 4.0 + - - +
182A PRO* 3.3 19.2 - - - +
199A TYR* 4.5 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 3.1 37.3 + - + +
176A LEU* 3.6 11.9 - - + +
178A ASP* 1.3 76.0 - - + +
180A LEU* 1.3 61.9 + - - +
182A PRO* 3.4 11.3 - - - +
183A VAL* 4.1 10.2 - - - +
212A GLN 5.6 2.5 - - - +
213A ILE* 4.1 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU 2.8 22.9 + - - +
177A THR* 3.8 4.3 - - - +
179A LYS* 1.3 75.3 - - - +
181A PHE* 1.3 64.7 + - - +
182A PRO 3.4 0.2 - - - -
183A VAL* 3.0 9.1 + - - +
184A VAL* 2.9 29.5 + - + +
202A SER* 3.7 24.5 - - - +
203A ILE* 3.9 17.0 - - + -
205A PHE 4.1 4.3 - - - +
206A LEU* 3.7 41.3 - - + +
209A ALA* 3.7 28.5 - - + -
213A ILE* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR 3.0 17.3 + - - +
178A ASP* 4.1 3.8 - - - +
180A LEU* 1.3 75.6 - - - +
182A PRO* 1.4 74.1 - - + +
184A VAL* 4.4 2.2 - - - +
185A GLU* 2.8 68.3 + - + +
188A GLN* 3.6 16.8 - - - -
197A THR* 3.7 19.5 - - + -
198A TYR 5.0 3.1 - - - -
199A TYR* 3.5 39.7 - + + -
202A SER* 3.4 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP 3.3 17.7 - - - +
179A LYS* 3.4 11.4 - - - +
180A LEU 3.5 0.2 - - - -
181A PHE* 1.4 96.2 - - + +
183A VAL* 1.3 64.9 + - + +
185A GLU* 4.1 11.3 + - + +
186A ALA 5.4 0.3 + - - -
311A PRO* 6.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS 4.1 13.2 - - - +
180A LEU* 3.0 9.8 + - - +
182A PRO* 1.3 79.5 - - + +
184A VAL* 1.3 64.1 + - + +
185A GLU 3.9 0.3 + - - -
186A ALA* 4.9 3.5 + - - +
187A MET* 4.3 5.8 + - + +
208A VAL* 5.6 0.7 - - + -
209A ALA* 3.9 20.0 - - + -
212A GLN* 3.3 33.4 - - + +
213A ILE* 5.6 0.9 - - + -
309A LEU* 4.0 39.5 - - + +
311A PRO* 5.9 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 2.9 27.5 + - + +
183A VAL* 1.3 84.4 - - + +
185A GLU* 1.3 66.8 + - - +
186A ALA 3.3 2.2 - - - -
187A MET* 3.0 24.1 + - + +
188A GLN* 3.3 22.9 - - - +
202A SER* 4.1 7.9 - - - +
205A PHE* 3.5 47.8 - - + +
208A VAL* 3.8 20.6 - - + -
209A ALA* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 2.8 52.9 + - + +
182A PRO* 4.4 9.5 - - - +
183A VAL 3.6 1.2 - - - -
184A VAL* 1.3 74.9 - - - +
186A ALA* 1.3 64.5 + - - +
188A GLN* 3.2 29.4 + - - +
189A LYS* 4.4 3.8 + - - +
197A THR* 3.9 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO 5.4 0.4 + - - -
183A VAL 4.9 3.7 + - - +
184A VAL 3.1 1.2 + - - -
185A GLU* 1.3 79.5 - - - +
187A MET* 1.3 60.5 + - - +
189A LYS* 3.5 20.2 - - - +
190A TYR* 3.5 21.1 - - - -
309A LEU 6.0 0.7 - - - +
311A PRO* 3.7 43.5 - - + +
314A VAL* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL 4.3 16.1 + - - +
184A VAL* 3.0 18.4 - - + +
186A ALA* 1.3 76.7 - - - +
188A GLN* 1.3 65.5 + - - +
189A LYS 3.2 2.9 - - - -
190A TYR* 3.1 12.9 + - - +
191A PHE* 3.1 31.8 - - + -
205A PHE* 3.8 27.1 - - + -
208A VAL* 4.1 22.9 - - + -
309A LEU* 4.3 13.2 - - + +
314A VAL* 3.8 24.4 - - + +
332A PHE* 4.0 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 3.6 15.4 - - - -
184A VAL* 3.3 29.4 + - + +
185A GLU* 3.2 11.3 + - - +
187A MET* 1.3 76.9 - - - +
189A LYS* 1.3 63.3 + - - +
192A SER* 2.9 39.6 + - - +
196A GLY 3.6 10.2 - - - +
197A THR* 4.2 10.8 - - + -
198A TYR 2.9 26.7 + - - +
201A ASP* 3.6 10.9 - - - +
202A SER* 2.6 36.0 + - - -
205A PHE* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 4.4 3.0 + - - +
186A ALA* 3.5 28.8 + - - +
187A MET 3.1 1.4 + - - -
188A GLN* 1.3 79.5 - - - +
190A TYR* 1.3 82.1 + - + +
192A SER 4.8 0.3 - - - +
194A GLY 3.8 9.8 - - - +
195A SER* 5.3 0.6 - - - -
196A GLY* 3.6 21.7 + - - +
197A THR* 4.2 16.2 + - - +
324A ARG* 2.7 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA* 3.5 24.0 - - + -
187A MET 3.1 5.3 + - - +
189A LYS* 1.3 95.8 - - + +
191A PHE* 1.3 72.5 + - + +
192A SER 3.8 0.9 - - - -
314A VAL* 3.8 24.7 - - + -
315A GLN* 3.4 37.4 + - + +
318A ALA* 3.5 22.0 - - + -
319A ASP* 4.7 9.1 + - - -
323A PHE 4.1 10.8 - - - +
324A ARG* 3.3 28.4 - - - +
325A GLY 2.7 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A MET* 3.1 40.6 + - + -
188A GLN 3.2 2.2 + - - -
190A TYR* 1.3 98.0 - + + +
192A SER* 1.3 59.4 + - - +
205A PHE* 3.6 22.9 - + + -
314A VAL* 4.4 5.6 - - + -
318A ALA* 5.1 0.2 - - + -
323A PHE* 3.4 37.2 - + + -
325A GLY 3.1 11.9 - - - -
326A HIS* 3.3 6.8 - - - -
328A GLY* 2.9 31.5 + - - +
331A ASP* 3.5 17.0 - - + -
332A PHE* 3.9 23.1 - + + -
335A MET* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLN* 2.9 21.9 + - - +
189A LYS 4.8 0.3 - - - +
191A PHE* 1.3 79.0 + - - +
193A ALA* 1.3 57.8 + - - +
194A GLY* 2.7 26.9 - - - +
196A GLY 4.5 6.5 - - - -
201A ASP* 3.5 32.3 - - - +
205A PHE* 3.4 24.3 - - - -
325A GLY 3.3 11.5 - - - +
326A HIS* 3.7 1.8 - - - +
61D SER* 4.6 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