Contacts of the helix formed by residues 179 - 196 (chain A) in PDB entry 1E0W
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 TRP 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASN* 3.8 42.4 - - + +
176A ASN* 3.2 45.5 + - + +
178A THR* 1.3 86.4 - - - +
180A ALA* 1.3 65.9 + - - +
181A LYS* 4.3 7.9 - - + +
182A THR* 3.2 12.0 + - - +
183A GLN* 3.1 22.6 + - - +
211A GLY 4.0 17.3 - - - -
212A SER* 4.0 19.1 - - - -
213A PRO* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY 4.0 7.3 + - - +
134A SER* 3.5 35.0 - - - +
135A SER 4.8 0.4 - - - -
136A GLY* 4.2 9.3 - - - +
178A THR 3.8 1.4 + - - -
179A TRP* 1.3 72.2 - - - +
181A LYS* 1.3 63.0 + - - +
183A GLN* 3.3 8.0 + - - +
184A ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.5 36.8 + - + -
131A ALA 3.6 16.4 - - - +
132A ASP* 2.8 31.9 + - - +
133A GLY 4.5 8.8 + - - +
136A GLY* 5.0 3.6 - - - -
171A ASP* 3.4 18.4 + - - -
172A TYR* 2.9 42.7 + - - +
173A ASN* 3.7 16.4 - - + +
174A VAL* 3.9 6.6 - - + +
179A TRP* 3.2 6.5 - - + +
180A ALA* 1.3 77.8 - - - +
182A THR* 1.3 62.7 + - - +
184A ALA* 3.3 7.8 + - - +
185A MET* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 3.3 42.5 - - + +
175A GLU 4.0 0.2 + - - -
176A ASN 2.8 28.4 + - - +
177A TRP* 4.2 15.0 - - + +
179A TRP* 3.2 13.0 + - - +
181A LYS* 1.3 78.4 - - - +
183A GLN* 1.3 58.0 + - - +
185A MET* 3.3 4.4 + - - +
186A TYR* 2.9 26.9 + - - +
221A THR* 4.1 17.3 - - + -
225A PHE* 3.9 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TRP* 2.9 60.0 + - - +
178A THR 5.1 3.1 - - - +
179A TRP 3.1 14.3 + - - +
180A ALA* 3.8 8.7 - - - +
182A THR* 1.3 73.9 - - - +
184A ALA* 1.3 62.8 + - - +
186A TYR* 3.4 17.8 + - - +
187A ASN* 3.0 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.8 21.0 - - + -
136A GLY* 3.5 29.8 - - - +
180A ALA 3.0 13.6 + - - +
181A LYS* 3.3 9.1 + - - +
183A GLN* 1.3 75.5 - - - +
185A MET* 1.3 63.1 + - - +
187A ASN* 3.5 5.8 + - - +
188A MET* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.9 15.8 - - + -
169A TYR* 3.6 38.6 - - + -
171A ASP* 4.5 1.8 - - - -
174A VAL* 3.7 31.6 - - + +
181A LYS 3.1 12.9 + - - +
182A THR 3.3 5.8 + - - +
184A ALA* 1.3 77.7 - - - +
186A TYR* 1.3 61.8 + - - +
188A MET* 3.3 4.5 + - + +
189A VAL* 3.1 32.7 + - + +
202A VAL* 3.6 22.4 - - + -
203A GLY 5.2 1.1 - - - +
204A PHE* 3.7 17.5 - - + -
225A PHE* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TRP* 3.9 31.0 - + + -
182A THR 2.9 16.7 + - - +
183A GLN* 3.6 21.1 - - - +
184A ALA 3.4 0.2 - - - -
185A MET* 1.3 75.8 - - - +
187A ASN* 1.3 72.6 + - - +
189A VAL* 3.3 3.1 + - - +
190A ARG* 3.0 40.4 + - - +
224A ASN* 3.8 19.6 + - + +
225A PHE* 3.5 22.3 - + + -
228A LEU* 3.7 37.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 3.0 35.2 + - - +
184A ALA* 3.9 6.0 - - - +
185A MET 3.4 0.2 - - - -
186A TYR* 1.3 81.8 - - - +
188A MET* 1.3 61.6 + - - +
190A ARG* 3.1 34.9 + - - +
191A ASP* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 4.0 25.1 - - + -
138A ARG* 4.7 8.7 - - - +
151A ILE* 4.0 23.6 - - + -
169A TYR* 3.9 37.5 - - + -
184A ALA 3.1 13.6 + - - +
185A MET* 3.6 7.4 - - + +
186A TYR 3.3 0.2 - - - -
187A ASN* 1.3 76.6 - - - +
189A VAL* 1.4 72.1 + - + +
191A ASP* 3.3 6.2 + - - +
192A PHE* 2.9 64.1 + - + -
199A ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 5.7 0.4 - - + -
185A MET* 3.1 19.0 + - + +
186A TYR 4.0 3.1 - - - +
188A MET* 1.4 83.8 - - + +
190A ARG* 1.3 62.6 + - - +
192A PHE* 3.3 7.5 + - - +
193A LYS* 3.0 26.7 + - + +
199A ILE* 4.3 16.6 - - + -
202A VAL* 4.0 21.5 - - + -
225A PHE* 4.3 7.4 - - + -
228A LEU* 3.8 22.4 - - + -
230A VAL* 4.1 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 3.0 29.9 + - + +
187A ASN* 3.1 31.1 + - - +
188A MET 3.3 0.2 - - - -
189A VAL* 1.3 76.8 - - - +
191A ASP* 1.3 61.3 + - - +
193A LYS* 3.4 6.1 + - - +
194A GLN* 3.1 47.9 + - + +
228A LEU* 4.0 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASN 3.1 18.5 + - - +
188A MET* 3.6 6.3 - - - +
190A ARG* 1.3 74.7 - - - +
192A PHE* 1.3 68.9 + - - +
194A GLN* 3.2 16.8 + - - +
195A ARG* 2.9 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 5.6 4.0 - - - -
151A ILE* 3.8 29.8 - - + -
152A GLU* 4.0 19.3 - - + -
155A PHE* 4.4 10.1 - + - -
188A MET* 2.9 47.6 + - + +
189A VAL* 3.3 5.1 + - - +
191A ASP* 1.3 80.0 - - - +
193A LYS* 1.3 62.7 + - - +
195A ARG* 3.3 22.6 + - - -
196A GLY 3.0 5.0 + - - -
197A VAL* 3.0 53.9 + - + -
199A ILE* 4.1 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 3.0 25.2 + - + +
190A ARG* 3.8 5.8 - - - +
192A PHE* 1.3 76.5 - - - +
194A GLN* 1.3 65.0 + - + +
195A ARG 3.4 0.2 + - - -
196A GLY* 3.5 8.8 + - - -
197A VAL 5.1 2.9 + - - +
199A ILE* 2.8 37.0 + - + +
200A ASP* 4.9 1.6 + - - +
228A LEU* 3.6 22.2 - - + +
229A GLY* 3.1 27.4 + - - -
230A VAL* 3.6 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 3.1 43.7 + - + +
191A ASP* 3.2 16.6 + - - +
193A LYS* 1.3 77.6 - - + +
195A ARG* 1.3 63.6 + - + +
196A GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLU* 3.0 36.0 + - - +
156A ARG* 3.7 12.1 + - - +
191A ASP* 2.9 49.6 + - - +
192A PHE* 3.9 20.4 - - - +
194A GLN* 1.3 81.1 - - + +
196A GLY* 1.3 61.3 + - - +
197A VAL* 3.4 7.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.5 15.2 + - - -
192A PHE 3.0 4.7 + - - -
193A LYS* 3.5 7.1 + - - -
194A GLN 3.4 4.0 + - - -
195A ARG* 1.3 78.2 - - - +
197A VAL* 1.3 62.7 + - - +
198A PRO* 3.5 4.7 - - - +
----------------------------------------------------------
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