Contacts of the helix formed by residues 176 - 190 (chain A) in PDB entry 1EZF
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 ALA 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A CYS 2.8 6.9 + - - +
173A HIS 3.7 0.2 + - - -
174A TYR 3.7 0.4 - - - -
175A VAL* 1.3 75.0 - - - +
177A GLY* 1.3 68.5 + - - +
178A LEU 3.3 1.3 - - - -
179A VAL* 3.1 11.8 + - - +
180A GLY 3.1 16.8 + - - -
208A GLY* 3.2 27.2 - - - +
212A GLN* 3.4 28.9 - - + +
991A IN0 3.4 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A CYS 2.9 10.5 + - - -
173A HIS* 3.3 4.9 - - - -
176A ALA* 1.3 76.3 - - - +
178A LEU* 1.3 56.0 + - - +
180A GLY* 2.8 19.2 + - - -
181A ILE* 2.9 20.1 + - - +
205A ASN* 3.3 40.5 - - - -
208A GLY* 4.0 1.2 - - - -
209A LEU* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.3 39.0 - - + +
149A ARG* 3.6 44.0 - - + +
150A MET* 3.8 9.9 - - - +
173A HIS* 2.7 44.9 + - + +
174A TYR* 3.6 30.1 - - + +
176A ALA 3.3 0.2 - - - -
177A GLY* 1.3 73.1 - - - +
179A VAL* 1.3 52.3 + - + +
181A ILE* 3.8 10.1 - - + -
182A GLY* 2.7 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.9 8.4 - - + -
76A LEU* 3.7 43.1 - - + -
146A ILE* 4.6 0.7 - - + -
150A MET* 4.5 4.3 - - + -
175A VAL 3.4 26.2 - - - +
176A ALA* 3.3 8.5 - - - +
177A GLY 3.1 1.0 - - - -
178A LEU* 1.3 74.2 - - - +
180A GLY* 1.3 61.3 + - - +
182A GLY* 3.7 0.3 - - - -
183A LEU* 2.9 33.8 + - + +
991A IN0 3.9 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA 3.1 6.3 + - - -
177A GLY 2.8 7.7 + - - -
179A VAL* 1.3 74.5 - - - +
181A ILE* 1.3 58.7 + - - +
183A LEU* 3.9 1.7 - - - +
184A SER* 2.9 34.7 + - - -
204A ALA* 3.6 14.1 - - - -
276A TYR* 4.8 1.2 + - - -
991A IN0 3.2 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 4.4 6.7 - - + -
173A HIS* 5.1 4.3 - - + -
177A GLY 2.9 18.8 + - - +
178A LEU* 3.5 22.2 - - + +
180A GLY* 1.3 77.7 - - - +
182A GLY* 1.3 61.1 - - - +
184A SER* 3.7 2.2 - - - -
185A ARG* 3.0 68.6 + - + +
198A GLY 5.4 0.4 - - - +
201A THR* 3.0 51.1 - - + +
204A ALA* 3.6 4.5 - - + -
205A ASN* 3.6 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.2 10.5 - - - -
142A VAL* 3.4 18.4 - - - +
146A ILE* 3.8 19.9 - - - +
178A LEU 2.7 19.9 + - - -
179A VAL 3.7 1.3 - - - -
181A ILE* 1.3 71.1 - - - +
183A LEU* 1.3 63.6 + - - +
185A ARG* 3.1 3.2 + - - -
186A LEU* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.9 18.6 - - + -
72A PHE* 3.8 24.7 - - + -
179A VAL* 2.9 21.7 + - + +
180A GLY* 3.9 2.9 - - - +
182A GLY* 1.3 72.1 - - - +
184A SER* 1.3 65.5 + - - +
186A LEU* 2.8 10.1 + - + +
187A PHE* 2.8 40.0 + - + -
276A TYR* 5.4 0.7 - - - +
288A PHE* 3.8 17.7 - - + -
991A IN0 3.6 66.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLY 2.9 20.7 + - - -
181A ILE* 3.7 5.6 - - - -
183A LEU* 1.3 74.0 - - - +
185A ARG* 1.3 60.4 + - - +
187A PHE* 3.3 13.5 + - - +
188A SER* 3.1 26.5 + - - -
197A VAL* 3.3 23.1 - - - +
198A GLY* 3.7 6.0 + - - -
204A ALA* 3.2 8.3 - - - +
276A TYR* 2.8 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 3.9 29.0 - - + +
145A ASP* 5.2 7.7 + - - -
146A ILE* 5.3 4.8 - - - +
149A ARG* 5.2 10.3 - - - +
181A ILE* 3.0 42.5 + - - +
182A GLY* 3.1 7.7 + - - +
184A SER* 1.3 72.8 - - - +
186A LEU* 1.3 61.2 + - - +
188A SER* 3.4 3.0 + - - -
189A ALA* 2.9 29.1 + - - +
198A GLY* 4.1 22.7 + - - +
201A THR* 3.8 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 4.9 3.3 - - + +
68A ALA* 4.4 24.0 - - + +
69A VAL* 4.6 11.9 - - + -
72A PHE* 4.0 28.9 - - + -
139A TYR* 3.6 47.1 - - + +
142A VAL* 3.9 18.4 - - + -
143A ILE* 4.4 6.7 - - + -
182A GLY 2.9 15.3 + - - +
183A LEU* 2.8 10.4 + - - +
185A ARG* 1.3 73.4 - - - +
187A PHE* 1.3 71.1 + - + +
189A ALA* 3.2 4.3 + - - +
190A SER* 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.1 1.8 - - + -
65A MET* 3.3 30.9 - - + +
69A VAL* 4.6 9.4 - - + -
183A LEU* 2.8 36.3 + - + -
184A SER* 3.4 8.3 - - - +
186A LEU* 1.3 79.8 - - + +
188A SER* 1.3 59.7 + - - +
190A SER* 2.7 19.2 + - - -
191A GLU 3.3 4.7 + - - -
193A GLU* 3.5 25.1 + - + -
197A VAL* 4.3 6.1 - - + -
276A TYR* 3.6 25.8 - - - -
280A LEU* 5.0 0.2 - - + -
285A VAL* 3.7 21.8 - - + -
288A PHE* 3.7 35.9 - + - -
289A CYS* 3.6 14.8 - - - -
991A IN0 5.7 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A SER 3.1 6.9 + - - -
185A ARG* 3.9 4.3 - - - -
186A LEU 3.3 0.2 - - - -
187A PHE* 1.3 77.1 - - - +
189A ALA* 1.3 58.3 + - - +
191A GLU* 3.0 24.8 + - - +
193A GLU 3.4 10.4 - - - +
194A ASP 2.8 23.4 + - - -
195A PRO* 3.6 13.4 + - - +
197A VAL* 3.8 1.9 - - - +
198A GLY* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS* 3.1 42.2 - - + +
139A TYR* 3.7 19.1 - - + -
142A VAL* 5.5 2.2 - - + -
185A ARG 2.9 18.6 + - - +
186A LEU* 3.2 5.6 + - + +
188A SER* 1.3 77.3 - - - +
190A SER* 1.3 61.7 + - - +
191A GLU* 4.2 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 5.1 1.1 - - - -
65A MET* 3.1 29.1 - - - +
138A LYS* 4.7 0.7 - - - +
139A TYR* 3.2 22.8 + - - -
186A LEU 3.1 10.0 + - - -
187A PHE 2.7 19.8 + - - -
189A ALA* 1.3 77.1 - - - +
191A GLU* 1.3 69.7 + - - +
192A PHE* 3.1 26.6 + - - -
----------------------------------------------------------
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