Contacts of the helix formed by residues 176 - 190 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B CYS 2.8 15.1 + - - +
174B TYR 3.5 0.8 + - - -
175B VAL* 1.3 76.8 - - - +
177B GLY* 1.3 63.4 + - - +
178B LEU 3.2 1.8 - - - -
179B VAL* 3.0 18.6 + - - +
180B GLY 3.2 9.9 + - - -
208B GLY* 3.4 31.9 - - - +
212B GLN* 3.7 19.3 - - + +
992B IN0 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B CYS 2.8 12.3 + - - -
173B HIS* 3.0 4.4 + - - -
176B ALA* 1.3 75.7 - - - +
178B LEU* 1.3 60.9 + - - +
180B GLY* 3.2 3.6 + - - -
181B ILE* 3.1 27.6 + - - +
205B ASN* 3.2 43.0 - - - -
208B GLY* 4.2 1.3 - - - -
209B LEU* 4.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.6 22.7 - - + +
149B ARG* 3.3 44.9 - - + +
150B MET* 3.6 37.0 - - + +
173B HIS* 2.7 39.9 + - + +
174B TYR* 3.7 29.4 - - + +
176B ALA 3.2 0.4 - - - -
177B GLY* 1.3 70.2 - - - +
179B VAL* 1.3 60.7 + - - +
181B ILE* 3.3 6.7 + - + -
182B GLY* 2.8 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.8 8.0 - - + -
76B LEU* 3.9 21.3 - - + -
150B MET* 3.8 15.3 - - + -
175B VAL 3.7 22.9 - - - +
176B ALA 3.0 7.7 + - - +
178B LEU* 1.3 75.3 - - - +
180B GLY* 1.3 60.3 + - - +
182B GLY 3.4 0.2 + - - -
183B LEU* 2.9 39.6 + - + +
992B IN0 3.7 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA 3.2 8.5 + - - -
177B GLY 3.2 3.9 + - - -
179B VAL* 1.3 78.8 - - - +
181B ILE* 1.3 52.0 + - - +
183B LEU* 3.3 3.3 + - - +
184B SER* 2.7 40.1 + - - -
204B ALA* 3.7 11.2 - - - -
276B TYR* 4.5 0.7 + - - -
992B IN0 3.1 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.2 13.9 - - + -
149B ARG* 4.7 10.3 - - - +
173B HIS* 4.0 24.9 - - + -
177B GLY 3.1 14.8 + - - +
178B LEU* 3.6 14.4 - - + +
180B GLY* 1.3 75.4 - - - +
182B GLY* 1.3 56.5 + - - +
184B SER* 3.3 3.4 + - - -
185B ARG* 2.9 40.9 + - + +
198B GLY 5.5 0.7 - - - +
201B THR* 3.8 51.4 - - + +
204B ALA* 3.8 10.7 - - + +
205B ASN* 4.2 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.9 11.4 - - - -
142B VAL* 3.3 10.8 - - - +
146B ILE* 3.6 22.0 - - - -
178B LEU 2.8 20.3 + - - -
179B VAL 3.8 0.7 - - - -
181B ILE* 1.3 71.5 - - - +
183B LEU* 1.3 64.0 + - - +
185B ARG* 3.1 2.5 + - - -
186B LEU* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.9 21.8 - - + -
72B PHE* 3.7 23.2 - - + -
179B VAL* 2.9 32.7 + - + +
180B GLY 3.7 3.6 - - - +
182B GLY* 1.3 73.5 - - - +
184B SER* 1.3 58.0 + - - +
186B LEU* 3.1 7.1 + - + +
187B PHE* 2.9 47.8 + - + -
288B PHE* 3.9 22.4 - - + -
992B IN0 3.7 48.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLY 2.7 24.7 + - - -
181B ILE* 3.5 5.6 - - - -
183B LEU* 1.3 77.4 - - - +
185B ARG* 1.3 59.7 + - - +
187B PHE* 3.4 12.4 + - - +
188B SER* 3.1 26.9 + - - -
197B VAL* 3.4 23.0 - - - +
198B GLY* 3.5 6.8 + - - -
204B ALA* 3.2 8.8 - - - +
276B TYR* 2.8 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 5.1 5.1 + - - +
142B VAL* 3.3 56.4 + - + +
145B ASP* 2.8 33.8 + - - +
146B ILE* 3.7 12.5 - - - +
149B ARG* 5.9 0.4 - - - +
181B ILE* 2.9 31.7 + - + +
182B GLY 3.6 6.5 - - - +
184B SER* 1.3 73.8 - - - +
186B LEU* 1.3 61.4 + - - +
188B SER* 3.6 2.8 + - - +
189B ALA* 2.9 30.9 + - - +
198B GLY* 4.1 22.2 - - - +
201B THR* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 3.6 15.7 - - + +
68B ALA* 4.5 8.1 - - + +
69B VAL* 4.2 20.6 - - + -
72B PHE* 3.9 34.1 - - + -
139B TYR* 3.6 36.3 - - + +
142B VAL* 3.8 23.3 - - + -
143B ILE* 4.3 5.8 - - + -
182B GLY 2.9 14.8 + - - +
183B LEU* 3.1 9.8 + - - +
185B ARG* 1.3 76.0 - - - +
187B PHE* 1.3 55.0 + - - +
189B ALA* 3.2 4.2 + - - +
190B SER* 2.8 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.9 3.4 - - + -
65B MET* 3.4 23.1 - - + -
69B VAL* 4.8 1.8 - - + -
183B LEU* 2.9 35.0 + - + -
184B SER* 3.6 6.5 - - - +
185B ARG 3.4 0.2 - - - -
186B LEU* 1.3 76.3 - - - +
188B SER* 1.3 60.6 + - - +
190B SER* 2.9 20.9 + - - -
191B GLU 3.2 5.9 + - - -
192B PHE* 4.2 0.6 - - - -
193B GLU* 3.4 30.4 + - + -
197B VAL* 4.3 7.0 - - + -
276B TYR* 3.4 26.7 - - - -
280B LEU* 4.9 0.9 - - + -
285B VAL* 4.0 29.2 - - + -
288B PHE* 3.8 35.0 - + - -
289B CYS* 3.7 15.5 - - - -
992B IN0 5.8 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B SER 3.1 8.6 + - - -
185B ARG* 4.0 2.7 - - - -
187B PHE* 1.3 75.1 - - - +
189B ALA* 1.3 61.5 + - - +
191B GLU* 2.8 26.3 + - - +
193B GLU 3.8 9.8 - - - +
194B ASP 3.0 16.4 + - - -
195B PRO* 3.5 14.1 + - - +
197B VAL* 3.8 1.4 - - - +
198B GLY* 2.9 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 2.8 44.7 + - + +
139B TYR* 4.0 14.8 - - + -
142B VAL* 5.0 7.2 - - + -
185B ARG 2.9 20.4 + - - +
186B LEU* 3.6 5.4 - - - +
188B SER* 1.3 76.7 - - - +
190B SER* 1.3 55.2 + - - +
191B GLU* 3.4 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 5.1 1.3 - - - -
65B MET* 3.3 31.7 - - - -
138B LYS* 4.1 4.1 + - - +
139B TYR* 3.2 24.7 + - - -
186B LEU 2.8 5.8 + - - -
187B PHE* 2.9 16.1 + - - -
189B ALA* 1.3 73.5 - - - +
191B GLU* 1.3 67.8 + - - +
192B PHE* 3.1 27.9 + - - +
----------------------------------------------------------
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