Contacts of the helix formed by residues 181 - 196 (chain A) in PDB entry 1F9E
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 GLY 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG 3.0 0.4 + - - -
180A ASN* 1.3 74.1 - - - +
182A THR* 1.3 66.9 + - - +
183A HIS* 3.0 17.6 + - - -
184A LEU* 2.7 30.0 + - - +
185A ASP 3.6 1.7 + - - -
341B ARG* 4.8 4.0 - - - -
342B ASN 4.5 3.6 - - - -
343B PRO* 3.9 18.1 + - - -
346B GLY* 4.1 7.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
169A ASN* 3.3 34.1 - - - +
170A ASN 3.6 5.0 + - - +
171A HIS* 4.1 4.7 - - - +
179A ARG* 2.5 58.3 + - - +
180A ASN 3.6 0.2 - - - -
181A GLY* 1.3 72.5 - - - +
183A HIS* 1.3 58.6 + - - +
185A ASP* 2.5 37.6 + - - +
186A ALA 2.8 11.3 + - - -
235A LEU* 3.4 20.2 - - + -
341B ARG* 4.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 3.9 11.0 - - - +
171A HIS* 3.3 45.2 + + + -
180A ASN* 4.1 1.8 - - - -
181A GLY* 3.2 29.6 + - - -
182A THR* 1.3 74.6 - - - +
184A LEU* 1.3 65.5 + - + +
186A ALA* 3.3 3.4 + - - +
187A GLY* 2.8 28.2 + - - -
204A HIS* 6.5 0.2 - - - -
175G LYS* 4.4 19.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
181A GLY* 2.7 19.7 + - - +
183A HIS* 1.3 83.9 - - + +
185A ASP* 1.3 54.6 + - - +
187A GLY* 3.5 1.5 + - - +
188A ALA* 2.9 30.5 + - - +
343B PRO 3.8 12.1 - - - +
344B ALA* 3.5 33.2 - - - +
345B GLU* 3.8 10.5 - - - +
346B GLY 3.9 11.0 - - - +
351B GLN* 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 4.6 1.7 + - - -
181A GLY 3.6 0.4 + - - -
182A THR* 2.5 23.1 + - - +
184A LEU* 1.3 69.9 - - - +
186A ALA* 1.3 58.2 + - - +
188A ALA* 3.0 2.8 + - - +
189A LEU* 2.6 39.5 + - - +
235A LEU* 3.7 15.7 - - + +
283A GLN* 4.3 2.8 - - - +
346B GLY* 3.6 2.6 - - - -
347B THR* 3.0 55.2 + - - +
350B ILE* 3.3 19.8 - - + +
351B GLN* 3.2 17.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
167A ILE* 4.1 11.1 - - + +
169A ASN* 3.1 30.1 - - + +
182A THR 2.8 5.3 + - - -
183A HIS* 3.5 8.1 - - - +
185A ASP* 1.3 76.7 - - - +
187A GLY* 1.3 52.6 + - - +
189A LEU* 3.3 6.3 + - - +
190A THR* 2.5 40.4 + - - +
202A PRO* 6.5 1.1 - - + -
204A HIS* 5.1 7.6 - - + -
235A LEU* 3.8 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A HIS 2.8 19.8 + - - -
184A LEU* 3.8 1.8 - - - -
186A ALA* 1.3 73.0 - - - +
188A ALA* 1.3 62.8 + - - +
190A THR* 3.1 7.6 + - - -
191A THR* 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU 2.9 18.8 + - - +
185A ASP* 3.5 3.4 - - - +
187A GLY* 1.3 73.3 - - - +
189A LEU* 1.3 54.0 + - - +
191A THR* 3.6 6.1 - - - -
192A THR* 2.6 38.6 + - - -
351B GLN* 3.9 21.1 - - - +
354B CYS* 3.6 18.6 - - + -
358B ARG* 4.8 10.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
167A ILE* 3.8 16.4 - - + -
185A ASP 2.6 23.0 + - - +
186A ALA 3.5 3.4 - - - +
188A ALA* 1.3 71.1 - - - +
190A THR* 1.3 59.3 + - - +
192A THR* 3.1 2.3 + - - -
193A PHE* 2.8 61.9 + - + +
233A CYS* 4.0 23.6 - - + -
235A LEU* 4.0 29.4 - - + -
350B ILE* 3.7 26.2 - - + -
353B LEU* 4.9 7.0 - - + -
354B CYS* 3.8 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.0 8.5 - - - +
186A ALA* 2.5 23.8 + - - +
187A GLY* 3.3 8.1 - - - -
189A LEU* 1.3 76.8 - - - +
191A THR* 1.3 53.4 + - - +
194A GLU* 2.7 54.3 + - - +
200A ILE* 3.6 34.2 - - + +
202A PRO* 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLY 2.9 15.2 + - - -
188A ALA* 3.6 8.6 - - - -
190A THR* 1.3 76.3 - - - +
192A THR* 1.3 58.9 + - - +
194A GLU* 3.5 8.6 - - - +
195A GLU* 2.9 59.9 + - + +
358B ARG* 4.3 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA 2.6 25.6 + - - -
189A LEU* 3.6 2.9 - - - -
191A THR* 1.3 74.5 - - - +
193A PHE* 1.3 63.9 + - + +
195A GLU* 3.2 13.6 + - - +
196A LEU* 3.1 27.0 + - + +
354B CYS* 3.4 23.0 - - - +
357B LEU* 3.8 38.4 - - + -
358B ARG* 3.8 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A CYS* 4.0 15.5 - - - -
189A LEU* 2.8 47.0 + - + +
192A THR* 1.3 74.2 - - - +
194A GLU* 1.3 65.9 + - - +
196A LEU* 3.1 25.2 + - + +
197A HIS 3.2 0.3 + - - -
198A PHE* 2.9 36.6 + + + +
200A ILE* 3.8 15.0 - - + -
231A ILE* 3.4 26.9 - - + -
233A CYS* 4.6 5.8 - - - -
281A PHE* 3.8 24.9 - + - -
353B LEU* 5.4 0.7 - - + -
357B LEU* 3.7 25.6 - - + -
400B PHE* 4.1 16.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A THR* 2.7 36.6 + - - +
191A THR* 3.5 8.4 - - - +
193A PHE* 1.3 77.3 - - - +
195A GLU* 1.3 61.2 + - + +
197A HIS* 2.8 25.1 + - - -
198A PHE 3.9 12.0 + - - +
200A ILE* 3.8 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 2.9 46.2 + - + +
192A THR 3.2 6.7 + - - +
194A GLU* 1.3 78.1 - - + +
196A LEU* 1.3 57.3 + - + +
197A HIS* 3.1 19.0 + - - -
358B ARG* 3.8 31.2 + - - +
402B SER* 4.2 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 3.6 14.9 + - - -
192A THR* 3.1 19.2 + - + +
193A PHE* 3.1 28.9 + - + +
194A GLU 3.0 0.8 - - - -
195A GLU* 1.3 80.6 - - + +
197A HIS* 1.3 74.7 + - - +
198A PHE* 3.6 13.5 - - + -
357B LEU* 4.6 5.6 - - + +
361B CYS* 4.0 20.4 - - + -
362B PRO* 5.8 0.4 - - + -
400B PHE* 3.6 52.7 - - + +
401B PRO 4.2 8.3 - - - +
402B SER* 4.5 8.7 - - - -
----------------------------------------------------------
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