Contacts of the helix formed by residues 181 - 196 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ARG 3.0 0.6 + - - -
180I ASN* 1.3 74.4 - - - +
182I THR* 1.3 55.7 + - - +
183I HIS* 2.9 18.3 + - - -
184I LEU* 2.6 41.0 + - - +
185I ASP 3.5 1.4 + - - -
341J ARG* 4.8 2.9 - - - -
342J ASN 4.5 3.8 - - - -
343J PRO* 3.9 17.2 + - - -
346J GLY* 4.2 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I ASN* 3.2 33.7 - - - +
170I ASN 3.5 5.0 + - - +
171I HIS* 4.1 4.3 - - - +
179I ARG* 2.6 58.2 + - - +
180I ASN 3.6 0.2 - - - -
181I GLY* 1.3 72.7 - - - +
183I HIS* 1.3 59.2 + - - +
185I ASP* 2.6 36.0 + - - +
186I ALA 2.8 11.3 + - - -
235I LEU* 3.4 22.2 - - + -
341J ARG* 4.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 183 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I ASN* 4.2 10.5 - - - +
171I HIS* 3.3 45.4 + + + -
179I ARG 4.2 0.2 - - - -
180I ASN* 4.1 1.8 - - + -
181I GLY* 3.2 30.0 + - - -
182I THR* 1.3 74.8 - - - +
184I LEU* 1.3 64.9 + - + +
186I ALA* 3.3 3.4 + - - +
187I GLY* 2.8 28.1 + - - -
204I HIS* 6.6 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I GLY* 2.6 21.7 + - - +
183I HIS* 1.3 83.6 - - + +
185I ASP* 1.3 56.1 + - - +
187I GLY* 3.4 1.4 + - - +
188I ALA* 2.9 30.8 + - - +
343J PRO 3.8 12.1 - - - +
344J ALA 3.6 32.3 - - - +
345J GLU* 3.8 13.0 - - - +
346J GLY 3.9 10.3 - - - +
351J GLN* 3.7 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ARG* 4.6 1.4 + - - -
182I THR* 2.6 22.2 + - - +
184I LEU* 1.3 70.6 - - - +
186I ALA* 1.3 56.5 + - - +
188I ALA* 3.0 2.8 + - - +
189I LEU* 2.6 41.2 + - - +
235I LEU* 3.7 15.3 - - + +
283I GLN* 4.3 2.4 - - - +
346J GLY* 3.6 2.0 - - - -
347J THR* 2.9 56.1 + - - +
350J ILE* 3.3 21.9 - - + +
351J GLN* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ILE* 4.1 10.9 - - + +
169I ASN* 3.1 30.3 - - + +
182I THR 2.8 4.6 + - - -
183I HIS* 3.5 8.1 - - - +
185I ASP* 1.3 76.2 - - - +
187I GLY* 1.3 59.4 + - - +
189I LEU* 3.5 6.6 - - - +
190I THR* 2.5 37.1 + - - +
202I PRO* 6.5 0.9 - - + -
204I HIS* 5.1 8.1 - - + -
235I LEU* 3.8 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I HIS 2.8 19.6 + - - -
184I LEU* 3.8 1.6 - - - -
186I ALA* 1.3 75.5 - - - +
188I ALA* 1.3 62.5 + - - +
190I THR* 3.1 6.5 + - - -
191I THR* 2.9 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I LEU 2.9 20.7 + - - +
185I ASP* 3.5 3.4 - - - +
187I GLY* 1.3 70.9 - - - +
189I LEU* 1.3 55.8 + - - +
191I THR* 3.6 4.8 - - - -
192I THR* 2.6 39.5 + - - -
350J ILE* 5.2 0.2 - - + -
351J GLN* 3.9 21.3 - - - +
354J CYS* 3.6 17.9 - - + -
358J ARG* 4.8 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ILE* 3.8 16.4 - - + -
185I ASP 2.6 23.6 + - - +
186I ALA 3.5 4.0 - - - +
188I ALA* 1.3 72.2 - - - +
190I THR* 1.3 54.4 - - - +
192I THR 3.2 1.2 + - - -
193I PHE* 2.8 66.0 + - + +
200I ILE* 5.4 0.2 - - - -
233I CYS* 4.0 23.1 - - + -
235I LEU* 4.0 29.8 - - + -
350J ILE* 3.8 25.4 - - + -
353J LEU* 4.9 7.6 - - + -
354J CYS* 3.9 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ILE* 4.0 8.6 - - - +
186I ALA* 2.5 27.0 + - - +
187I GLY* 3.3 8.7 - - - -
189I LEU* 1.3 71.9 - - - +
191I THR* 1.3 52.3 + - - +
194I GLU* 2.8 55.8 + - - +
200I ILE* 3.6 35.5 - - + +
202I PRO* 6.0 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I GLY 2.9 15.5 + - - -
188I ALA* 3.6 9.5 - - - -
190I THR* 1.3 76.0 - - - +
192I THR* 1.3 59.4 + - - +
194I GLU* 3.5 9.1 - - - +
195I GLU* 2.9 59.0 + - + +
358J ARG* 4.3 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I ALA 2.6 22.0 + - - -
189I LEU 3.6 2.7 - - - -
191I THR* 1.3 77.7 - - - +
193I PHE* 1.3 66.1 + - + +
195I GLU* 3.2 12.8 + - - +
196I LEU* 3.1 30.9 + - + +
354J CYS* 3.4 23.0 - - - +
357J LEU* 3.8 38.1 - - + -
358J ARG* 3.8 24.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I CYS* 4.0 15.7 - - - -
189I LEU* 2.8 50.8 + - + +
192I THR* 1.3 75.8 - - - +
194I GLU* 1.3 66.5 + - - +
196I LEU* 3.1 25.8 + - + +
197I HIS 3.2 0.2 + - - -
198I PHE* 2.9 34.3 + + + +
200I ILE* 3.8 16.6 - - + -
231I ILE* 3.4 26.2 - - + -
233I CYS* 4.6 4.5 - - - -
281I PHE* 3.8 24.9 - + - -
353J LEU* 5.4 0.4 - - + -
354J CYS* 5.6 0.2 - - - -
357J LEU* 3.7 24.7 - - + -
400J PHE* 4.1 16.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I THR* 2.8 37.6 + - - +
191I THR* 3.5 8.7 - - - +
193I PHE* 1.3 78.1 - - - +
195I GLU* 1.3 54.7 + - + +
197I HIS* 2.7 29.8 + - - -
198I PHE 3.8 12.7 - - - +
200I ILE* 3.8 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I THR* 2.9 48.0 + - + +
192I THR* 3.4 7.4 - - - +
194I GLU* 1.3 77.4 - - + +
196I LEU* 1.3 58.3 + - + +
197I HIS* 3.1 19.2 + - - -
358J ARG* 3.8 31.4 + - + +
402J SER* 4.2 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I ARG* 3.6 12.0 + - - -
192I THR* 3.1 17.9 + - + +
193I PHE* 3.1 27.1 + - + +
194I GLU 3.0 1.4 - - - -
195I GLU* 1.3 79.8 - - + +
197I HIS* 1.3 76.1 + - - +
198I PHE* 3.6 15.7 - - + -
357J LEU* 4.6 4.9 - - + +
361J CYS* 4.0 21.1 - - + -
362J PRO* 5.8 0.9 - - + -
400J PHE* 3.5 53.2 - - + +
401J PRO 4.1 8.7 - - - +
402J SER* 4.5 9.2 - - - +
----------------------------------------------------------
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