Contacts of the helix formed by residues 181 - 191 (chain A) in PDB entry 4OHN
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 THR 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 4.5 6.1 - - - +
48A THR* 3.7 31.8 - - + +
151A GLN* 3.9 6.7 - - - +
179A TYR* 3.5 12.6 - - - +
180A GLN* 1.3 101.2 - - + +
182A PHE* 1.3 63.8 + - - +
183A ASN* 3.5 6.2 + - - +
184A GLU* 3.3 23.9 + - - +
185A ALA 3.4 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 5.5 0.7 - - - -
48A THR* 4.5 2.2 + - - -
49A PHE* 3.9 22.2 - + - -
127A GLN* 5.5 0.9 - - - -
151A GLN* 3.3 49.5 - - + +
154A SER* 4.4 7.9 - - - -
181A THR* 1.3 71.5 - - - +
183A ASN* 1.3 60.9 + - - +
185A ALA* 3.1 4.0 + - + +
186A LEU* 2.8 33.3 + - - +
197A LEU* 4.3 12.3 - - + -
198A LEU 3.3 23.3 - - - -
199A ILE* 3.6 34.1 - - + -
200A ASP* 3.5 25.4 - - - -
203A TYR* 3.7 22.7 - + + -
301A HIS* 4.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.0 39.1 + - + +
50A VAL* 6.0 1.8 - - - +
181A THR* 3.2 6.2 - - - +
182A PHE* 1.3 75.2 - - - +
184A GLU* 1.3 61.5 + - - +
186A LEU* 3.3 7.2 + - - +
187A ILE* 3.1 28.1 + - + +
203A TYR* 2.7 26.5 + - - -
207A TYR* 4.5 15.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 3.5 29.2 - - + +
180A GLN* 4.4 9.9 + - - +
181A THR* 3.3 16.9 + - - +
182A PHE 3.3 0.4 - - - -
183A ASN* 1.3 77.7 - - - +
185A ALA* 1.3 66.4 + - - +
187A ILE* 3.2 10.0 + - + +
188A ASP* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA 5.2 0.7 - - - +
179A TYR* 3.6 36.7 - - + -
181A THR 3.4 7.5 + - - +
182A PHE* 3.1 12.7 + - + +
184A GLU* 1.3 79.0 - - - +
186A LEU* 1.3 56.5 + - - +
188A ASP* 3.2 3.8 + - - +
189A LEU* 2.9 24.4 + - - +
194A ILE* 3.6 8.2 - - + +
197A LEU* 3.6 28.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
130A VAL* 4.8 9.6 - - + -
182A PHE 2.8 18.1 + - - +
183A ASN 3.7 4.7 - - - +
185A ALA* 1.3 74.3 - - - +
187A ILE* 1.3 60.0 + - - +
189A LEU* 3.3 16.5 + - + +
190A LYS* 2.9 29.3 + - - +
197A LEU* 3.6 19.3 - - + -
199A ILE* 4.2 9.4 - - + -
203A TYR* 3.5 33.0 - - + +
204A ALA* 6.1 1.6 - - + -
207A TYR* 3.9 29.4 - - + +
208A LEU* 5.2 3.6 - - + -
302A ACT 3.6 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 3.1 15.8 + - + +
184A GLU* 3.2 10.9 + - + +
186A LEU* 1.3 76.5 - - - +
188A ASP* 1.3 63.3 + - - +
190A LYS* 3.3 23.0 + - + +
191A ASN* 2.9 43.4 + - - +
193A ARG* 4.1 10.8 - - - +
207A TYR* 4.8 11.2 - - - +
302A ACT 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 2.7 42.4 + - + +
184A GLU* 3.0 18.1 + - - +
185A ALA 3.2 7.6 + - - +
187A ILE* 1.3 79.4 - - - +
189A LEU* 1.3 59.7 + - - +
191A ASN 3.2 2.1 + - - -
192A ASP 3.2 3.6 + - - -
193A ARG* 2.9 70.3 + - + +
194A ILE* 4.0 5.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
130A VAL* 3.7 34.8 - - + +
131A THR* 4.4 3.1 - - - -
132A LYS* 3.5 15.7 - - + +
185A ALA 2.9 13.8 + - - +
186A LEU* 3.3 20.6 + - + +
188A ASP* 1.3 75.5 - - - +
190A LYS* 1.3 62.1 + - - +
192A ASP* 3.1 12.8 + - - +
194A ILE* 3.6 20.2 - - + +
195A ASP* 3.5 34.5 - - - +
196A GLY* 3.7 6.1 - - - +
197A LEU* 4.4 5.2 - - + -
217A TYR* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 2.8 24.0 + - - +
186A LEU 2.9 17.2 + - - +
187A ILE* 3.5 23.6 - - + +
188A ASP 3.3 0.2 - - - -
189A LEU* 1.3 76.2 - - - +
191A ASN* 1.3 64.9 + - - +
192A ASP 3.4 0.4 - - - -
217A TYR* 3.5 17.4 + - - +
302A ACT 3.5 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE* 2.9 40.7 + - - +
188A ASP 3.2 1.3 + - - +
189A LEU 3.1 0.4 - - - -
190A LYS* 1.3 88.7 - - - +
192A ASP* 1.3 67.8 + - - +
193A ARG* 3.1 38.1 + - - +
----------------------------------------------------------
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