Contacts of the helix formed by residues 199 - 211 (chain A) in PDB entry 3OAX
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 ASN 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY 5.2 1.0 - - - +
175A TRP* 3.3 21.4 + - + +
194A PRO 5.0 0.2 - - - -
195A HIS 3.3 1.0 + - - -
196A GLU* 2.8 22.4 + - - +
197A GLU 4.7 1.2 - - - +
198A THR* 1.3 82.6 - - - +
200A ASN* 1.3 64.8 + - - +
201A GLU 3.3 2.9 - - - +
202A SER* 3.1 27.3 + - - +
203A PHE* 3.5 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.1 20.3 + - - +
177A ARG* 3.8 1.8 - - - +
190A ASP* 2.6 46.1 + - - +
193A THR 3.3 17.2 + - - +
194A PRO 3.6 6.8 + - - +
195A HIS* 3.1 24.9 + - - +
198A THR* 2.6 28.7 - - - +
199A ASN* 1.3 75.9 - - - +
201A GLU* 1.3 62.8 + - - +
203A PHE* 3.5 3.6 + - - +
204A VAL* 3.2 27.4 + - - +
276A PHE* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR 4.5 0.9 - - - +
194A PRO* 3.7 29.4 + - + +
199A ASN* 3.3 1.0 - - - +
200A ASN* 1.3 73.2 - - - +
202A SER* 1.3 66.7 + - - +
204A VAL* 3.1 12.6 + - - +
205A ILE* 3.2 23.0 + - + +
276A PHE* 3.7 21.3 - - + -
279A GLN* 2.8 12.6 + - - +
957A ZN 2.1 36.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TRP* 3.1 28.2 + - - -
199A ASN* 3.1 19.0 + - - +
201A GLU* 1.3 77.2 - - - +
203A PHE* 1.3 61.8 + - - +
205A ILE* 3.4 12.1 + - - +
206A TYR* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A CYS* 3.2 26.2 - - - -
170A PRO* 3.5 23.3 - - + -
171A PRO* 3.8 8.3 - - + -
175A TRP* 3.6 47.1 - + + +
176A SER* 3.5 26.7 - - - -
189A ILE* 3.6 29.6 - - + -
199A ASN 3.5 1.6 + - - +
200A ASN 3.8 3.8 - - - +
201A GLU 3.2 0.6 - - - -
202A SER* 1.3 82.1 + - - +
204A VAL* 1.3 54.4 + - - +
206A TYR* 3.1 18.4 + + - +
207A MET* 2.7 49.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 4.2 15.3 - - + -
190A ASP 3.6 20.6 - - - +
191A TYR* 4.3 6.3 - - + -
200A ASN 3.2 14.3 + - - +
201A GLU 3.1 7.7 + - - +
203A PHE* 1.3 79.8 - - + +
205A ILE* 1.3 58.2 + - - +
207A MET* 3.2 4.3 + - + +
208A PHE* 2.9 53.9 + - + -
276A PHE* 3.6 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 3.2 20.1 + - + +
202A SER* 3.8 9.2 - - - +
204A VAL* 1.3 77.0 - - - +
206A TYR* 1.3 57.3 + - - +
208A PHE* 3.5 4.6 + - - +
209A VAL* 3.0 48.0 + - + +
276A PHE* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA* 2.7 35.8 + - - +
175A TRP* 3.4 40.2 - + + -
202A SER 3.0 14.5 + - - +
203A PHE* 3.3 26.9 - + - +
205A ILE* 1.3 79.2 - - - +
207A MET* 1.3 58.0 + - - +
209A VAL* 4.9 1.6 - - - -
210A VAL* 2.9 57.6 + - + +
211A HIS* 2.9 26.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 5.8 0.2 - - - -
167A CYS* 3.9 21.3 - - - -
189A ILE* 3.7 28.3 - - + -
191A TYR* 3.9 19.5 - - + +
203A PHE* 2.7 32.0 + - + +
204A VAL* 3.2 4.5 + - + +
206A TYR* 1.3 75.1 - - - +
208A PHE* 1.3 89.1 + - + +
211A HIS* 2.9 43.8 + - + +
212A PHE* 4.0 0.5 - - - +
1296A RET 3.6 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 4.7 5.4 - + - -
204A VAL* 2.9 46.4 + - + +
205A ILE* 4.1 5.4 - - - +
207A MET* 1.3 94.8 - - + +
209A VAL* 1.3 61.0 - - + +
212A PHE* 3.3 29.5 - + + +
213A ILE* 3.0 36.9 + - + +
269A ALA* 3.9 17.0 - - + -
272A ALA* 4.0 9.9 - - + -
273A PHE* 3.9 52.5 - + + -
276A PHE* 5.3 0.4 - - + -
1296A RET 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.0 32.6 + - + +
206A TYR* 4.2 2.0 - - - +
208A PHE* 1.3 81.3 - - + +
210A VAL* 1.3 69.5 + - + +
211A HIS 3.6 0.3 + - - -
213A ILE* 3.6 16.6 + - + -
214A ILE* 3.0 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TRP* 3.3 18.2 - - + -
163A MET* 4.4 12.6 - - + -
206A TYR* 2.9 44.1 + - + +
209A VAL* 1.3 79.7 - - + +
211A HIS* 1.3 81.6 + - + +
214A ILE* 4.3 14.3 - - + +
215A PRO* 3.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 2.9 31.2 - - - +
125A LEU* 3.1 12.8 - - - +
126A TRP* 3.3 11.7 + - - -
163A MET* 3.3 20.4 - - + -
166A ALA* 4.3 2.7 - - + -
167A CYS* 3.5 22.3 - - + +
206A TYR* 2.9 43.7 + + - -
207A MET* 2.9 16.3 + - + +
210A VAL* 1.3 96.4 - - + +
212A PHE* 1.3 60.9 + - - +
215A PRO* 4.2 2.5 - - - -
962A ZN 2.4 29.2 - - - -
1296A RET 4.0 2.8 - - - +
----------------------------------------------------------
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