Contacts of the helix formed by residues 201 - 215 (chain A) in PDB entry 1UWY
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 ASP 201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A THR* 3.0 4.2 - - - -
200A PRO* 1.3 79.6 - - - +
202A ASP* 1.3 62.4 + - - +
203A ASP* 3.1 11.0 - - - +
204A VAL* 3.1 21.1 - - + +
205A PHE* 3.0 23.6 + - + -
253A TYR* 2.5 24.4 + - - +
259A PHE* 3.4 17.7 - - + -
320A ARG* 2.5 40.7 + - - +
322A HIS* 3.2 17.2 - - - -
337A LEU 5.3 2.2 - - - -
338A LEU* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.0 21.5 + - - -
182A PRO 4.3 0.2 - - - +
198A LEU* 2.9 45.7 - - + +
199A THR* 3.3 23.0 + - - +
200A PRO 3.6 1.8 + - - -
201A ASP* 1.3 76.6 - - - +
203A ASP* 1.3 58.2 + - - +
205A PHE* 3.8 2.4 - - - +
206A GLN* 2.8 63.8 + - - +
237A ASN* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 3.4 8.5 - - - -
202A ASP* 1.3 73.4 + - - +
204A VAL* 1.3 73.4 + - - +
206A GLN* 3.3 7.7 + - - +
207A TYR* 2.8 31.2 + - - +
320A ARG* 2.9 33.4 + - - -
339A LEU* 3.8 26.0 + - + +
343A TYR* 5.0 2.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
201A ASP* 3.1 22.2 - - + +
203A ASP* 1.3 84.5 + - - +
205A PHE* 1.3 61.5 + - - +
207A TYR* 3.2 2.4 + - - +
208A LEU* 2.8 48.3 + - + +
259A PHE* 3.1 33.7 - - + -
296A LEU* 4.0 21.5 - - + -
320A ARG* 5.7 0.4 - - - +
337A LEU* 4.4 17.7 - - + +
338A LEU* 5.1 1.8 - - - -
339A LEU* 4.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.6 23.8 - + + +
182A PRO* 3.7 20.2 - - + -
199A THR* 3.3 26.5 - - + -
201A ASP 3.0 14.8 + - - +
202A ASP* 3.9 2.7 - - - +
204A VAL* 1.3 83.7 - - - +
206A GLN* 1.3 63.4 + - - +
208A LEU* 3.2 7.2 + - + +
209A ALA* 3.0 23.2 + - - +
253A TYR* 3.4 49.4 - + - -
259A PHE* 3.6 36.3 - + + -
260A GLU 3.4 23.1 - - - -
261A ILE* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.0 35.4 + - + +
202A ASP* 2.8 46.7 + - - +
203A ASP* 3.7 6.5 - - - +
205A PHE* 1.3 73.2 - - - +
207A TYR* 1.3 64.9 + - - +
209A ALA* 3.1 3.6 + - - +
210A HIS* 3.0 43.1 + - + -
235A VAL* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASP 2.8 21.0 + - - +
204A VAL 3.6 2.2 - - - +
206A GLN* 1.3 72.5 - - - +
208A LEU* 1.3 68.1 + - + +
210A HIS* 3.4 7.3 + - - +
211A THR* 2.8 46.9 + - - -
293A GLN* 2.8 38.5 + - - -
296A LEU* 3.8 19.2 - - + +
339A LEU* 3.8 31.4 - - + -
340A PRO* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.9 29.4 - - + -
204A VAL* 2.8 29.2 + - + +
205A PHE* 3.4 12.6 - - + +
206A GLN 3.1 0.2 - - - -
207A TYR* 1.3 77.6 - - + +
209A ALA* 1.3 65.6 + - - +
211A THR* 3.3 11.8 + - - -
212A TYR* 3.4 8.7 + - - +
259A PHE* 4.2 24.0 - - + -
261A ILE* 4.4 5.4 - - + -
290A TYR* 3.6 26.8 - - + +
293A GLN* 3.9 20.4 - - + -
296A LEU* 3.8 27.4 - - + -
337A LEU* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 3.9 24.7 - - + +
181A TYR* 4.1 14.4 - - + -
205A PHE 3.0 13.3 + - - +
206A GLN* 3.1 6.9 + - - +
208A LEU* 1.3 74.5 - - - +
210A HIS* 1.3 64.4 + - - +
212A TYR* 3.3 4.7 + - - +
213A ALA* 3.0 24.8 + - - +
235A VAL* 3.8 15.7 - - + +
261A ILE* 3.8 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLN* 3.0 39.7 + - + +
207A TYR* 3.7 7.2 - - - +
209A ALA* 1.3 75.7 - - - +
211A THR* 1.3 68.5 + - - +
213A ALA 4.6 0.4 - - - +
214A SER* 2.8 33.8 + - - +
233A ASN* 3.7 30.6 + - + +
235A VAL* 3.3 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 2.8 46.1 + - - -
208A LEU* 3.4 11.2 - - - -
209A ALA 3.1 0.6 - - - -
210A HIS* 1.3 80.7 - - - +
212A TYR* 1.3 62.4 + - - +
214A SER* 3.0 16.3 + - - -
215A ARG* 3.4 17.2 + - - +
289A GLU* 3.6 40.3 - - + +
290A TYR* 4.2 4.9 - - - +
293A GLN* 3.8 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.8 0.2 - - - -
208A LEU 3.4 2.6 + - - +
209A ALA 3.3 6.8 + - - +
210A HIS 3.2 0.2 - - - -
211A THR* 1.3 84.5 - - - +
213A ALA* 1.3 63.8 + - - +
215A ARG 3.2 3.3 + - - -
216A ASN* 3.6 3.4 + - - -
219A MET* 3.9 13.9 - - - -
263A LEU* 3.2 44.6 - - + -
265A LEU* 3.3 25.1 - - + +
283A ASN* 2.4 35.5 + - - +
286A SER* 2.5 72.6 + - - +
287A LEU* 3.7 14.1 - - + +
290A TYR* 4.0 20.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 4.5 1.1 - - + -
209A ALA 3.0 15.5 + - - +
210A HIS* 4.8 0.2 - - - -
212A TYR* 1.3 72.5 - - - +
214A SER* 1.3 59.5 + - - +
215A ARG 2.9 2.5 - - - -
216A ASN 2.7 33.1 + - - +
219A MET* 3.7 32.8 - - + +
220A LYS* 3.7 5.5 - - - +
233A ASN 3.6 22.0 - - - +
234A GLY 4.0 1.8 - - - +
235A VAL* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A HIS* 2.8 25.0 + - - +
211A THR* 3.0 14.0 + - - -
213A ALA* 1.3 73.3 - - - +
215A ARG* 1.3 77.6 + - - +
216A ASN 3.6 0.2 + - - -
220A LYS* 3.5 33.9 + - - +
233A ASN 5.0 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A THR* 3.4 18.7 + - - +
212A TYR 3.2 3.0 + - - +
213A ALA 2.9 1.2 - - - -
214A SER* 1.3 104.8 + - - +
216A ASN* 1.3 56.0 + - - +
217A PRO* 3.4 10.4 - - - +
220A LYS* 5.6 0.4 - - - -
282A ASN 4.2 3.5 - - - +
283A ASN 5.8 0.2 - - - -
285A ALA* 4.2 25.0 - - + +
286A SER* 2.9 29.9 + - - +
289A GLU* 2.9 46.7 + - - +
----------------------------------------------------------
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