Contacts of the helix formed by residues 218 - 238 (chain D) in PDB entry 1UNL
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 SER 218 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LEU* 3.4 10.4 - - - +
216D VAL* 3.4 8.2 - - - +
217D GLY* 1.3 79.4 - - - +
219D ASP* 1.3 63.0 + - - +
220D HIS* 3.5 11.7 + - - +
221D GLU* 3.0 27.5 + - - +
222D LEU 3.2 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LEU* 3.4 33.7 - - - +
168D HIS* 4.1 7.3 + - - +
169D LEU* 3.6 38.5 + - + +
173D ASP* 4.6 2.9 - - - +
177D TRP* 3.8 11.6 - - + -
218D SER* 1.3 71.0 - - - +
220D HIS* 1.3 66.2 + - - +
222D LEU* 3.3 3.8 + - - +
223D GLN* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D SER* 3.2 9.8 + - - +
219D ASP* 1.3 79.8 - - - +
221D GLU* 1.3 64.1 + - - +
223D GLN* 3.2 12.1 + - - +
224D ALA* 3.0 22.5 + - + +
250D VAL* 2.9 38.4 + - + +
251D GLU* 4.5 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D GLU 5.3 0.2 - - - +
216D VAL* 3.8 20.9 - - + +
217D GLY* 3.0 23.4 + - - -
218D SER* 3.0 22.1 + - - +
219D ASP 3.3 0.2 - - - -
220D HIS* 1.3 78.4 + - - +
222D LEU* 1.3 64.5 + - - +
224D ALA* 3.2 7.5 + - + +
225D VAL* 3.0 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 4.3 19.1 - - + -
163D CYS* 4.0 20.9 - - - -
166D LEU* 4.0 12.1 - - + -
169D LEU* 3.7 38.6 - - + -
174D PRO* 5.0 1.3 - - + -
177D TRP* 4.1 11.4 - - + -
212D ILE* 4.1 28.3 - - + -
216D VAL* 3.6 8.0 - - + +
218D SER 3.2 10.2 + - - +
219D ASP 3.3 8.3 + - - +
221D GLU* 1.3 77.7 - - - +
223D GLN* 1.3 58.3 + - - +
225D VAL* 3.2 4.0 + - + -
226D LEU* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D TRP* 3.3 64.3 - - + +
219D ASP 3.1 11.0 + - - +
220D HIS* 3.6 14.3 - - - +
222D LEU* 1.3 78.1 - - - +
224D ALA* 1.3 56.0 + - - +
226D LEU* 3.8 2.0 - - - +
227D LEU* 3.0 48.9 + - + +
250D VAL* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D HIS* 3.0 15.2 + - + +
221D GLU* 3.2 12.1 + - + +
223D GLN* 1.3 76.0 - - - +
225D VAL* 1.3 54.5 + - + +
227D LEU* 3.6 2.7 + - - +
228D THR* 2.6 32.9 + - - -
248D PHE 5.2 0.8 - - - +
250D VAL* 3.7 13.3 - - + +
251D GLU* 3.8 24.2 - - + +
257D PHE* 4.9 1.6 - - - -
260D ARG* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 4.0 19.5 - - + +
212D ILE* 3.5 31.0 - - + -
216D VAL* 5.2 7.2 - - + -
221D GLU* 3.0 30.3 + - + +
222D LEU* 3.8 5.4 - - + +
224D ALA* 1.3 72.8 - - - +
226D LEU* 1.3 66.9 + - - +
228D THR* 3.2 4.9 + - - -
229D CYS* 3.1 21.9 + - - -
260D ARG* 4.0 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.9 1.3 - - + -
159D LEU* 4.2 14.4 - - + -
174D PRO* 4.1 19.7 - - + +
177D TRP* 4.0 26.2 - - + -
178D LEU* 4.0 27.8 - - + -
204D LEU* 4.4 7.4 - - + -
208D CYS* 3.6 28.3 - - - -
212D ILE* 4.4 11.6 - - + +
222D LEU* 2.9 19.2 + - + +
223D GLN 3.8 2.2 - - - +
225D VAL* 1.3 77.8 - - - +
227D LEU* 1.3 61.0 + - + +
229D CYS* 3.3 5.8 + - - +
230D LEU* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D TRP* 4.5 16.4 - - + +
178D LEU* 4.5 7.6 - - + -
181D VAL* 4.3 11.0 - - + -
223D GLN* 3.0 42.0 + - + +
224D ALA* 4.0 3.6 - - - +
226D LEU* 1.3 78.9 - - + +
228D THR* 1.3 61.3 + - - +
230D LEU* 4.1 21.3 - - + -
231D TYR* 3.0 28.4 + - - +
247D PRO 4.2 10.3 - - - +
248D PHE* 3.5 38.8 - - + +
250D VAL* 3.9 15.3 - - + -
257D PHE* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ALA 2.6 20.5 + - - -
225D VAL* 3.3 9.4 - - - -
227D LEU* 1.3 75.9 - - - +
229D CYS* 1.3 64.6 + - - +
231D TYR* 3.3 3.1 + - - +
232D LEU* 3.1 27.8 + - + +
257D PHE* 3.4 15.3 - - + +
260D ARG* 2.9 33.6 + - + +
261D CYS* 3.7 42.2 - - - +
264D VAL* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 3.8 14.8 - - + -
207D LEU* 3.5 30.3 - - + +
208D CYS* 4.4 9.9 - - - -
211D VAL* 4.0 34.1 - - - -
212D ILE* 5.0 0.7 - - - -
225D VAL* 3.1 19.3 + - - -
226D LEU* 3.5 9.0 - - - +
228D THR* 1.3 76.3 - - - +
230D LEU* 1.3 58.2 + - - +
232D LEU* 3.6 4.6 + - - -
233D SER* 2.9 30.8 + - - -
264D VAL* 4.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU* 3.6 33.7 - - + +
181D VAL* 3.9 22.9 - - + -
195D PHE* 4.6 7.9 - - + -
196D ILE* 4.3 15.3 - - + -
204D LEU* 3.7 19.0 - - + +
226D LEU 2.9 17.4 + - - +
227D LEU* 3.7 14.1 - - + +
228D THR 3.2 0.2 - - - -
229D CYS* 1.3 76.4 - - - +
231D TYR* 1.3 57.2 + - - +
233D SER* 3.2 4.0 + - - -
234D TYR* 2.9 50.8 + - + -
248D PHE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.6 14.9 - - - +
46A SER* 3.4 24.1 + - - -
49A LEU* 3.5 23.8 - - + -
227D LEU 3.0 18.8 + - - +
228D THR 3.3 2.7 + - - +
230D LEU* 1.3 76.3 - - - +
232D LEU* 1.3 59.6 + - - +
234D TYR* 3.4 2.8 + - - +
235D SER* 2.8 43.7 + - - -
243D TYR* 4.0 21.4 + - + -
244D PRO 4.2 9.2 - - - -
245D LEU* 4.6 6.0 + - + +
248D PHE* 3.5 39.0 - + + -
257D PHE* 3.7 29.6 - + + -
258D TRP* 3.6 8.7 - + - -
261D CYS* 4.0 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.1 23.6 - - + -
53A CYS* 5.4 3.4 - - - -
207D LEU* 4.6 6.3 - - + -
228D THR 3.1 22.8 + - - +
229D CYS* 3.9 4.9 - - - +
231D TYR* 1.3 72.6 - - - +
233D SER* 1.3 61.6 + - - +
235D SER* 4.0 4.7 - - - -
236D TYR* 3.0 31.2 + - - +
261D CYS* 3.8 20.2 - - - +
264D VAL* 3.6 39.3 - - + -
265D ILE* 3.6 33.0 - - + -
272D MET* 4.2 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D PHE* 3.3 18.0 - - - -
200D ASN 5.2 0.4 - - - -
203D PHE* 3.3 35.0 - - - -
204D LEU* 3.9 13.8 - - - +
207D LEU* 3.5 4.7 - - - +
229D CYS 2.9 21.0 + - - -
230D LEU* 3.2 11.2 + - - -
232D LEU* 1.3 74.8 - - - +
234D TYR* 1.3 57.9 + - - +
237D MET* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.8 0.2 + - - -
181D VAL* 4.0 0.8 - - + +
182D ASP* 2.7 40.5 + - - +
185D LEU* 3.6 16.0 - - + +
191D GLN* 3.5 13.5 - - - -
195D PHE* 3.3 42.4 - + + +
196D ILE* 4.4 1.4 - - - +
230D LEU* 2.9 48.5 + - + +
231D TYR* 3.6 8.3 - - - +
232D LEU 3.4 0.2 - - - -
233D SER* 1.3 76.3 - - - +
235D SER* 1.3 59.1 + - - +
238D GLY* 2.9 21.1 + - - +
243D TYR* 3.1 50.1 - + + -
248D PHE* 3.5 20.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 2.8 46.7 + - - -
49A LEU* 4.8 8.7 - - - +
50A ARG* 2.7 39.2 + - - +
231D TYR* 2.8 33.0 + - - -
232D LEU* 4.0 7.9 - - - -
233D SER 3.3 0.2 - - - -
234D TYR* 1.3 76.9 - - - +
236D TYR* 1.3 59.0 + - - +
238D GLY 4.8 0.2 + - - -
243D TYR* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.3 20.2 + - + +
53A CYS* 3.6 32.2 + - + -
54A LEU* 3.6 27.9 - - + +
149A ARG* 4.6 13.7 + - - +
150A ALA* 3.7 20.2 + - + +
203D PHE* 3.6 21.1 - + + -
232D LEU 3.0 18.0 + - - +
233D SER 4.2 0.7 - - - +
235D SER* 1.3 78.9 - - - +
237D MET* 1.3 64.0 + - - +
238D GLY 3.7 1.1 - - - +
269D SER 4.5 1.7 + - - -
272D MET* 3.4 45.8 - - + -
273D LEU* 3.4 28.2 + - - +
276D ASN* 4.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.1 37.0 + - - +
150A ALA 5.1 2.0 - - - +
153A ILE* 3.6 36.8 - - + -
155A VAL* 5.0 3.1 - - + -
195D PHE* 3.8 8.3 - - + -
200D ASN* 3.8 22.0 + - - +
203D PHE* 3.7 32.5 - - + -
233D SER 2.8 18.4 + - - +
236D TYR* 1.3 85.2 - - - +
238D GLY* 1.3 63.8 + - - +
239D ASN* 3.9 1.7 + - - +
276D ASN* 3.7 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.7 6.1 + - - -
125A ARG* 5.6 2.6 + - - -
149A ARG* 3.7 6.9 + - - -
195D PHE* 3.7 16.4 - - - -
233D SER 3.7 1.4 + - - -
234D TYR 2.9 21.1 + - - +
236D TYR 3.7 2.0 - - - +
237D MET* 1.3 81.3 - - - +
239D ASN* 1.3 62.9 + - - -
240D GLU 3.4 9.0 + - - +
243D TYR* 3.4 9.6 - - - -
----------------------------------------------------------
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