Contacts of the helix formed by residues 218 - 244 (chain A) in PDB entry 3U44
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 PHE 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.6 22.0 - - + +
213A ILE* 5.5 4.3 - - + -
216A LEU* 3.2 41.1 - - + -
217A PRO* 1.3 79.2 - - - +
219A TYR* 1.3 71.9 + + + +
220A GLN 3.0 2.1 + - - -
221A TYR* 3.2 14.2 + - - +
222A VAL* 3.8 4.0 + - + -
332A LEU* 6.2 1.3 - - + -
335A LEU* 4.3 6.7 - - + -
828A LEU* 3.5 24.9 - - + -
846A LEU* 4.0 30.7 - - + -
847A PRO* 3.4 40.8 - - + +
850A ALA* 3.5 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 3.0 48.7 - - + +
214A GLU* 3.5 30.1 - - + +
216A LEU* 3.4 10.6 + - + +
217A PRO 3.1 1.8 + - - -
218A PHE* 1.3 85.3 - + + +
220A GLN* 1.3 55.5 + - - +
221A TYR 3.1 0.2 - - - -
222A VAL* 3.0 33.2 + - + -
223A LYS* 2.7 56.0 + - + +
226A ILE* 4.1 6.8 - - - +
271A GLN 4.1 8.4 + - - -
272A ASP* 3.7 12.0 + - - -
274A PHE* 3.4 28.4 - + + +
846A LEU* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU 4.4 1.2 + - - -
217A PRO 3.2 16.1 + - - +
218A PHE 3.0 0.2 - - - -
219A TYR* 1.3 79.3 - - - +
221A TYR* 1.3 71.1 + - + +
223A LYS* 3.3 22.6 + - - +
224A GLU* 3.1 60.0 + - - +
827A GLU* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PRO 5.1 0.9 - - - -
218A PHE* 3.2 14.6 + - - +
219A TYR 3.1 0.4 - - - -
220A GLN* 1.3 88.5 - - + +
222A VAL* 1.3 61.5 + - - +
224A GLU* 3.9 8.4 - - - +
225A ASP* 3.1 28.9 + - - +
827A GLU* 3.1 23.9 + - - -
828A LEU* 3.8 20.0 - - + -
850A ALA* 3.7 20.9 - - - +
853A LYS* 4.4 6.4 - - + +
854A LYS* 3.3 52.0 - - + +
857A ARG* 3.3 38.7 + - - +
858A GLU* 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 4.3 7.2 - - + -
219A TYR* 3.0 43.8 + - + +
221A TYR* 1.3 75.7 - - - +
223A LYS* 1.3 65.7 + - - +
225A ASP* 3.3 1.7 + - - +
226A ILE* 3.1 37.5 + - + +
274A PHE* 4.2 3.4 - - + -
323A TYR* 3.5 41.3 - - + -
846A LEU* 4.8 5.2 - - + +
850A ALA* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 2.7 39.5 + - + +
220A GLN* 3.3 28.5 + - - +
222A VAL* 1.3 74.7 - - - +
224A GLU* 1.3 65.1 + - + +
226A ILE* 3.3 5.7 + - - +
227A ALA* 3.1 22.1 + - + +
271A GLN* 5.5 7.4 - - - +
272A ASP* 4.7 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLN* 3.1 40.9 + - - +
221A TYR* 3.9 6.6 - - - +
222A VAL 3.4 0.2 - - - -
223A LYS* 1.3 77.0 - - + +
225A ASP* 1.3 65.6 - - - +
227A ALA* 3.4 9.0 - - - +
228A MET* 3.2 27.8 + - - +
499A LYS* 3.2 34.0 + - + +
857A ARG* 2.8 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR 3.1 20.8 + - - +
222A VAL 3.6 4.9 - - - +
223A LYS 3.2 0.2 - - - -
224A GLU* 1.3 76.4 - - - +
226A ILE* 1.3 62.1 + - - +
228A MET* 3.3 11.7 + - - +
229A VAL* 3.1 34.6 + - - +
319A LEU* 5.0 2.3 - - - +
322A ASP* 4.8 0.2 - - - +
323A TYR* 2.5 34.4 + - - +
853A LYS* 3.2 35.1 + - + +
857A ARG* 5.4 1.0 - - - +
911A TYR* 4.5 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 4.1 11.4 - - - +
222A VAL* 3.1 34.1 + - + +
223A LYS* 3.7 4.9 - - - +
225A ASP* 1.3 72.7 - - - +
227A ALA* 1.3 67.7 - - - +
229A VAL* 3.1 8.9 - - - +
230A LEU* 2.9 50.6 + - + +
271A GLN* 4.7 10.8 - - + +
274A PHE* 4.4 5.8 - - + -
277A LEU* 3.9 30.1 - - + -
319A LEU* 3.8 22.9 - - + -
323A TYR* 4.3 6.7 - - + -
324A PHE* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS* 3.1 14.3 + - + +
224A GLU* 3.4 14.4 - - - +
226A ILE* 1.3 76.2 - - - +
228A MET* 1.3 63.0 + - + +
230A LEU* 3.9 1.4 - - - +
231A ASN* 2.9 27.9 + - - +
271A GLN* 4.0 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU* 3.2 12.6 + - - +
225A ASP* 3.5 13.5 - - - +
226A ILE 3.3 0.2 - - - -
227A ALA* 1.3 77.6 - - - +
229A VAL* 1.3 54.9 + - + +
231A ASN* 2.9 6.0 + - - +
232A GLY* 2.5 37.4 + - - -
499A LYS* 5.2 11.2 - - + -
857A ARG* 6.0 3.8 - - - -
907A GLU* 4.8 25.1 - - + +
908A PHE* 3.5 33.5 - - + +
911A TYR* 3.4 48.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 3.1 25.8 + - - +
226A ILE* 3.1 20.6 - - - +
228A MET* 1.3 78.8 - - + +
230A LEU* 1.3 60.8 + - - +
232A GLY* 3.6 1.1 - - - +
233A ALA* 2.8 34.3 + - - +
315A LEU* 4.2 25.7 - - + +
316A LEU* 6.0 1.3 - - - -
319A LEU* 3.7 29.4 - - + -
853A LYS* 6.1 0.9 - - - +
908A PHE* 4.2 23.8 - - + -
911A TYR* 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 2.9 42.7 + - + +
229A VAL* 1.3 74.6 - - - +
231A ASN* 1.3 58.4 + - - +
233A ALA* 3.1 7.6 + - - +
234A LYS* 3.0 27.0 + - - +
264A ILE* 4.2 8.9 - - + +
267A LEU* 3.9 42.8 - - + +
268A ILE* 4.2 9.2 - - + +
271A GLN* 3.6 31.6 - - + +
277A LEU* 4.8 5.8 - - + -
316A LEU* 4.0 12.1 - - + -
319A LEU* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA 2.9 20.0 + - - +
228A MET* 3.5 3.8 - - - +
230A LEU* 1.3 73.9 - - - +
232A GLY* 1.3 58.0 + - - +
234A LYS* 3.2 20.4 + - - +
235A GLU* 2.8 43.5 + - - +
268A ILE* 4.9 5.4 - - + -
271A GLN* 4.7 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET 2.5 20.3 + - - -
229A VAL* 3.6 2.9 - - - -
231A ASN* 1.3 72.2 - - - +
233A ALA* 1.3 56.3 + - - +
235A GLU* 4.3 5.5 - - - +
236A LYS* 2.9 33.3 + - - +
315A LEU* 4.1 7.0 - - - -
908A PHE* 4.3 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL 2.8 13.8 + - - +
230A LEU* 3.2 12.3 - - - +
231A ASN 3.1 0.2 - - - -
232A GLY* 1.3 73.4 - - - +
234A LYS* 1.3 60.4 + - - +
236A LYS* 3.0 4.5 + - - +
237A LEU* 2.8 37.9 + - - +
264A ILE* 3.6 19.1 - - + -
312A ALA* 4.6 13.9 - - - +
315A LEU* 4.0 10.7 - - + +
316A LEU* 4.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU 3.0 9.7 + - - +
231A ASN* 3.6 22.3 + - - +
233A ALA* 1.3 77.6 - - - +
235A GLU* 1.3 60.1 + - - +
237A LEU* 2.9 4.5 + - - +
238A LEU* 2.8 48.5 + - + +
261A LEU* 3.9 18.6 - - + -
264A ILE* 4.0 15.8 - - + +
265A ASP* 3.8 14.6 - - - +
268A ILE* 3.6 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 2.8 31.2 + - - +
232A GLY* 4.3 4.5 - - - +
234A LYS* 1.3 76.6 - - - +
236A LYS* 1.3 60.5 + - - +
238A LEU* 3.8 23.2 + - - +
239A ARG* 4.0 36.2 + - - +
900A GLN* 5.3 16.0 - - - +
906A PRO* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLY 2.9 22.5 + - - +
233A ALA* 3.0 5.8 + - - +
235A GLU* 1.3 77.5 - - - +
237A LEU* 1.3 66.5 + - + +
239A ARG* 4.1 8.9 + - - +
240A ALA 4.2 2.3 + - - -
308A LEU* 4.0 40.8 - - + +
311A GLY* 4.2 26.0 - - - -
312A ALA 5.5 0.4 - - - +
315A LEU* 4.3 21.9 - - + +
908A PHE* 4.9 10.5 - - + -
909A ASP* 5.3 8.6 + - - -
912A GLN* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA 2.8 26.1 + - - +
234A LYS 2.9 6.5 + - - +
236A LYS* 1.3 77.3 - - + +
238A LEU* 1.3 57.4 + - - +
239A ARG 3.0 2.9 - - - -
240A ALA* 2.6 36.3 + - - +
241A LEU* 3.2 5.0 + - - +
257A PHE* 4.3 17.9 - - + +
260A ASP* 3.8 14.4 - - + -
261A LEU* 3.8 35.9 - - + +
264A ILE* 3.6 22.9 - - + -
308A LEU 4.5 6.7 - - - +
309A ARG* 5.1 4.3 - - + -
312A ALA* 3.3 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 2.8 41.2 + - + +
235A GLU* 4.1 22.4 - - - +
236A LYS 3.6 0.4 - - - -
237A LEU* 1.3 72.9 - - - +
239A ARG* 1.3 60.0 + - + +
241A LEU* 3.1 18.5 + - + +
242A GLU* 3.0 24.6 + - - +
261A LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU* 4.0 31.1 + - + +
236A LYS* 4.3 8.3 - - - +
237A LEU 2.9 0.8 + - - -
238A LEU* 1.3 76.4 - - - +
240A ALA* 1.3 61.0 + - - +
242A GLU* 2.7 43.9 + - - +
243A LEU* 2.8 37.3 + - + +
308A LEU* 4.8 9.6 - - + -
896A ALA 6.1 1.1 - - - +
899A SER* 4.2 25.2 + - - +
900A GLN* 5.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LYS 4.2 1.0 + - - -
237A LEU* 2.6 21.9 + - - +
239A ARG* 1.3 74.4 - - - +
241A LEU* 1.3 57.9 + - - +
243A LEU* 3.4 26.1 + - - +
244A THR* 3.6 5.5 + - - +
257A PHE* 3.4 43.9 - - + -
305A ALA* 4.3 11.4 - - + +
308A LEU* 4.3 11.3 - - + +
309A ARG 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU 3.2 5.4 + - - +
238A LEU* 3.1 20.6 + - + +
239A ARG 3.1 0.2 - - - -
240A ALA* 1.3 75.6 - - - +
242A GLU* 1.3 60.1 + - - +
244A THR* 3.0 31.8 + - + +
255A ASP 5.1 7.9 - - - +
257A PHE* 4.9 13.6 - - + -
258A LEU* 4.6 30.3 - - + -
261A LEU* 4.5 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU 3.0 11.3 + - - +
239A ARG* 2.7 48.5 + - - +
241A LEU* 1.3 75.7 - - - +
243A LEU* 1.3 71.2 + - + +
244A THR* 3.3 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 2.8 21.8 + - + +
240A ALA* 3.5 8.5 - - - +
241A LEU 3.2 0.6 - - - -
242A GLU* 1.3 79.2 - - + +
244A THR* 1.3 77.7 + - - +
301A LEU* 3.3 48.8 - - + +
304A GLU* 4.2 10.3 - - - +
305A ALA* 3.5 30.5 - - + -
308A LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA 3.6 5.8 + - - +
241A LEU* 3.0 25.6 + - + +
242A GLU* 3.1 10.1 + - - +
243A LEU* 1.3 98.6 + - - +
301A LEU* 4.7 4.5 - - - +
----------------------------------------------------------
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