Contacts of the helix formed by residues 247 - 273 (chain B) in PDB entry 1UU1
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 HIS 247 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 5.7 1.1 - - - -
37B LEU* 3.8 43.0 - - + +
40B GLU* 4.9 11.2 - - + -
44B ARG* 6.3 0.4 - - - -
243B VAL* 3.2 17.2 + - + -
244B ALA 3.0 6.9 + - - +
246B ASP* 1.3 95.7 + - + +
248B ARG* 1.3 57.5 + - - +
249B GLU* 3.0 13.9 - - - -
250B ILE* 2.9 39.4 + - + +
251B PHE* 3.6 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 3.9 7.3 + - - +
67B SER* 3.3 27.0 + - - -
68B TYR* 3.7 52.7 + - + +
204B PHE* 4.9 7.2 - - + -
244B ALA 3.2 8.5 + - - +
245B LEU* 3.2 29.9 + - - +
246B ASP 3.7 0.6 - - - -
247B HIS* 1.3 75.0 - - - +
249B GLU* 1.3 71.3 + - + +
251B PHE* 3.2 9.9 + - - +
252B GLU* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASP 4.4 6.3 - - - +
247B HIS* 3.0 18.8 + - - +
248B ARG* 1.3 92.4 + - + +
250B ILE* 1.3 68.3 + - + +
252B GLU* 3.3 14.9 + - - +
253B GLU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PRO* 4.1 27.1 - - + -
37B LEU* 5.1 3.8 - - + -
247B HIS* 3.2 31.2 - - + +
249B GLU* 1.3 82.4 - - + +
251B PHE* 1.3 64.0 + - + +
253B GLU* 3.1 21.9 + - - +
254B ARG* 3.2 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.5 23.1 - + - -
34B PRO* 3.7 26.9 - - + -
37B LEU* 3.9 12.8 - - + -
203B ALA* 3.3 24.9 - - + +
204B PHE* 3.4 49.8 - + + -
244B ALA* 3.6 24.0 - - - -
247B HIS 3.6 12.3 - - - -
248B ARG* 3.2 4.9 + - - +
250B ILE* 1.3 73.5 - - + +
252B GLU* 1.3 59.6 + - - +
253B GLU 3.1 1.8 - - - -
254B ARG* 3.7 20.8 - - - +
255B THR* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG* 2.8 23.2 + - - +
249B GLU* 3.6 14.2 - - - +
250B ILE 3.2 0.2 - - - -
251B PHE* 1.3 76.2 - - - +
253B GLU* 1.3 64.5 + - - +
255B THR* 3.9 5.7 - - - -
256B LYS* 3.0 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU 3.1 11.3 + - - +
250B ILE* 3.1 11.8 + - - +
252B GLU* 1.3 80.8 - - - +
254B ARG* 1.3 63.5 + - + +
256B LYS* 3.2 25.7 + - - +
257B PHE* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 4.9 9.0 - - - +
31B PHE* 3.5 42.8 - - + +
32B PRO* 2.7 34.7 + - - +
34B PRO* 3.6 33.3 - - - +
203B ALA 5.3 2.0 - - - +
205B SER* 3.7 14.1 + - - -
250B ILE* 3.2 18.7 + - + +
251B PHE* 3.5 22.7 + - - +
253B GLU* 1.3 77.6 - - + +
255B THR* 1.3 58.3 + - - +
257B PHE* 3.1 9.2 + - - +
258B ILE* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 5.6 0.8 + - - +
178B GLU* 3.2 30.3 - - + +
179B PHE* 3.9 17.6 - - + -
203B ALA* 3.7 24.3 + - - +
251B PHE 2.9 24.0 + - - -
252B GLU* 3.9 6.1 - - - -
254B ARG* 1.3 77.1 - - - +
256B LYS* 1.3 58.5 + - - +
258B ILE* 3.2 9.0 + - - +
259B VAL* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLU* 3.0 18.9 + - + +
253B GLU* 3.4 24.1 + - - +
255B THR* 1.3 79.8 - - - +
257B PHE* 1.3 56.5 + - - +
259B VAL* 3.4 5.2 + - - +
260B GLU* 2.9 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.3 36.6 - + + -
253B GLU 3.0 12.4 + - - +
254B ARG* 3.4 9.9 - - - +
256B LYS* 1.3 77.6 - - - +
258B ILE* 1.3 63.3 + - + +
260B GLU* 3.4 13.5 + - + +
261B GLU* 2.8 62.8 + - + +
319B GLY 4.0 16.8 - - - -
321B ARG* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 4.8 5.4 - - - +
30B PRO* 3.3 40.6 - - + -
31B PHE* 3.8 4.7 - - + -
179B PHE* 3.7 32.1 - - + -
254B ARG 2.9 23.9 + - - +
255B THR* 3.5 6.5 - - - +
257B PHE* 1.3 89.6 - - + +
259B VAL* 1.3 53.1 + - - +
261B GLU* 3.0 6.2 + - - +
262B ARG* 2.7 32.4 + - - +
282B ASN* 3.9 19.3 - - + -
318B ILE* 3.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 3.4 39.3 - - + +
255B THR* 2.9 22.7 + - + +
256B LYS* 3.8 5.4 - - - +
258B ILE* 1.3 76.9 - - - +
260B GLU* 1.3 67.5 + - + +
262B ARG* 3.1 29.9 + - - +
263B GLU* 3.0 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS* 2.9 66.8 + - + +
257B PHE* 3.7 10.9 - - + +
259B VAL* 1.3 79.3 - - + +
261B GLU* 1.3 62.5 + - - +
263B GLU* 4.2 4.3 - - - +
264B ARG* 3.4 21.7 + - - +
321B ARG* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PHE* 2.8 52.2 + - + +
258B ILE* 3.3 5.6 - - - +
260B GLU* 1.3 79.0 - - - +
262B ARG* 1.3 64.0 + - - +
264B ARG* 3.3 17.7 + - - +
265B MET* 3.1 25.1 + - - +
318B ILE* 3.9 10.5 - - + -
321B ARG* 2.8 44.9 + - - -
324B ASN* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE 2.8 27.3 + - - -
258B ILE* 2.7 8.6 + - + +
259B VAL* 3.3 36.7 - - - +
261B GLU* 1.3 77.0 - - - +
263B GLU* 1.3 82.8 + - - +
265B MET* 3.2 5.1 + - - +
266B LYS* 2.8 40.9 + - + +
279B SER 3.3 18.9 + - - -
280B ARG* 2.9 27.8 + - - +
281B GLY 3.0 20.1 + - - -
283B PHE 3.9 9.4 - - - +
284B VAL* 4.0 3.8 - - + +
318B ILE* 3.0 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B VAL* 3.0 19.4 + - + +
260B GLU* 4.5 4.5 - - - +
262B ARG* 1.3 99.4 + - - +
264B ARG* 1.3 67.6 + - - +
266B LYS* 2.8 39.0 + - - +
267B SER* 2.9 29.4 + - - +
270B ARG* 4.6 7.1 + - - -
280B ARG* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU 3.4 18.2 + - - +
261B GLU* 3.3 24.9 + - - +
262B ARG 3.2 0.2 - - - -
263B GLU* 1.3 81.2 - - - +
265B MET* 1.3 66.5 + - - +
267B SER* 3.2 6.3 + - - -
268B ALA* 3.1 22.3 + - + +
321B ARG* 2.8 39.3 - - - +
324B ASN* 4.8 0.8 - - - +
325B ASP* 2.7 31.9 + - - +
328B LEU* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLU 3.1 12.8 + - - +
262B ARG* 3.6 6.5 - - - +
264B ARG* 1.3 79.8 - - - +
266B LYS* 1.3 64.4 + - - +
268B ALA* 3.8 1.2 - - - +
269B LEU* 3.0 34.9 + - + +
284B VAL* 4.1 28.7 - - + -
316B ILE* 4.3 5.8 - - + +
318B ILE* 4.9 8.1 - - + -
324B ASN* 3.3 48.9 - - + +
327B ILE* 4.1 29.2 - - + -
328B LEU* 3.9 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ARG* 2.8 34.9 + - + +
263B GLU* 2.8 39.1 + - - +
265B MET* 1.3 73.6 - - - +
267B SER* 1.3 63.2 + - - +
269B LEU* 3.4 2.4 + - - +
270B ARG* 3.2 50.6 + - - +
276B ILE* 3.4 20.2 - - + +
277B THR 3.9 14.4 - - - +
278B ASP* 3.3 18.8 + - - -
279B SER* 2.9 22.9 + - - +
280B ARG* 4.6 2.6 - - - +
284B VAL* 3.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLU* 2.9 16.6 + - - +
264B ARG* 3.4 10.7 - - - -
266B LYS* 1.3 76.3 - - - +
268B ALA* 1.3 62.7 + - - +
270B ARG* 3.1 21.0 + - - +
271B GLU* 3.0 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 3.1 12.7 + - + +
265B MET 3.8 0.7 - - - +
266B LYS 3.4 0.2 - - - -
267B SER* 1.3 80.5 - - - +
269B LEU* 1.3 55.8 + - - +
271B GLU* 3.4 16.1 + - - +
272B MET* 3.0 38.6 + - + +
328B LEU* 3.7 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B MET* 3.0 32.5 + - + +
266B LYS* 3.7 6.1 - - - +
267B SER 3.2 0.2 - - - -
268B ALA* 1.3 72.5 - - - +
270B ARG* 1.3 67.3 + - - +
272B MET* 3.2 7.3 + - - +
273B GLY 3.1 4.7 + - - -
274B TYR* 3.1 39.7 + - + +
276B ILE* 3.9 27.1 - - + -
284B VAL* 4.1 22.2 - - + -
286B VAL* 4.0 15.9 - - + -
316B ILE* 5.2 0.7 - - + -
328B LEU* 3.9 14.1 - - + -
331B LEU* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLU* 4.6 8.1 + - - -
266B LYS* 3.2 46.7 + - - +
267B SER* 3.1 17.7 + - - +
269B LEU* 1.3 76.4 - - - +
271B GLU* 1.3 55.5 + - + +
273B GLY* 2.6 27.5 + - - -
274B TYR 4.1 8.7 - - - +
276B ILE* 3.4 29.4 - - + +
277B THR 4.7 3.0 + - - -
278B ASP* 4.4 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER* 3.0 34.9 + - - +
268B ALA* 3.5 13.4 + - - +
269B LEU 3.3 0.2 - - - -
270B ARG* 1.3 76.5 - - + +
272B MET* 1.3 59.9 + - + +
273B GLY 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ALA* 3.0 27.8 + - + +
269B LEU* 3.5 10.5 - - - +
270B ARG 3.1 0.4 - - - -
271B GLU* 1.3 75.7 - - + +
273B GLY* 1.3 59.8 + - - +
274B TYR* 3.5 26.6 - - + -
328B LEU* 3.6 40.4 - - + +
331B LEU* 4.0 3.8 - - - -
332B GLU* 3.5 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ARG 2.6 21.9 + - - -
271B GLU 3.1 1.3 - - - -
272B MET* 1.3 73.9 - - - +
274B TYR* 1.3 64.2 - - - +
275B ARG* 3.8 5.4 + - - +
----------------------------------------------------------
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