Contacts of the helix formed by residues 246 - 265 (chain A) in PDB entry 1UJN
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 PRO 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 3.4 30.1 - - - +
243A HIS 5.4 0.9 - - - +
244A ALA 3.2 10.9 - - - +
245A LEU* 1.3 95.1 - - + +
247A HIS* 1.3 67.4 + - - +
249A MET* 3.0 27.8 + - + +
250A ALA* 3.0 10.2 + - - +
284A PRO* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.6 17.3 - - + -
125A ASP* 5.5 3.5 + - - -
169A GLU* 3.7 3.9 + - - +
173A GLU* 3.7 19.2 + - - -
231A HIS* 3.6 35.0 + + - -
238A GLU* 3.2 38.6 + - - +
245A LEU 3.5 1.8 + - - -
246A PRO* 1.3 71.3 - - - +
248A GLY* 1.3 59.4 + - - +
250A ALA* 3.1 4.2 + - - +
251A VAL* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 5.3 2.4 - - - +
169A GLU* 3.0 38.7 + - - -
172A VAL* 3.5 15.8 - - - +
173A GLU* 5.4 2.5 - - - -
247A HIS* 1.3 81.1 - - - +
249A MET* 1.3 61.4 + - - +
251A VAL* 3.4 7.4 + - - -
252A ALA* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 4.1 33.7 - - + +
169A GLU* 4.4 6.3 - - + -
245A LEU* 3.6 17.0 - - + -
246A PRO* 3.0 26.6 + - + +
248A GLY* 1.3 74.6 - - - +
250A ALA* 1.3 66.4 + - - +
252A ALA* 3.2 7.5 + - - +
253A TYR* 3.1 27.9 + - - -
281A LEU* 3.5 45.5 - - + +
282A SER 4.6 2.0 - - - +
283A PRO* 3.8 12.6 - - + +
284A PRO* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLY* 3.6 26.5 - - - +
237A LEU* 4.7 0.7 - - + -
238A GLU* 3.5 33.0 - - + +
245A LEU* 3.7 19.9 - - + +
246A PRO 3.0 6.1 + - - +
247A HIS 3.1 8.7 + - - +
249A MET* 1.3 77.8 - - - +
251A VAL* 1.3 56.3 + - + +
253A TYR* 3.2 6.6 + - - +
254A GLY 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.8 17.3 - - + -
173A GLU* 3.8 16.6 - - - +
176A LYS* 4.5 6.3 - - + -
229A LEU 4.5 2.2 - - - +
230A GLY 4.2 7.2 - - - +
231A HIS* 3.8 24.9 - - + +
234A GLY* 5.0 1.1 - - - -
247A HIS* 2.9 44.8 + - + +
248A GLY* 3.6 9.2 - - - +
250A ALA* 1.3 77.7 - - + +
252A ALA* 1.3 56.5 + - - +
254A GLY* 3.0 2.3 + - - -
255A LEU* 2.8 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 4.1 11.9 - - + -
248A GLY 3.1 9.3 + - - +
249A MET 3.2 7.2 + - - +
251A VAL* 1.3 75.5 - - - +
253A TYR* 1.3 63.3 + - - +
255A LEU* 3.2 17.4 + - - +
256A LEU* 3.3 10.7 + - - +
274A VAL* 4.5 2.4 - - - +
277A LEU* 4.5 6.5 - - + +
278A LEU* 3.7 21.2 - - + +
281A LEU* 3.3 33.9 - - + -
283A PRO* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.8 0.7 - - - -
237A LEU* 3.6 15.3 - - + -
245A LEU* 4.1 13.7 - - + -
249A MET 3.1 22.9 + - - -
250A ALA 3.5 6.1 - - - +
251A VAL 3.2 0.2 - - - -
252A ALA* 1.3 76.3 - - - +
254A GLY* 1.3 61.7 + - - +
256A LEU* 3.3 10.2 + - - +
257A TYR* 3.3 1.0 + - - +
278A LEU* 4.6 6.1 - - + -
283A PRO* 3.5 27.0 - - + +
284A PRO 2.7 26.3 + - - -
285A PRO* 4.0 0.2 - - - +
286A LEU* 3.5 35.2 - - + +
337A TRP* 3.0 26.5 + + + -
341A LEU* 3.7 44.9 - - + -
346A LEU* 3.7 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLY* 3.3 29.7 - - - -
233A LEU* 4.3 18.3 - - - +
234A GLY 4.4 1.1 - - - +
250A ALA 2.9 12.0 + - - -
251A VAL 3.0 0.8 + - - -
253A TYR* 1.3 73.6 - - - +
255A LEU* 1.3 58.7 + - - +
257A TYR* 3.2 4.1 + - - +
258A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 4.2 11.4 - - + +
175A PHE* 3.9 27.6 - - + -
176A LYS* 4.3 9.2 - - + -
179A LEU* 4.3 7.5 - - + +
229A LEU* 3.8 47.6 - - + +
251A VAL* 2.8 28.7 + - + +
252A ALA* 3.2 7.6 + - - +
254A GLY* 1.3 75.1 - - - +
256A LEU* 1.3 59.6 + - - +
258A ALA* 3.4 4.3 + - + +
259A ALA* 2.9 29.6 + - - +
274A VAL* 4.1 16.4 - - + +
277A LEU* 4.0 13.0 - - + -
314A PRO* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA 3.3 3.8 + - - +
253A TYR* 3.5 9.2 - - + +
254A GLY 3.3 0.2 - - - -
255A LEU* 1.3 78.1 - - - +
257A TYR* 1.3 62.5 + - - +
259A ALA* 3.2 4.2 + - - +
260A LEU* 3.0 31.6 + - + +
271A LEU* 3.4 31.2 - - + -
274A VAL* 3.6 23.7 - - + +
275A ARG* 5.0 6.5 - - + -
278A LEU* 3.8 15.9 - - + -
337A TRP* 3.8 16.4 - - + +
340A GLU* 4.0 24.0 - - + +
341A LEU* 3.6 30.1 - - + -
344A LEU* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.4 34.5 - - + -
253A TYR 3.3 2.4 + - - -
254A GLY 3.2 6.9 + - - +
255A LEU 3.2 0.4 - - - -
256A LEU* 1.3 79.8 - - - +
258A ALA* 1.3 62.9 + - - +
260A LEU* 3.0 6.1 + - - +
261A LEU* 3.0 42.4 + - + +
291A PHE* 4.4 3.8 - - - -
294A LEU* 5.3 3.0 - - + +
311A TRP* 3.5 35.6 - + - -
330A LEU* 2.9 37.9 + - - +
333A ALA* 3.7 10.5 - - + -
334A PHE* 3.4 37.0 - + + +
337A TRP* 3.6 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.8 17.7 - - + -
230A GLY* 4.6 4.3 - - - +
254A GLY 2.9 16.4 + - - +
255A LEU* 3.6 8.1 - - - +
256A LEU 3.3 0.2 - - - -
257A TYR* 1.3 77.0 - - - +
259A ALA* 1.3 57.2 + - - +
261A LEU* 3.1 15.0 + - - +
262A GLY 2.9 24.4 + - - -
312A VAL 4.1 5.4 - - - +
314A PRO* 3.4 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU 2.9 17.0 + - - +
256A LEU 3.4 6.7 - - - +
258A ALA* 1.3 78.2 - - - +
260A LEU* 1.3 56.0 + - - +
262A GLY* 3.3 1.8 + - - -
263A ARG* 3.0 27.4 + - - +
268A GLU 5.5 0.7 - - - +
270A LEU* 4.2 24.1 + - + +
271A LEU* 3.8 25.0 - - + +
274A VAL* 4.3 8.3 - - + -
314A PRO* 4.2 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.0 24.2 + - + +
257A TYR* 3.0 7.6 + - - +
259A ALA* 1.3 73.2 - - - +
261A LEU* 1.3 66.0 + - - +
263A ARG* 3.3 38.7 + - - +
264A ALA* 3.1 23.4 + - - +
271A LEU* 3.6 22.4 - - + -
333A ALA* 3.9 18.3 - - + +
336A ALA* 4.0 7.2 - - + +
337A TRP* 3.4 47.8 - - + +
340A GLU* 4.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 3.0 41.0 + - + +
258A ALA* 3.1 13.9 + - + +
260A LEU* 1.3 76.5 - - - +
262A GLY* 1.3 64.1 + - - +
264A ALA* 3.3 2.9 + - - +
265A LEU* 3.1 27.7 + - - +
311A TRP* 4.0 19.1 - - + -
312A VAL 5.4 1.3 - - - +
313A VAL* 4.0 15.3 - - + -
325A LEU* 3.9 22.0 - - + -
329A LEU* 3.5 28.4 - - + +
330A LEU* 3.9 10.3 - - + -
333A ALA* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA 2.9 11.8 + - - -
259A ALA 3.3 2.7 + - - -
261A LEU* 1.3 78.2 - - - +
263A ARG* 1.3 59.1 + - - +
265A LEU* 3.2 8.1 + - - +
267A GLY* 2.8 29.0 + - - -
268A GLU 5.2 1.3 - - - -
313A VAL* 3.5 20.1 - - - +
314A PRO 3.7 16.2 - - - -
315A LEU* 4.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA 3.0 16.3 + - - +
260A LEU* 3.6 33.3 + - - +
262A GLY* 1.3 76.4 - - - +
264A ALA* 1.3 63.1 + - - +
266A GLY* 3.0 14.9 + - - -
267A GLY 4.3 12.8 - - - +
268A GLU 5.0 3.7 + - - +
269A ASP* 4.7 11.7 - - + +
271A LEU* 4.3 19.0 - - + +
275A ARG* 5.1 4.0 - - - +
336A ALA* 4.3 15.4 - - - +
340A GLU* 4.6 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 3.1 16.8 + - - +
261A LEU 3.7 5.4 - - - +
262A GLY 3.3 0.2 - - - -
263A ARG* 1.3 78.8 - - - +
265A LEU* 1.3 59.5 + - - +
266A GLY 3.2 3.0 + - - -
329A LEU* 4.3 24.5 - - + +
332A GLU* 6.1 5.4 - - + -
333A ALA* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 3.1 13.6 + - - +
262A GLY 3.8 4.0 - - - +
263A ARG 3.1 0.6 - - - -
264A ALA* 1.3 76.3 - - - +
266A GLY* 1.3 59.6 + - - +
267A GLY 3.4 1.7 + - - -
313A VAL* 4.0 25.6 - - + -
315A LEU* 4.2 14.6 - - + +
321A VAL* 5.2 1.8 - - + -
323A ARG* 3.9 28.7 - - - +
325A LEU* 3.7 21.8 - - + -
329A LEU* 3.4 30.3 - - + -
----------------------------------------------------------
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