Contacts of the helix formed by residues 253 - 270 (chain A) in PDB entry 3U86
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 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.6 27.5 + - - +
52A ARG* 5.7 0.3 - - - -
245A PRO* 2.6 18.6 + - - +
247A ILE* 4.0 10.7 - - - +
252A ASP* 1.3 68.5 - - - +
254A LEU* 1.3 66.2 + - - +
255A GLU* 3.8 14.3 + - - +
256A LEU* 3.6 28.7 + - - +
257A LEU* 3.1 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 3.5 34.5 - - + -
70A ASP* 5.1 4.9 - - - +
252A ASP 3.4 5.9 + - - +
253A SER* 1.3 72.4 + - - +
255A GLU* 1.3 73.9 + - - +
257A LEU* 3.4 14.2 + - + -
258A GLN* 3.1 49.0 + - + +
290A GLU* 5.3 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.6 27.8 - - + +
48A LEU* 3.9 27.8 - - + -
52A ARG* 6.0 0.2 + - - -
69A PRO* 5.1 2.8 - - - +
76A THR* 3.0 30.4 + - - +
77A TYR 5.6 1.1 - - - +
78A PHE* 4.8 7.8 - - + -
253A SER* 3.8 12.4 + - - +
254A LEU* 1.3 95.3 + - - +
256A LEU* 1.3 60.0 + - - +
258A GLN* 4.4 2.8 - - - +
259A LEU* 2.8 32.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
41A LEU 5.6 0.4 - - - +
44A VAL* 4.4 9.2 - - + -
45A GLU* 3.9 26.9 - - + +
48A LEU* 4.0 22.0 - - + -
49A ALA* 3.9 22.4 - - + -
243A ILE* 4.1 17.0 - - + +
244A ASN 3.8 21.1 - - - +
245A PRO* 3.7 19.0 - - + +
253A SER* 3.2 24.3 + - - +
255A GLU* 1.3 77.1 - - - +
257A LEU* 1.3 57.7 + - - +
259A LEU* 4.0 13.3 - - + +
260A GLN* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO* 3.4 27.4 - - + -
252A ASP* 4.2 20.9 - - + +
253A SER 3.1 16.1 + - - +
254A LEU* 3.7 18.4 - - + +
255A GLU 3.1 0.2 - - - -
256A LEU* 1.3 77.1 - - - +
258A GLN* 1.3 59.6 + - - +
260A GLN* 3.5 2.9 + - - +
261A GLN* 2.9 34.5 + - - +
286A LEU* 3.5 30.9 - - + +
289A LEU* 4.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.6 22.4 - - + +
69A PRO* 4.8 4.9 - - - +
254A LEU* 3.1 48.6 + - + +
255A GLU* 3.7 6.3 - - - +
257A LEU* 1.3 75.2 - - + +
259A LEU* 1.3 60.2 + - - +
261A GLN* 3.1 11.2 + - - +
262A LYS* 2.8 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.6 29.1 - - + +
19A VAL* 4.0 25.8 - - + -
20A VAL* 4.4 1.1 - - + -
41A LEU* 4.3 22.4 - - + -
44A VAL* 4.5 21.5 - - + -
78A PHE* 5.8 2.5 - - + -
243A ILE* 4.5 7.9 - - + -
255A GLU 2.8 21.2 + - - +
256A LEU* 4.1 13.7 - - + +
258A GLN* 1.3 74.5 - - - +
260A GLN* 1.3 57.0 + - - +
262A LYS* 3.9 0.9 - - - +
263A LEU* 3.0 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 2.7 36.0 + - - +
241A CYS* 3.2 25.1 + - - +
243A ILE* 3.5 20.6 + - + +
245A PRO* 3.8 19.4 - - - +
256A LEU 3.3 15.8 + - - +
257A LEU 3.9 3.1 - - - +
258A GLN 3.3 0.4 - - - -
259A LEU* 1.3 79.6 - - - +
261A GLN* 1.3 58.5 + - - +
264A LEU* 3.0 41.2 + - + +
282A ASN* 3.7 14.5 + - - -
286A LEU* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 2.9 21.0 + - - +
258A GLN* 3.4 11.9 - - - +
260A GLN* 1.3 74.4 - - - +
262A LYS* 1.3 68.1 + - + +
264A LEU* 3.0 5.9 + - - +
265A TRP* 3.0 32.0 + - + +
283A LEU* 4.3 2.6 - - + +
286A LEU* 4.0 32.9 + - + +
287A GLU* 3.1 29.7 + - - +
290A GLU* 3.0 32.3 + - - +
292A THR* 3.5 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.0 24.9 - - + -
17A ASP* 4.0 23.2 + - - +
20A VAL* 4.0 19.6 - - + +
258A GLN* 2.8 37.6 + - - +
259A LEU 4.0 2.7 - - - +
261A GLN* 1.3 75.6 - - + +
263A LEU* 1.3 58.2 + - - +
265A TRP* 3.3 9.3 + - - +
266A LEU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.7 42.2 - - + -
23A PHE* 4.1 37.0 - - + -
41A LEU* 4.5 10.5 - - + -
240A VAL* 3.5 27.4 - - + -
243A ILE* 4.5 2.9 - - + -
259A LEU* 3.0 42.1 + - + +
262A LYS* 1.3 76.9 - - - +
264A LEU* 1.3 60.8 + - - +
266A LEU* 3.5 6.6 - - + +
267A LEU* 3.2 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA 4.9 1.1 - - - +
240A VAL* 3.9 18.2 - - + -
241A CYS* 4.5 14.4 - - - -
260A GLN* 3.0 31.2 + - + +
261A GLN 3.0 4.0 + - - +
263A LEU* 1.3 77.1 - - - +
265A TRP* 1.3 60.5 + - - +
267A LEU* 3.2 12.9 + - + +
268A TYR 2.8 25.5 + - - -
273A LEU* 3.4 13.4 - - + +
279A ALA* 4.4 18.8 - - + +
282A ASN* 4.2 7.6 - - - +
283A LEU* 3.9 34.8 - - + +
286A LEU* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN* 3.0 27.0 + - + -
262A LYS* 3.7 9.4 - - - +
264A LEU* 1.3 73.8 - - - +
266A LEU* 1.3 67.3 + - - +
268A TYR* 3.0 42.5 + + + +
269A ASP* 2.9 29.7 + - - -
283A LEU* 3.9 18.1 - - + +
287A GLU* 2.6 41.8 + - + -
292A THR* 3.5 14.2 - - + +
295A ARG* 3.4 53.8 - - + +
296A PRO* 4.0 20.2 - - + -
301A LEU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.0 20.0 - - + +
23A PHE* 3.9 17.0 - - + -
24A ALA* 3.6 45.5 - - + +
27A LEU* 4.2 13.5 - - + -
262A LYS 2.9 14.2 + - - +
263A LEU* 3.5 13.9 - - + +
265A TRP* 1.3 76.5 - - - +
267A LEU* 1.3 63.3 + - + +
269A ASP* 3.5 6.9 + - + +
270A LEU* 3.3 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 6.3 0.7 - - + -
27A LEU* 3.7 27.1 - - + -
233A LYS 4.3 13.5 - - - +
236A VAL* 4.5 5.8 - - + -
237A ALA* 3.7 27.8 - - + -
240A VAL* 3.9 19.5 - - + -
263A LEU 3.2 17.4 + - - +
264A LEU* 3.2 8.6 + - + +
265A TRP 3.1 0.8 - - - -
266A LEU* 1.3 75.3 - - + +
268A TYR* 1.3 67.5 + - - +
270A LEU* 3.2 7.4 + - - -
272A HIS* 3.0 46.1 + - + +
273A LEU* 3.4 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 2.8 16.7 + - - +
265A TRP* 3.3 39.0 - + + +
267A LEU* 1.3 71.3 - - - +
269A ASP* 1.3 80.8 + - - +
271A GLY* 2.8 23.4 + - - -
273A LEU* 3.6 18.4 + - + +
280A LEU* 4.4 18.4 - - + -
283A LEU* 4.5 0.7 - - + -
295A ARG* 4.4 2.2 - - - -
296A PRO* 5.0 9.1 - - + +
301A LEU* 4.6 6.3 - - + -
304A LYS* 3.3 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TRP 2.9 18.0 + - - +
266A LEU* 3.7 6.5 - - - +
268A TYR* 1.3 88.8 - - - +
270A LEU* 1.3 66.1 + - + +
271A GLY* 3.0 5.5 + - - -
295A ARG* 3.2 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.4 4.5 - - + +
27A LEU* 4.2 28.0 - - + +
28A GLY* 6.3 0.4 - - - -
266A LEU* 3.3 27.1 + - + +
267A LEU 3.2 3.9 + - - +
269A ASP* 1.3 79.3 - - + +
271A GLY* 1.3 61.6 + - - +
272A HIS* 3.2 42.1 + - + +
----------------------------------------------------------
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