Contacts of the helix formed by residues 272 - 282 (chain B) in PDB entry 2CUY
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 GLU 272 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.5 33.9 + - + +
15A GLY* 3.7 4.0 - - - -
18A ARG* 2.6 43.9 + - - -
46A TRP 3.6 1.9 - - - +
50A GLU* 5.2 1.2 + - - -
267B GLU* 3.4 5.6 - - - -
271B GLY* 1.3 77.3 - - - +
273B VAL* 1.3 66.1 + - - +
275B LYS* 3.0 32.3 + - - +
276B GLY* 2.9 19.4 + - - -
289B SER* 3.4 16.2 + - - +
291B GLN* 3.6 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 5.7 0.2 - - - -
50A GLU* 4.0 41.2 + - + +
9B GLN 6.2 0.7 - - - +
10B GLY 4.6 4.3 - - - +
11B SER* 3.1 33.4 - - - +
267B GLU* 3.4 2.6 + - - +
271B GLY* 5.2 1.1 - - - -
272B GLU* 1.3 77.9 - - - +
274B LEU* 1.3 70.7 + - + +
276B GLY* 2.9 13.3 + - - +
277B LEU* 3.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.7 19.3 - - + -
6B PHE 3.4 35.7 - - - +
7B PRO* 3.7 7.2 - - + -
8B GLY 5.5 0.2 - - - +
88B HIS* 3.9 18.4 - - + -
250B TRP* 3.7 42.1 + - + +
267B GLU* 2.8 24.7 + - + +
273B VAL* 1.3 79.8 - - + +
275B LYS* 1.3 57.3 + - - +
277B LEU* 3.1 17.1 + - + +
278B VAL* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.2 0.6 - - - +
18A ARG* 3.9 4.2 - - - +
46A TRP 3.3 17.0 + - - -
47A GLU* 4.0 15.2 - - - +
5B LEU* 6.1 0.2 - - - -
267B GLU* 2.8 18.9 + - + +
272B GLU* 3.0 52.2 + - - +
274B LEU* 1.3 75.6 - - - +
276B GLY* 1.3 62.2 + - - +
278B VAL* 3.2 8.3 + - - +
279B LEU* 3.0 39.4 + - + +
287B ALA* 3.9 35.7 - - + +
288B LEU* 4.3 5.8 - - - -
289B SER* 3.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 6.0 0.7 - - - -
47A GLU 3.7 23.8 - - - +
48A GLY* 5.6 0.2 - - - -
49A PRO* 5.2 8.4 - - - +
50A GLU 5.8 0.9 - - - -
160B GLN* 4.8 2.0 + - - -
272B GLU 2.9 12.7 + - - -
273B VAL* 2.9 5.8 + - - -
275B LYS* 1.3 80.3 - - - +
277B LEU* 1.3 62.7 + - - +
279B LEU* 3.6 5.7 + - - +
280B ARG* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 5.2 2.2 - - + -
88B HIS* 4.6 3.6 - - + +
156B ASN* 3.7 44.9 - - + +
157B ALA* 4.3 0.7 - - + -
160B GLN* 3.7 33.0 - - - +
250B TRP* 3.8 21.5 - - + +
254B LEU* 4.3 1.3 - - - -
273B VAL* 3.1 22.6 + - + +
274B LEU* 3.1 22.6 + - + +
276B GLY* 1.3 77.0 - - - +
278B VAL* 1.3 64.1 + - - +
280B ARG* 3.6 2.5 + - - +
281B THR* 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.6 27.1 - - + -
250B TRP* 5.2 0.4 - - - +
254B LEU* 3.9 22.4 - - + -
265B PHE* 4.0 26.5 - - + -
274B LEU 2.8 18.9 + - - +
275B LYS* 3.2 8.9 + - - +
277B LEU* 1.3 78.1 - - - +
279B LEU* 1.3 56.7 + - + +
282B LEU* 2.7 43.7 + - + +
285B ALA* 4.7 7.2 - - + -
286B GLU 5.3 0.2 - - - -
287B ALA* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.7 48.0 - - + +
275B LYS* 3.0 36.6 + - + +
276B GLY 3.8 3.6 - - - +
277B LEU 3.3 0.2 - - - -
278B VAL* 1.3 79.8 - - + +
280B ARG* 1.3 69.4 + - - +
281B THR 3.1 1.6 + - - -
282B LEU 3.4 15.8 + - - +
283B LYS* 4.4 6.1 - - - +
285B ALA 4.8 13.5 - - - +
287B ALA* 4.7 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.1 36.4 - - - +
47A GLU* 5.1 3.6 + - - -
49A PRO* 4.4 20.2 - - + +
157B ALA* 4.4 6.5 - - + -
158B PRO* 3.5 15.9 - - + +
159B GLU* 5.9 3.4 - - + +
160B GLN* 4.0 22.0 - - + +
276B GLY 3.2 14.9 + - - +
277B LEU 4.2 2.7 - - - +
279B LEU* 1.3 84.7 + - - +
281B THR* 1.3 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASN 3.7 3.8 + - - -
157B ALA* 3.6 9.7 - - - -
158B PRO* 3.4 23.0 - - + +
251B VAL* 4.5 10.3 - - + -
254B LEU* 3.8 24.6 - - + +
255B ARG* 3.5 35.9 + - - +
277B LEU 2.7 22.1 + - - -
280B ARG* 1.3 79.7 - - - +
282B LEU* 1.3 73.9 + - + +
283B LYS* 4.2 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.3 37.0 - - + +
255B ARG* 3.7 31.2 - - - +
258B GLU* 4.0 26.0 - - + -
265B PHE* 3.9 22.7 - - + -
278B VAL* 2.7 27.9 + - + +
279B LEU* 3.4 10.3 - - - +
281B THR* 1.3 89.8 - - + +
283B LYS* 1.4 62.3 + - - +
284B GLU 3.7 1.1 - - - +
285B ALA* 3.9 22.6 + - + +
----------------------------------------------------------
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