Contacts of the helix formed by residues 264 - 276 (chain C) in PDB entry 3HH2
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 264 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PRO* 5.9 0.5 - - - +
252C GLU* 3.7 20.7 + - - -
254C VAL* 3.9 6.5 - - - +
262C TYR* 3.1 6.4 + - - +
263C ALA* 1.3 84.8 - - - +
265C GLU* 1.3 63.5 + - - +
266C CYS* 2.9 26.2 + - - +
267C ALA* 3.2 12.3 + - - +
268C MET* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLU* 4.6 4.3 + - - +
254C VAL* 3.7 15.9 - - + +
264C SER* 1.3 74.8 + - - +
266C CYS* 1.3 62.4 + - - +
268C MET* 3.3 15.7 + - + +
269C LYS* 3.1 41.5 + - + +
281C VAL* 3.6 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLU* 5.7 5.6 - - - -
244C LEU 4.2 4.9 - - - -
245C CYS* 2.0 64.6 - - + -
246C PRO* 4.3 8.5 - - + -
264C SER* 2.9 11.1 + - - +
265C GLU* 1.3 78.6 - - - +
267C ALA* 1.3 62.5 + - - +
269C LYS* 3.4 14.0 + - - +
270C GLU 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C CYS* 4.0 4.2 - - + -
262C TYR* 4.2 7.4 - - + -
263C ALA* 4.4 13.0 - - + +
264C SER* 3.2 23.4 + - - +
266C CYS* 1.3 76.6 - - - +
268C MET* 1.3 66.0 + - - +
270C GLU* 3.3 9.3 + - - +
271C ALA* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C VAL* 4.4 3.1 - - + -
256C ALA* 3.7 19.1 - - + -
262C TYR* 3.9 20.3 - - + +
264C SER 3.1 11.7 + - - +
265C GLU* 3.4 23.1 - - + +
266C CYS 3.2 0.2 - - - -
267C ALA* 1.3 78.0 - - - +
269C LYS* 1.3 70.8 + - + +
271C ALA* 3.1 4.5 + - - +
272C ALA* 2.8 27.4 + - - +
279C LEU* 3.6 36.8 - - + +
280C GLU* 3.6 25.1 - - - +
281C VAL* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 4.5 17.9 - - - +
265C GLU* 3.1 35.7 + - + +
266C CYS* 3.6 16.2 - - - +
267C ALA 3.3 0.2 - - - -
268C MET* 1.3 92.2 - - + +
270C GLU* 1.3 56.4 + - - +
272C ALA* 3.4 7.9 + - - +
273C CYS* 2.9 37.6 + - - +
279C LEU 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C CYS* 4.9 7.4 - - - -
266C CYS 3.1 13.3 + - - +
267C ALA* 3.5 12.6 - - - +
268C MET 3.2 0.6 - - - -
269C LYS* 1.3 76.3 - - - +
271C ALA* 1.3 57.5 + - - +
273C CYS* 3.4 6.4 + - - +
274C SER* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C TYR* 3.5 34.1 - - + +
267C ALA 3.0 9.8 + - - +
268C MET 3.5 7.0 - - - +
270C GLU* 1.3 75.4 - - - +
272C ALA* 1.3 57.1 + - - +
274C SER* 3.8 6.4 - - - -
275C SER* 2.7 36.3 + - - -
279C LEU* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 3.3 15.2 - - + +
268C MET 2.8 12.7 + - - +
269C LYS* 3.6 12.3 - - - +
271C ALA* 1.3 76.0 - - - +
273C CYS* 1.3 59.3 + - - +
275C SER* 3.8 1.8 - - - -
276C GLY 2.9 26.2 + - - -
277C VAL 3.1 28.9 + - - +
278C LEU* 5.8 0.2 - - + -
279C LEU* 4.0 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LYS* 2.8 32.4 + - - +
228C LEU* 3.8 12.8 - - - -
239C SER* 5.2 1.1 - - - -
241C CYS* 2.0 58.1 - - + +
269C LYS* 2.9 26.5 + - - +
270C GLU* 3.6 6.7 - - - +
272C ALA* 1.3 78.4 - - - +
274C SER* 1.3 57.8 + - - +
275C SER 3.4 0.3 + - - -
276C GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LYS* 3.1 15.5 + - - +
270C GLU 2.8 21.4 + - - -
271C ALA* 3.8 7.4 - - - -
272C ALA 3.3 0.2 - - - -
273C CYS* 1.3 74.1 - - - +
275C SER* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LYS* 4.7 1.3 - - - -
271C ALA 2.7 22.4 + - - -
272C ALA* 3.3 6.2 + - - -
274C SER* 1.3 77.0 - - - +
276C GLY* 1.3 61.3 + - - +
277C VAL* 3.4 26.7 + - - +
279C LEU* 5.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C CYS* 4.4 3.0 - - - -
226C LYS* 4.2 10.2 - - - +
227C CYS 3.6 16.7 - - - +
228C LEU* 3.5 7.3 - - - -
229C TRP* 2.8 28.0 + - - +
272C ALA 2.9 7.7 + - - -
273C CYS 3.7 1.8 + - - -
274C SER 3.5 2.8 + - - -
275C SER* 1.3 77.9 - - - +
277C VAL* 1.3 59.7 + - - +
----------------------------------------------------------
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