Contacts of the helix formed by residues 236 - 249 (chain C) in PDB entry 6AH0
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 MET 236 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C HIS* 6.2 1.3 - - - +
234C GLY 3.4 4.1 + - - -
235C VAL* 1.3 74.3 - - - +
237C LEU* 1.3 69.0 + - - +
238C ASN 3.2 2.5 - - - -
239C THR* 2.6 22.8 + - - +
240C GLU 3.3 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C MET* 1.3 69.8 - - - +
238C ASN* 1.3 60.7 + - - +
240C GLU* 3.2 10.7 + - - -
241C ARG* 3.2 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLY* 5.6 1.3 - - - -
137C HIS* 4.9 13.2 - - - +
207C GLY 5.6 4.5 - - - -
236C MET 2.8 2.4 + - - -
237C LEU* 1.3 71.7 - - - +
239C THR* 1.3 60.2 + - - +
241C ARG* 3.8 2.6 - - - +
242C LEU* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C CYS 5.9 0.9 - - - -
136C GLY* 5.6 2.7 - - - -
137C HIS* 4.6 13.9 - - - +
236C MET* 2.6 20.7 + - - +
238C ASN* 1.3 70.4 - - - +
240C GLU* 1.3 55.1 + - - +
242C LEU* 3.3 2.1 + - - +
243C ILE* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C MET 3.3 5.6 + - - +
237C LEU 3.2 8.2 + - - -
239C THR* 1.3 77.0 - - - +
241C ARG* 1.3 56.4 + - - +
243C ILE* 3.2 2.5 + - - +
244C LYS* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU 3.2 12.1 + - - -
238C ASN* 3.3 3.5 + - - +
239C THR 3.3 0.2 - - - -
240C GLU* 1.3 77.4 - - - +
242C LEU* 1.3 61.4 + - - +
244C LYS* 3.2 2.4 + - - +
245C HIS* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C CYS* 6.0 3.4 - - - +
238C ASN 2.9 15.9 + - - -
239C THR* 3.7 1.6 - - - +
241C ARG* 1.3 77.4 - - - +
243C ILE* 1.3 61.5 + - - +
245C HIS* 3.2 1.8 + - - +
246C ALA* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C THR 2.9 15.3 + - - -
240C GLU* 3.2 2.9 + - - +
242C LEU* 1.3 75.7 - - - +
244C LYS* 1.3 57.7 + - - +
246C ALA* 3.2 2.9 + - - +
247C VAL* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C GLU 2.9 14.3 + - - -
241C ARG* 3.7 3.4 - - - +
243C ILE* 1.3 75.8 - - - +
245C HIS* 1.3 63.6 + - - +
247C VAL* 3.2 2.4 + - - +
248C GLN* 2.9 20.8 + - - -
292C TYR* 6.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ARG 2.9 14.5 + - - -
242C LEU* 3.7 3.4 - - - +
244C LYS* 1.3 75.6 - - - +
246C ALA* 1.3 63.1 + - - +
248C GLN* 3.2 1.8 + - - +
249C GLU* 2.9 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU 2.9 14.0 + - - -
243C ILE* 3.2 3.1 + - - +
245C HIS* 1.3 77.0 - - - +
247C VAL* 1.3 61.9 + - - +
249C GLU* 3.2 2.6 + - - +
250C ARG 3.0 18.7 + - - -
251C LEU* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ILE 2.9 14.5 + - - -
244C LYS* 3.7 2.7 - - - +
246C ALA* 1.3 75.6 - - - +
248C GLN* 1.3 63.6 + - - +
250C ARG* 3.2 13.4 + - - +
251C LEU 5.4 1.1 - - - -
292C TYR* 6.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C LYS 2.9 15.1 + - - -
245C HIS* 3.7 2.7 - - - +
247C VAL* 1.3 77.6 - - - +
249C GLU* 1.3 57.1 + - - +
250C ARG* 3.2 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C HIS 2.9 14.1 + - - -
246C ALA* 3.2 3.1 + - - +
248C GLN* 1.3 75.3 - - - +
250C ARG* 1.3 64.4 + - - +
251C LEU* 3.3 3.7 + - - -
447C PRO 5.6 3.5 - - - +
448C LYS* 5.9 2.1 - - - -
----------------------------------------------------------
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