Contacts of the helix formed by residues 236 - 245 (chain H) in PDB entry 6V96
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 ASP 236 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H ASP* 3.6 10.1 - - - +
228H THR 4.2 2.8 - - - +
229H SER* 3.2 29.2 - - - +
230H SER* 2.6 39.6 + - - -
231H ARG 3.0 1.2 + - - -
232H ASP* 2.8 29.4 + - - +
234H GLY 3.5 0.4 - - - -
235H LYS* 1.3 81.1 - - - +
237H ILE* 1.3 65.9 + - - +
238H ILE 3.5 1.1 - - - -
239H PRO* 3.4 2.6 - - - +
240H TYR* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H ALA* 3.7 15.3 - - + -
211H PHE* 4.4 5.6 - - + -
216H LEU* 4.8 2.0 - - + -
219H ALA* 4.2 20.9 - - + +
220H LEU* 4.3 6.5 - - + -
223H ASP* 3.5 39.7 - - + +
232H ASP 3.2 13.0 + - - +
233H PHE* 3.4 35.0 + - + +
236H ASP* 1.3 76.4 - - - +
238H ILE* 1.3 66.4 + - + +
240H TYR* 3.4 4.6 + - - +
241H ILE* 3.2 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H VAL* 4.4 7.9 - - + -
158H ILE* 3.6 34.1 - - + -
174H MET* 4.0 16.6 - - + -
185H PHE* 5.0 3.1 - - + -
209H TYR* 3.7 28.7 - - + -
211H PHE* 4.0 24.0 - - + -
233H PHE* 3.1 24.0 + - + +
234H GLY* 4.4 4.3 - - - +
237H ILE* 1.3 78.4 - - - +
239H PRO* 1.3 75.1 - - + +
241H ILE* 3.0 7.6 + - - +
242H VAL* 2.8 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 239 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H PHE* 3.8 19.3 - - + -
234H GLY 3.2 27.1 - - - +
235H LYS* 3.4 18.4 - - - +
236H ASP 3.4 13.7 - - - +
238H ILE* 1.3 90.2 - - + +
240H TYR* 1.3 62.7 + - - +
242H VAL* 3.1 15.1 - - + +
243H GLU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H ALA* 6.3 0.7 - - + -
222H ARG* 4.0 38.5 - - + +
226H ASP* 5.8 4.7 - - - -
236H ASP 3.1 20.2 + - - +
237H ILE* 3.7 4.9 - - - +
238H ILE 3.2 0.2 - - - -
239H PRO* 1.3 75.6 - - - +
241H ILE* 1.3 63.1 + - + +
243H GLU* 3.3 10.0 + - - +
244H HIS* 3.0 65.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ASP* 3.6 26.9 - - + -
156H VAL* 3.8 21.5 - - + -
211H PHE* 3.7 29.6 - - + -
215H PHE* 3.8 22.4 - - + -
219H ALA* 5.1 2.9 - - + -
222H ARG* 5.4 2.0 - - - +
237H ILE* 3.2 25.9 + - + +
238H ILE* 3.0 7.7 + - - +
240H TYR* 1.3 81.4 - - + +
242H VAL* 1.3 62.8 + - - +
243H GLU 3.0 1.6 - - - -
244H HIS* 5.4 0.2 - - - -
245H GLY* 2.6 38.9 + - - +
246H LYS 4.1 9.2 - - - +
247H ALA 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H ILE* 4.0 35.2 - - + +
183H ILE* 4.8 7.6 - - - +
184H ASP* 4.9 5.4 - - - +
185H PHE* 4.7 18.4 - - + +
238H ILE* 2.8 34.9 + - + +
239H PRO* 3.1 24.5 - - + +
241H ILE* 1.3 72.1 - - - +
243H GLU* 1.3 61.6 + - + +
245H GLY 4.2 6.0 - - - +
247H ALA* 3.4 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H PRO 3.0 17.4 + - - +
240H TYR* 3.4 9.5 - - - +
242H VAL* 1.3 82.7 - - + +
244H HIS* 1.3 99.0 + - + +
245H GLY 4.0 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 244 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H TYR* 3.0 57.7 + + + +
241H ILE* 5.4 0.2 - - - -
243H GLU* 1.3 114.2 + - + +
245H GLY* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 245 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ASP* 3.3 11.4 - - - -
215H PHE* 6.3 0.4 - - - -
241H ILE* 2.6 28.8 + - - +
242H VAL* 4.2 7.3 - - - +
243H GLU 4.6 1.0 - - - +
244H HIS* 1.3 76.5 - - - +
246H LYS* 1.3 59.3 + - - -
247H ALA 4.1 0.7 + - - -
----------------------------------------------------------
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