Contacts of the helix formed by residues 245 - 249 (chain B) in PDB entry 6DC0
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 CYS 245 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A HIS 5.2 1.3 - - - -
501A GLU* 4.0 20.6 - - - -
502A THR 3.5 21.1 - - - +
503A SER* 3.3 11.7 + - - +
205B ASP* 3.8 2.8 + - - +
206B LEU 5.8 0.2 + - - -
207B LYS* 4.1 11.2 - - + -
244B GLY* 1.3 71.2 - - - -
246B PRO* 1.4 72.2 - - - +
247B ALA* 4.1 8.3 - - - -
248B TYR* 3.0 47.4 + - + +
249B VAL* 3.6 8.3 - - - +
282B TYR* 5.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A THR* 3.7 13.5 - - + +
504A ILE* 3.9 26.7 - - + -
244B GLY 3.7 5.4 - - - +
245B CYS* 1.4 86.5 - - - +
247B ALA* 1.3 63.4 + - - +
248B TYR 3.1 1.4 + - - -
249B VAL* 3.1 15.8 + - + +
289B PRO* 4.3 12.1 - - + -
292B LEU* 4.1 17.3 - - + -
293B PHE* 3.7 27.4 - - + -
296B ILE* 3.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B CYS* 3.2 5.5 + - - -
246B PRO* 1.3 79.2 - - - +
248B TYR* 1.3 62.7 + - + +
249B VAL 3.7 0.9 + - - +
268B TRP* 4.9 0.5 + - - -
272B VAL* 3.6 17.2 - - - +
282B TYR* 3.6 49.8 - - + -
283B PRO* 5.4 0.5 - - - +
284B PHE* 4.3 12.8 - - - +
292B LEU* 4.0 16.6 - - + +
296B ILE* 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A GLU* 2.3 36.8 + - - -
206B LEU 3.4 21.5 - - - +
207B LYS* 3.5 24.5 - - + -
208B LEU* 3.3 22.5 + - - +
245B CYS* 3.0 30.3 + - + +
247B ALA* 1.3 77.1 - - - +
249B VAL* 1.3 62.0 + - - +
250B SER 3.6 0.5 + - - -
265B ALA 5.0 0.3 - - - +
268B TRP* 3.5 11.5 - - - -
269B SER* 3.0 28.4 + - - +
272B VAL* 3.5 28.7 - - + -
273B MET* 3.8 17.3 - - + -
282B TYR* 3.4 20.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ILE* 4.0 22.2 - - + -
243B HIS 5.9 0.4 - - - -
244B GLY* 4.6 6.1 - - - -
245B CYS 3.6 16.4 - - - +
246B PRO* 3.1 18.6 + - + +
247B ALA 3.5 0.2 - - - -
248B TYR* 1.3 76.9 - - - +
250B SER* 1.3 74.6 + - - +
253B ILE* 3.6 30.7 - - + -
254B LEU* 3.9 16.2 - - + -
268B TRP* 3.3 9.9 + - - -
293B PHE* 4.5 6.7 - - + -
296B ILE* 3.5 21.2 - - + +
----------------------------------------------------------
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