Contacts of the helix formed by residues 246 - 250 (chain J) in PDB entry 6C6U
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 PRO 246 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328I LYS* 4.3 9.0 - - + -
62J PHE* 4.5 0.4 - - + -
98J ARG 3.9 0.7 - - - +
99J ARG* 3.6 31.2 - - - +
100J GLU 4.2 2.7 - - - -
101J ARG 3.3 25.6 - - - +
102J MET* 3.8 19.7 - - + -
245J LEU* 1.3 101.8 - - + +
247J PRO* 1.3 72.8 - - + +
248J ASP 3.3 0.7 - - - -
249J LEU* 3.1 25.2 + - + +
250J ARG* 3.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 247 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J LEU 4.5 2.0 - - - +
57J PHE* 3.8 22.0 - - + -
58J CYS 5.2 0.2 - - - +
62J PHE* 3.5 47.1 - - + -
98J ARG* 3.3 42.3 + - - +
246J PRO* 1.3 80.7 - - + +
248J ASP* 1.3 64.0 + - - +
250J ARG* 3.6 35.7 + - - +
251J PRO* 4.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253I LEU* 4.1 13.2 - - + +
1254I VAL* 4.0 14.0 - - - -
95J THR* 3.8 8.0 + - - +
96J LYS* 5.0 0.5 - - - -
98J ARG* 3.2 51.6 + - - +
99J ARG* 3.2 32.4 + - + +
246J PRO 3.3 0.8 - - - -
247J PRO* 1.3 77.6 - - - +
249J LEU* 1.3 62.5 + - - +
250J ARG 3.5 0.5 + - - -
251J PRO* 3.9 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254I VAL* 3.6 37.6 - - + +
1325I VAL* 3.7 29.8 - - + -
1328I LYS* 3.7 32.8 - - + -
1329I GLU* 5.1 1.7 - - - +
99J ARG* 3.8 35.4 - - + +
245J LEU* 4.0 20.2 - - + +
246J PRO* 3.1 20.7 + - + +
248J ASP* 1.3 80.7 - - - +
250J ARG* 1.3 58.5 + - - +
251J PRO* 3.6 4.8 - - - +
265J LEU* 4.7 2.9 - - - +
330J MET* 4.7 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J VAL* 5.8 0.2 - - - +
56J LEU* 3.1 57.9 + - - +
57J PHE* 3.8 9.3 - - + +
62J PHE* 4.0 8.1 - - - -
244J VAL* 4.6 9.7 - - - +
245J LEU* 3.3 34.0 + - + -
246J PRO 3.4 9.4 - - - +
247J PRO* 3.6 26.5 - - - +
248J ASP 3.2 0.2 - - - -
249J LEU* 1.3 78.5 - - - +
251J PRO* 1.3 67.5 - - - +
252J LEU 3.7 0.3 + - - -
263J SER* 5.1 5.6 - - - +
265J LEU* 3.9 25.8 - - + -
266J ASN* 3.3 31.6 + - - +
269J TYR* 4.2 19.9 - - - -
----------------------------------------------------------
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