Contacts of the helix formed by residues 225 - 230 (chain V) in PDB entry 3FKS
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 225 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302U TYR* 3.4 25.7 - - + +
19V ALA* 5.2 8.7 - - + -
63V ALA 4.9 3.8 - - - +
64V MET 3.4 27.8 - - - +
65V ASP* 3.5 26.0 - - - +
66V GLY* 4.6 3.4 - - - +
223V ASN 4.4 1.1 - - - +
224V GLU* 1.3 92.3 - - + +
226V PRO* 1.3 78.3 - - + +
227V GLY 4.5 3.6 - - - +
228V ALA* 3.1 12.6 + - + +
229V ARG* 3.2 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 226 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299U ASP* 5.1 3.1 - - + -
302U TYR* 4.1 20.9 - - + -
19V ALA* 5.1 7.4 - - + -
225V PRO* 1.3 86.5 - - + +
227V GLY* 1.3 64.3 + - - +
229V ARG* 2.9 16.4 + - - +
230V ALA* 2.9 26.2 + - - +
264V ALA* 3.9 3.1 - - + +
267V GLU* 3.3 37.2 - - + +
268V VAL* 3.7 20.6 - - + +
271V LEU* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 227 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62V ILE* 3.7 18.6 - - - +
63V ALA 3.2 23.7 + - - -
64V MET* 3.4 6.5 - - - +
225V PRO* 3.3 1.2 - - - +
226V PRO* 1.3 81.3 - - - +
228V ALA* 1.3 56.5 - - - +
230V ALA* 4.0 2.2 + - - +
231V ARG* 3.2 29.8 + - - +
268V VAL* 3.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63V ALA 3.9 3.0 + - - -
64V MET* 3.1 34.8 - - - +
98V VAL* 3.8 12.8 - - + +
224V GLU* 3.9 23.8 - - + +
225V PRO* 3.1 9.9 + - + +
226V PRO 3.0 0.6 - - - -
227V GLY* 1.3 77.2 - - - +
229V ARG* 1.3 59.8 + - - +
230V ALA 3.3 0.4 - - - -
231V ARG 3.2 1.4 + - - -
232V VAL* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301U PHE* 3.2 29.6 - - - -
302U TYR* 5.0 3.8 - - - +
187V VAL* 3.5 12.6 - - + +
188V GLY* 4.3 11.9 - - - +
220V GLY 3.8 20.0 - - - +
221V GLN 3.8 3.1 - - - +
222V MET* 3.7 26.3 + - - +
224V GLU* 3.2 27.3 + - + +
225V PRO 3.2 1.6 + - - +
226V PRO* 2.9 23.6 + - - +
228V ALA* 1.3 79.3 - - - +
230V ALA* 1.3 58.3 + - - +
231V ARG 3.2 1.1 - - - -
232V VAL* 3.3 20.6 + - + +
233V ALA 4.6 0.7 + - - -
260V ARG* 4.6 8.5 + - - +
261V PHE* 4.5 3.5 - - - -
263V GLN* 4.6 4.8 + - - +
264V ALA* 3.7 25.0 - - + +
267V GLU* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226V PRO 2.9 15.3 + - - +
227V GLY* 4.5 4.0 - - - +
228V ALA 3.3 0.2 - - - -
229V ARG* 1.3 76.7 - - - +
231V ARG* 1.3 80.0 + - + +
233V ALA 4.9 0.4 + - - -
234V LEU* 4.4 3.1 - - - +
261V PHE* 3.6 27.8 - - + +
264V ALA* 3.5 26.2 - - + +
265V GLY* 4.1 8.3 - - - +
268V VAL* 4.9 8.3 - - + -
----------------------------------------------------------
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