Contacts of the helix formed by residues 230 - 235 (chain C) in PDB entry 3DLX
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 PHE 230 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLY 4.1 12.3 - - - +
64C PHE* 4.8 3.1 - + - -
90C ASN* 3.3 46.0 - - + -
138C GLN* 3.6 26.0 - - + -
141C LEU* 4.0 12.3 - - + -
142C ALA* 3.7 31.4 - - + -
145C ILE* 4.0 18.6 - - + -
229C ASN* 1.3 82.3 + - + +
231C ASN* 1.3 63.8 + - - +
232C LEU 3.2 2.7 - - - -
233C PRO* 3.3 8.6 - - + +
234C MET* 2.9 48.0 + - + +
382C SER* 3.6 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLY* 3.2 23.4 - - - -
63C GLY 3.8 0.2 - - - +
68C GLY* 2.9 22.1 + - - +
210C VAL* 3.7 8.8 - - + +
211C LYS 3.1 38.4 + - - +
223C PHE* 3.6 11.4 - - + -
227C ALA 2.8 24.7 + - - -
228C ARG 2.8 12.5 + - - +
229C ASN* 3.7 7.5 + - - -
230C PHE* 1.3 78.1 - - - +
232C LEU* 1.3 60.9 + - - +
234C MET* 4.7 1.6 - - - -
235C CYS* 3.3 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 4.0 17.9 - - + -
228C ARG* 3.5 41.2 + - + +
231C ASN* 1.3 80.6 - - - +
233C PRO* 1.4 75.7 - - + +
235C CYS* 3.3 15.2 + - - +
236C LYS* 3.8 25.7 - - - +
260C HIS* 3.5 26.7 - - + +
261C ILE* 3.7 15.3 - - + +
381C SER* 4.1 14.8 - - - +
383C ASP* 4.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ALA 4.4 8.7 - - - +
145C ILE* 3.4 23.7 - - + +
146C ARG* 4.5 8.7 - - + +
229C ASN 3.4 13.7 - - - +
230C PHE* 3.3 27.8 - - + +
232C LEU* 1.4 96.1 - - + +
234C MET* 1.3 60.6 + - - +
235C CYS 3.3 0.7 + - - -
236C LYS* 3.3 18.9 + - + +
237C ALA* 3.7 4.9 + - - +
381C SER* 4.1 0.2 - - - -
383C ASP* 3.3 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 3.7 22.5 - - + +
61C VAL 3.4 36.3 - - - +
62C GLY* 3.5 10.5 - - - -
88C VAL* 3.4 27.4 - - + +
89C SER* 4.4 3.8 - - - +
90C ASN 4.7 2.2 - - - +
141C LEU* 6.0 0.4 - - + -
145C ILE* 3.8 33.9 - - + -
208C ALA* 3.4 17.3 - - + +
210C VAL* 4.4 8.7 - - + -
230C PHE* 2.9 36.6 + - + +
231C ASN 4.0 4.0 - - - +
233C PRO* 1.3 75.8 - - - +
235C CYS* 1.3 60.8 + - - +
236C LYS 3.2 0.9 + - - -
237C ALA 3.3 9.4 + - - -
238C ALA 3.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C VAL* 3.7 27.1 - - - +
221C VAL* 5.7 0.7 - - - -
223C PHE* 4.6 2.7 - - - -
231C ASN 3.3 18.9 + - - -
232C LEU 3.3 10.6 + - - +
233C PRO 3.2 0.6 - - - -
234C MET* 1.3 75.6 - - - +
236C LYS* 1.3 57.5 + - + +
237C ALA 3.5 0.2 - - - -
238C ALA 5.0 0.2 - - - +
241C THR* 2.8 30.6 - - - +
243C VAL* 4.3 12.6 - - - -
261C ILE* 3.9 36.6 - - + -
265C TYR* 3.2 14.7 - - + +
266C VAL* 5.1 0.4 - - - -
267C HIS* 5.4 0.2 - - - -
393D HIS* 5.5 0.3 - - - -
----------------------------------------------------------
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