Contacts of the helix formed by residues 230 - 235 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 4.1 12.1 - - - +
64A PHE* 4.6 2.9 - + - -
90A ASN* 3.4 46.0 - - + -
138A GLN* 3.7 25.8 - - + -
141A LEU* 4.1 11.7 - - + -
142A ALA* 3.7 30.3 - - + -
145A ILE* 4.2 17.7 - - + -
229A ASN* 1.3 85.8 + - + +
231A ASN* 1.3 63.5 + - - +
232A LEU 3.2 3.4 + - - -
233A PRO* 3.4 8.9 - - + +
234A MET* 3.1 44.5 + - + +
382A SER* 3.6 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY* 3.3 20.9 - - - -
63A GLY 3.5 8.3 - - - +
68A GLY 2.7 26.8 + - - +
210A VAL* 3.5 13.2 - - + +
211A LYS 3.0 39.9 + - - +
223A PHE* 3.6 10.8 - - + -
227A ALA 3.1 19.2 + - - +
228A ARG 3.0 8.5 + - - +
229A ASN* 3.7 2.8 + - - -
230A PHE* 1.3 76.6 - - - +
232A LEU* 1.3 62.0 + - - +
234A MET* 4.7 2.0 - - - -
235A CYS* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 4.0 17.9 - - + -
228A ARG* 3.4 39.4 + - + +
229A ASN 4.4 0.2 - - - +
230A PHE 3.2 1.0 - - - -
231A ASN* 1.3 78.0 - - - +
233A PRO* 1.3 76.7 - - + +
235A CYS* 3.1 20.0 - - - +
236A LYS* 3.7 29.9 - - - +
260A HIS* 3.8 22.0 - - + +
261A ILE* 3.7 10.2 - - + +
381A SER* 3.9 20.4 - - - +
383A ASP* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.5 4.5 - - - +
145A ILE* 3.5 23.6 - - + +
146A ARG* 4.4 14.0 - - + +
229A ASN 3.5 10.3 - - - +
230A PHE* 3.4 22.9 - - + +
232A LEU* 1.3 98.3 - - + +
234A MET* 1.3 53.6 - - - +
236A LYS* 3.1 30.5 + - + +
237A ALA* 3.7 3.3 + - - +
383A ASP* 3.3 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.8 19.2 - - + +
61A VAL 3.5 35.0 - - - +
62A GLY* 3.6 7.6 - - - -
88A VAL* 3.2 30.3 - - + +
89A SER* 4.3 3.6 - - - -
90A ASN 4.8 1.1 - - - +
141A LEU* 5.9 0.7 - - + -
145A ILE* 3.7 37.7 - - + -
208A ALA* 3.1 25.2 - - + +
210A VAL* 4.6 4.0 - - + -
230A PHE* 3.1 34.2 + - + +
231A ASN* 4.0 2.9 - - - +
233A PRO* 1.3 74.8 - - + +
235A CYS* 1.3 62.3 + - - +
236A LYS 3.3 0.7 + - - -
237A ALA* 3.4 8.5 + - - -
241A THR* 4.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL* 3.9 28.2 - - - +
221A VAL* 6.0 0.9 - - - -
223A PHE* 5.1 1.3 - - - -
231A ASN 3.2 9.1 + - - +
232A LEU 3.1 15.9 - - - +
234A MET* 1.3 76.6 - - - +
236A LYS* 1.3 55.8 + - - +
241A THR* 2.9 25.4 - - - +
243A VAL* 4.0 17.3 - - - -
261A ILE* 4.0 33.9 - - + -
265A TYR* 3.2 21.9 - - - +
266A VAL* 4.8 0.4 - - - -
267A HIS* 5.4 0.3 - - - -
393B HIS* 5.4 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