Contacts of the helix formed by residues 232 - 242 (chain A) in PDB entry 4N6N
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 TRP 232 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.2 14.6 + - + +
218A ALA 3.5 20.2 + - - -
219A CYS* 3.3 31.1 - - + +
220A TYR* 4.6 22.7 - + - -
231A ASP* 1.3 70.6 - - - +
233A TYR* 1.3 59.4 + - - +
235A VAL* 4.0 2.1 - - + +
236A ASN* 2.8 59.1 + - - +
261A HIS 5.2 4.9 - - - -
262A THR* 4.2 9.9 - - + -
263A GLN 5.9 1.1 - - - -
264A THR* 3.3 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 4.8 1.3 - + - -
185A TYR* 3.3 16.7 - + - +
186A ILE 3.6 22.9 - - - -
187A GLU* 3.4 19.6 + - + +
207A THR* 2.6 35.5 + - - -
208A THR 3.9 4.7 - - - -
209A ALA* 3.4 32.1 - - + -
216A SER* 5.7 0.4 - - - -
231A ASP 3.5 0.4 - - - -
232A TRP* 1.3 77.8 - - - +
234A SER* 1.3 67.6 + - - +
236A ASN* 3.4 1.9 + - - +
237A TRP* 3.1 42.2 + + + -
258A VAL* 3.7 22.0 - - + +
262A THR* 3.8 19.5 + - + +
265A SER* 5.5 0.2 - - - +
267A VAL* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 3.4 18.9 + - - -
144A TYR* 2.7 29.2 + - - -
187A GLU* 2.6 39.1 + - - +
231A ASP 3.2 4.7 + - - -
233A TYR* 1.3 76.5 - - - +
235A VAL* 1.3 62.2 + - - +
237A TRP* 3.3 15.3 - - - -
238A MET* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 4.2 0.9 - - - +
51A HIS* 5.5 0.4 - - - +
88A ASN* 3.7 36.1 - - - +
219A CYS* 4.1 5.4 - - - -
220A TYR* 3.3 24.0 - - + +
230A GLY* 4.0 2.0 - - - -
231A ASP 2.8 33.3 + - - +
232A TRP* 4.0 3.1 - - + +
234A SER* 1.3 73.0 - - - +
236A ASN* 1.3 63.0 + - - +
238A MET* 4.3 5.6 - - - -
239A GLU* 2.8 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 5.7 0.2 + - - -
232A TRP* 2.8 41.2 + - - +
233A TYR 3.7 4.3 - - - +
235A VAL* 1.3 80.2 - - - +
237A TRP* 1.3 61.3 + - - +
239A GLU* 4.2 5.8 - - - +
240A ASP* 3.2 23.6 + - - +
258A VAL* 3.9 15.5 - - + +
261A HIS* 3.4 40.5 + - + +
262A THR* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 4.2 13.2 - - + -
55A ILE* 4.2 8.7 - - + -
56A ILE* 5.8 0.9 - - + -
142A PHE* 4.0 16.4 - + - -
144A TYR* 3.6 45.2 - + - -
185A TYR* 3.5 25.9 - + + -
233A TYR* 3.1 30.6 + + + +
234A SER* 3.3 19.1 + - - +
236A ASN* 1.3 75.6 - - - +
238A MET* 1.3 82.7 + - + +
240A ASP* 3.4 2.1 + - - -
241A SER* 2.9 33.8 + - - -
254A GLN* 3.4 12.7 + - - +
258A VAL* 3.5 22.3 - - + +
284A GLN* 3.6 36.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 3.3 29.2 - - - +
51A HIS* 3.6 15.0 - - + -
52A ALA* 3.3 25.1 - - - -
55A ILE* 3.5 16.0 - - + +
88A ASN* 3.5 22.0 - - - +
144A TYR* 4.0 2.9 - - - +
234A SER* 3.0 43.4 + - - +
235A VAL 4.0 1.6 - - - +
237A TRP* 1.3 101.0 - - + +
239A GLU* 1.3 60.2 + - - +
241A SER 3.3 0.5 + - - -
242A ASP* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 4.4 13.3 - - + -
88A ASN 4.8 0.5 - - - +
89A ARG* 3.9 21.5 - - - +
220A TYR* 2.8 30.0 + - - -
235A VAL* 2.8 38.8 + - + +
236A ASN* 4.5 6.1 - - - +
238A MET* 1.3 71.2 - - - +
240A ASP* 1.3 61.3 + - - +
242A ASP* 3.6 11.1 + - - +
243A VAL* 3.4 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASN 3.2 21.4 + - - +
237A TRP* 3.4 6.1 - - - +
238A MET 3.2 0.2 - - - -
239A GLU* 1.3 75.5 - - - +
241A SER* 1.3 60.2 + - - +
243A VAL* 3.0 9.3 + - - +
244A GLU* 2.9 55.3 + - - +
249A GLU* 2.6 25.4 - - - +
254A GLN* 2.9 22.8 + - + +
257A LEU* 3.3 18.1 - - + +
258A VAL* 5.2 1.8 - - + -
261A HIS* 5.7 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 4.2 16.4 - - - -
58A ARG* 4.1 6.1 + - - -
237A TRP* 2.9 15.2 + - - -
238A MET* 3.3 5.1 + - - -
240A ASP* 1.3 76.2 - - - +
242A ASP* 1.3 62.0 + - - +
243A VAL 3.4 1.0 + - - -
244A GLU 4.0 2.9 + - - +
246A LEU* 3.6 33.1 - - - +
254A GLN* 2.9 22.1 + - - +
280A VAL* 4.1 2.6 - - - +
284A GLN* 2.6 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 2.7 29.9 + - - -
55A ILE* 3.3 13.7 - - - +
58A ARG* 2.8 38.6 + - - +
238A MET 2.9 19.5 + - - +
239A GLU* 3.6 12.0 - - - +
240A ASP 3.1 0.6 - - - -
241A SER* 1.3 78.0 - - - +
243A VAL* 1.3 63.4 + - + +
244A GLU 5.2 0.2 - - - -
----------------------------------------------------------
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