Contacts of the helix formed by residues 233 - 241 (chain A) in PDB entry 6D1U
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 ALA 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.8 8.1 - - - +
216A GLU* 4.7 9.3 - - + +
229A ASN* 3.6 33.7 - - + +
230A GLY 3.1 14.2 + - - +
232A TRP* 1.3 79.7 - - - +
234A TRP* 1.3 66.3 - - + +
235A SER 3.3 1.3 + - - -
236A ASN* 3.4 15.9 + - - +
237A ILE* 3.4 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 5.6 0.6 - - - -
118A ILE* 4.2 18.2 - - + +
229A ASN 5.3 0.6 + - - -
230A GLY 3.8 14.6 + - - -
231A PRO* 3.2 34.9 + - + +
233A ALA* 1.3 77.8 - - - +
235A SER* 1.3 59.5 + - - +
237A ILE* 3.2 7.1 + - + +
238A ASP* 2.9 33.2 + - - +
244A TYR* 3.6 10.0 + + - +
246A VAL* 3.8 22.8 - - + +
300A PRO* 3.7 17.5 - - + -
316A ASP* 4.5 0.4 - - - -
318A ARG* 3.5 78.7 - - + +
319A ILE* 3.7 24.5 - - + -
322A THR* 3.5 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP 4.2 0.2 + - - -
233A ALA 3.3 0.8 - - - -
234A TRP* 1.3 77.0 - - - +
236A ASN* 1.3 63.6 + - - +
238A ASP* 3.3 12.1 + - - +
239A THR* 3.0 27.1 + - - -
297A LYS 4.7 2.4 + - - -
298A ASP 2.8 27.2 + - - -
299A LYS* 3.5 17.1 - - - -
300A PRO* 3.2 21.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
216A GLU* 2.8 34.4 + - - +
220A ASN* 3.7 12.1 - - - +
232A TRP 5.8 0.8 + - - -
233A ALA* 3.4 7.2 + - - +
234A TRP 3.3 0.6 - - - -
235A SER* 1.3 77.5 - - - +
237A ILE* 1.3 63.7 + - - +
239A THR* 3.4 10.2 + - - -
240A SER* 3.1 22.0 + - - -
299A LYS* 3.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 3.8 38.6 - - + -
216A GLU* 6.2 0.4 - - + -
219A PHE* 3.9 19.3 - - + -
220A ASN* 3.4 18.8 - - - +
227A THR* 5.3 2.0 - - + -
233A ALA* 3.4 20.4 - - + +
234A TRP* 3.2 12.0 + - - +
236A ASN* 1.3 74.3 - - - +
238A ASP* 1.3 66.4 + - - +
240A SER* 2.7 30.7 + - - +
241A LYS* 3.3 3.3 + - - -
242A VAL* 4.1 7.7 + - + +
244A TYR* 3.4 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP 2.9 16.5 + - - +
235A SER* 3.5 12.5 - - - +
237A ILE* 1.3 74.0 - - - +
239A THR* 1.3 62.1 + - - +
241A LYS* 3.1 28.1 + - - +
242A VAL 5.7 0.4 - - - -
244A TYR* 2.6 33.8 + - - -
300A PRO* 6.1 0.7 - - - +
318A ARG* 4.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 3.0 15.3 + - - -
236A ASN* 3.6 13.1 + - - -
237A ILE 3.3 0.4 - - - -
238A ASP* 1.3 74.8 - - - +
240A SER* 1.3 61.1 + - - +
241A LYS* 3.3 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASN* 3.3 30.9 + - - +
236A ASN 3.1 12.5 + - - -
237A ILE* 2.7 19.6 + - - -
239A THR* 1.3 74.8 - - - +
241A LYS* 1.3 67.4 + - - +
242A VAL* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE 3.3 0.6 + - - -
238A ASP* 3.1 29.7 + - - +
239A THR* 3.6 14.5 + - - +
240A SER* 1.3 79.4 + - - +
242A VAL* 1.3 64.7 + - - +
243A ASN* 3.5 3.5 + - - +
----------------------------------------------------------
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