Contacts of the helix formed by residues 226 - 235 (chain E) in PDB entry 1M54
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 226 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E HIS* 5.0 4.9 - - + -
224E ARG 3.6 1.2 + - - -
225E ASN* 1.3 75.7 + - - +
227E SER* 1.3 64.4 + - - +
228E ASN 2.8 4.2 + - - -
229E PRO* 3.0 4.3 - - - +
230E LEU* 2.9 38.6 + - + +
1520E HEM 3.3 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ARG* 3.3 10.7 - - - +
126E MET* 3.6 30.7 - - - -
129E ASP* 2.8 37.0 + - - +
225E ASN* 2.4 32.9 + - - -
226E ALA* 1.3 67.4 - - - +
228E ASN* 1.3 55.0 + - - -
230E LEU* 3.2 12.4 - - - +
231E ALA* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ILE* 3.0 53.2 - - + +
126E MET* 4.1 10.7 - - + +
222E GLN* 4.7 7.0 - - - +
223E TYR 5.4 1.2 - - - +
225E ASN* 3.6 10.3 + - - +
226E ALA 2.8 0.2 - - - -
227E SER* 1.3 79.0 - - - +
229E PRO* 1.4 78.3 - - + +
230E LEU 2.9 1.1 - - - -
231E ALA 3.6 3.8 + - - -
232E HIS* 3.8 7.4 + - - -
257E THR* 3.5 28.5 + - - -
259E GLY* 3.1 18.0 - - - +
314E VAL* 5.3 3.4 - - - +
1510E PLP 4.5 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ASN 3.7 8.1 - - - +
226E ALA 3.0 10.7 - - - +
228E ASN* 1.4 100.0 - - + +
230E LEU* 1.3 68.9 - - - +
232E HIS 3.4 1.4 + - - -
233E TYR 3.1 3.5 + - - -
259E GLY* 3.8 16.8 - - - +
262E THR* 4.8 2.9 - - + -
263E GLY* 3.1 25.7 - - - +
314E VAL* 4.2 18.4 - - + -
315E LEU 5.1 2.5 - - - +
1520E HEM 3.1 48.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E HIS* 3.9 40.2 - - + +
66E HIS 5.3 2.9 - - - +
67E HIS* 4.0 20.6 - - + +
125E ARG* 2.9 31.0 - - - +
129E ASP* 4.0 5.8 - - - +
226E ALA* 2.9 38.6 - - + +
227E SER* 3.2 3.8 - - - +
228E ASN 2.9 0.2 - - - -
229E PRO* 1.3 83.5 - - - +
231E ALA* 1.3 52.3 + - - +
233E TYR* 2.5 26.8 + - + +
234E ASP* 2.8 16.1 + - - +
1520E HEM 3.5 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 4.6 8.3 - - + -
122E ILE* 4.4 16.2 - - + +
125E ARG* 3.6 28.6 - - + +
227E SER 2.8 19.8 + - - +
228E ASN 3.9 5.6 - - - +
229E PRO 3.4 0.2 - - - -
230E LEU* 1.3 70.2 - - - +
232E HIS* 1.3 57.4 + - - +
234E ASP* 2.9 5.4 + - - +
235E THR* 2.7 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E VAL* 3.6 20.7 - - + +
121E ARG* 3.5 22.3 - - + -
122E ILE* 3.4 21.9 - - + +
228E ASN* 3.8 10.0 + - - -
229E PRO 3.4 1.0 + - - +
230E LEU 3.3 0.8 - - - -
231E ALA* 1.3 79.8 - - - +
233E TYR* 1.3 55.8 + - - +
236E THR* 2.9 33.4 + - + +
237E ALA* 2.6 33.8 + - - +
259E GLY 3.0 33.4 - - - +
260E THR* 3.0 32.5 - - + +
263E GLY* 3.9 9.8 - - - +
264E ILE* 4.4 2.3 - - + +
1510E PLP 4.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ALA* 4.8 8.7 - - - +
67E HIS* 3.6 25.2 - + - -
229E PRO 3.1 10.3 + - - +
230E LEU* 2.5 16.7 + - + +
232E HIS* 1.3 74.5 - - - +
234E ASP* 1.3 76.8 + - - -
237E ALA* 3.2 10.8 - - - +
238E ASP* 3.4 0.2 - - - +
263E GLY 3.2 15.2 + - - +
266E ARG* 4.2 2.0 - - + -
267E LYS* 2.6 87.8 + - + +
270E GLU* 3.3 29.3 + - - -
1520E HEM 3.6 40.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E HIS* 2.9 57.1 + - - +
68E THR* 3.1 26.2 + - - +
70E PRO* 3.3 22.9 - - - +
125E ARG* 4.0 10.8 + - - -
230E LEU* 2.8 14.4 + - - +
231E ALA* 2.9 6.3 + - - +
233E TYR* 1.3 91.6 - - - +
235E THR* 1.3 60.6 + - + +
238E ASP* 3.7 10.1 - - - +
267E LYS* 4.1 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E THR* 4.7 5.2 - - - +
69E ALA 4.4 5.4 - - - +
70E PRO* 3.9 26.4 - - + +
71E ALA 5.2 0.9 - - - +
121E ARG* 3.7 15.1 + - - +
125E ARG* 6.3 2.0 - - - -
231E ALA* 2.7 25.9 + - + +
234E ASP* 1.3 80.7 - - + +
236E THR* 1.3 69.1 + - - -
237E ALA 2.8 14.1 + - - -
238E ASP* 3.0 13.5 + - - +
239E GLU* 3.1 22.5 + - - +
----------------------------------------------------------
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