Contacts of the helix formed by residues 225 - 233 (chain A) in PDB entry 1MF8
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 GLY 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLU* 3.5 4.7 - - - -
222A PRO* 5.2 0.4 - - - -
224A TYR* 1.3 96.1 - - - +
226A PRO* 1.3 70.9 - - - +
227A MET 3.3 2.9 - - - -
228A CYS* 3.3 2.5 + - - -
229A ASP* 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 3.6 11.4 - - - +
205A GLU* 3.2 37.9 - - + +
206A ILE* 3.5 22.9 - - + -
215A LEU* 3.6 24.0 - - + -
225A GLY* 1.3 83.1 - - - +
227A MET* 1.3 57.4 + - - +
229A ASP* 3.6 0.7 - - - +
230A ILE* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 4.8 3.1 - - - -
187A LEU* 3.5 28.3 - - + -
215A LEU* 4.1 10.9 - - + +
216A ASP 2.8 17.3 - - - +
217A ARG* 2.8 52.7 - - + +
219A LYS* 4.3 8.5 - - + +
221A PRO* 4.3 11.4 - - + -
222A PRO* 4.0 28.6 - - + +
225A GLY 3.3 1.0 - - - -
226A PRO* 1.3 74.8 - - - +
228A CYS* 1.3 67.5 + - - +
230A ILE* 3.6 6.9 - - - +
231A LEU* 3.2 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 5.0 4.7 - - - -
222A PRO* 3.2 27.5 - - - +
223A ALA* 4.1 6.3 - - - -
224A TYR* 3.8 24.9 - - - +
225A GLY 3.3 7.7 + - - +
227A MET* 1.3 78.8 - - - +
229A ASP* 1.3 54.6 + - - +
231A LEU* 5.0 0.7 - - - -
232A TRP* 2.6 55.4 + - + +
256A CYS* 4.9 5.6 - - - -
257A SER* 4.2 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY 3.9 0.3 - - - +
202A LEU 3.5 4.3 - - - +
203A SER* 3.8 17.0 + - - -
204A PRO* 3.8 7.5 - - - +
205A GLU* 4.7 2.8 - - - +
224A TYR* 5.0 1.7 - - - -
225A GLY* 2.9 30.1 + - - +
226A PRO 3.7 4.0 - - - +
227A MET 3.1 0.2 - - - -
228A CYS* 1.3 78.7 - - - +
230A ILE* 1.3 65.6 + - - +
233A SER* 2.7 34.6 + - - +
257A SER* 2.8 38.4 + - - -
258A TYR* 3.1 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 3.3 36.6 - - + +
188A ALA* 5.2 0.7 - - + -
196A LEU* 6.5 0.4 - - + -
198A VAL* 3.2 19.9 - - + +
200A GLY* 3.0 7.6 + - - -
201A GLY 2.8 43.5 + - - +
202A LEU* 4.8 2.9 - - + -
203A SER* 4.6 3.8 - - - -
206A ILE* 3.1 33.7 - - + -
212A ILE* 4.6 12.3 - - + -
215A LEU* 4.8 4.5 - - + -
226A PRO 2.8 26.8 + - - +
227A MET* 3.3 9.8 + - + +
229A ASP* 1.3 71.5 - - - +
231A LEU* 1.3 68.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 2.7 55.9 - - + +
149A GLY* 4.1 8.5 - - - +
150A ASN* 2.2 35.8 + - - +
187A LEU* 5.0 5.6 - - + +
199A HIS* 3.5 10.2 - - + -
200A GLY* 3.3 15.4 - - - +
221A PRO* 3.8 30.1 - - + -
227A MET* 3.2 22.2 + - + +
230A ILE* 1.3 94.2 - - + +
232A TRP* 1.3 61.6 + - + +
281A HIS* 3.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASN* 3.5 29.5 + - + +
156A LEU* 3.7 43.3 - - + -
221A PRO* 5.5 6.9 - - + +
228A CYS* 2.6 36.1 + - - +
231A LEU* 1.3 82.6 - - + +
233A SER* 1.3 64.4 + - - +
234A ASP 3.6 0.7 + - - -
251A ASN* 4.5 0.5 + - - -
254A ARG* 3.5 58.3 - - + +
256A CYS* 3.7 26.5 - - - -
257A SER* 3.3 18.9 + - - -
281A HIS* 3.6 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLY* 2.7 28.4 - - - +
201A GLY* 3.9 3.4 - - - -
202A LEU 2.6 26.8 + - - -
229A ASP* 2.7 27.8 + - - +
231A LEU 3.8 0.6 - - - -
232A TRP* 1.3 73.5 - - - +
234A ASP* 1.3 56.9 + - - +
257A SER* 2.8 17.9 + - - -
258A TYR* 3.2 11.4 + - - +
260A TYR* 3.4 17.5 - - - -
279A ARG* 3.1 5.9 + - - -
281A HIS* 3.8 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