Contacts of the helix formed by residues 275 - 283 (chain A) in PDB entry 1M0E
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 HIS 275 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.5 12.7 - - + +
201A GLU* 4.2 19.8 + - - +
202A VAL* 3.9 10.5 - - + -
204A HIS* 4.2 16.0 + - - -
205A LEU* 3.6 12.5 - - + +
274A LEU* 1.3 73.1 - - - +
276A PRO* 1.3 83.2 - - + +
277A ARG* 3.0 39.8 + - + +
278A GLU* 2.8 31.7 + - + +
279A CYS* 3.0 9.5 + - - -
291A VAL* 6.4 1.1 - - + -
299A TYR* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 5.3 0.2 - - + -
275A HIS* 1.3 98.0 - - + +
277A ARG* 1.3 55.7 + - - +
279A CYS* 3.2 12.4 + - + +
280A ALA* 2.9 26.7 + - - +
291A VAL* 4.5 15.5 - - + -
295A THR* 4.3 23.1 - - + -
298A ALA* 4.2 25.4 - - + -
299A TYR* 3.5 29.2 - - + +
302A PHE* 3.7 8.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.0 14.4 - - + -
275A HIS* 3.0 23.3 + - + +
276A PRO* 1.3 77.4 - - - +
278A GLU* 1.3 57.8 + - - +
280A ALA* 3.2 23.9 - - - +
281A ARG* 3.0 49.2 + - - +
286A PRO 3.0 24.0 + - - -
287A ASP* 3.5 30.2 + - - +
289A TYR* 3.0 31.9 + - - +
290A LYS* 5.0 0.8 - - - +
291A VAL* 3.8 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.3 8.9 - - - +
196A LEU* 3.1 13.0 - - + -
197A LEU* 2.7 40.4 + - + +
202A VAL* 4.6 0.2 - - - -
272A ARG* 2.8 40.5 + - - -
274A LEU* 3.4 16.1 - - + +
275A HIS* 2.8 31.4 + - + +
277A ARG* 1.3 75.8 - - - +
279A CYS* 1.3 53.8 + - - +
281A ARG* 3.3 9.4 + - - +
282A VAL* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.1 17.3 - - + -
262A THR* 3.6 32.3 - - - -
274A LEU* 3.9 10.1 - - - -
275A HIS 3.0 15.0 + - - -
276A PRO* 3.2 10.3 + - + +
278A GLU* 1.3 74.7 - - - +
280A ALA* 1.3 66.3 + - - +
282A VAL* 3.2 4.0 + - - +
283A MET* 3.0 29.6 + - - +
299A TYR* 4.0 14.6 - - + -
302A PHE* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO 2.9 10.5 + - - +
277A ARG* 3.2 37.2 - - - +
279A CYS* 1.3 73.6 - - - +
281A ARG* 1.3 62.8 + - + +
283A MET* 3.0 9.2 + - - +
284A GLY 3.1 0.2 + - - -
285A TYR* 2.8 32.5 + - + +
291A VAL* 4.7 0.2 - - + -
302A PHE* 3.5 33.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 4.3 5.5 - - - +
195A LEU* 2.8 59.6 + - + +
196A LEU 3.6 13.3 + - - -
197A LEU* 3.6 29.7 - - - +
277A ARG* 3.0 24.9 + - - +
278A GLU* 3.5 7.6 - - - +
279A CYS 3.2 0.2 - - - -
280A ALA* 1.3 78.1 - - + +
282A VAL* 1.3 56.5 + - - +
284A GLY* 2.8 21.3 + - - -
285A TYR 4.1 9.2 - - - +
287A ASP* 2.7 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.1 18.7 - - - +
160A PRO* 4.6 4.5 - - + +
161A GLN* 3.0 42.9 + - + +
192A VAL* 5.7 7.6 - - + -
195A LEU* 4.0 21.3 - - + -
248A ALA* 3.8 22.0 - - + -
251A LEU* 4.1 12.3 - - + -
274A LEU* 4.3 11.9 - - + -
278A GLU* 2.8 23.7 + - + +
279A CYS* 3.2 7.4 + - - +
281A ARG* 1.3 71.8 - - - +
283A MET* 1.3 55.5 + - - +
284A GLY 3.3 0.9 - - - -
307A VAL* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLN* 3.3 23.6 - - - -
163A ARG* 3.6 15.3 - - - +
251A LEU* 3.6 19.1 - - + -
279A CYS 3.0 17.2 + - - +
281A ARG 3.0 1.2 - - - -
282A VAL* 1.3 76.5 - - - +
284A GLY* 1.3 62.2 + - - +
285A TYR* 3.3 19.8 + - + -
302A PHE* 3.4 23.6 - - + +
305A SER* 3.3 38.6 - - - +
306A VAL 3.4 16.4 - - - +
307A VAL* 3.3 11.3 - - - +
308A ILE* 3.1 24.3 + - - +
----------------------------------------------------------
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