Contacts of the helix formed by residues 240 - 251 (chain I) in PDB entry 3MQT
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 ASP 240 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I THR 4.3 4.2 - - - +
236I LEU* 4.5 5.4 - - + +
237I GLN* 2.9 24.4 + - + +
238I HIS 3.3 0.2 - - - -
239I ASP* 1.3 76.9 - - - +
241I LEU* 1.3 60.5 + - - +
242I ILE 3.6 2.6 + - - -
243I GLY* 3.0 23.3 + - - -
244I HIS* 2.8 25.0 + - - +
300J GLU 4.4 5.3 - - - +
301J HIS 4.1 9.9 - - - +
303J ASN* 3.0 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I HIS 4.1 7.0 - - - +
239I ASP 3.0 13.0 + - - +
240I ASP* 1.3 70.3 + - - +
242I ILE* 1.3 61.4 + - - +
244I HIS* 3.1 2.3 + - - +
245I GLN* 2.9 26.6 + - - +
269I GLU* 3.6 37.2 - - + +
270I TRP* 3.7 49.6 - - + +
273I LYS* 3.9 27.6 - - + +
274I THR* 3.4 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I ASP* 3.4 1.0 + - - -
241I LEU* 1.3 80.6 - - + +
243I GLY* 1.3 56.2 + - - +
245I GLN* 3.2 12.1 + - + +
246I LYS* 3.0 48.2 + - + +
273I LYS* 4.3 20.6 - - - +
301J HIS* 3.5 50.2 + - + +
302J HIS* 3.6 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 243 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I TRP* 3.6 7.8 - - - +
236I LEU* 3.3 15.7 - - - +
240I ASP* 3.0 27.9 + - - -
242I ILE* 1.3 74.7 - - - +
244I HIS* 1.3 65.6 + - - +
246I LYS* 3.5 1.9 + - - +
247I LEU* 3.1 17.7 + - - +
303J ASN* 3.9 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 244 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234I ALA* 5.6 1.2 - - - -
235I CYS 4.8 4.0 + - - -
236I LEU* 3.5 38.8 + - + +
237I GLN 3.3 24.2 - - - -
238I HIS* 4.7 0.2 - - - -
240I ASP 2.8 24.5 + - - -
241I LEU 3.1 9.0 + - - +
243I GLY* 1.3 75.5 - - - +
245I GLN* 1.3 58.5 + - - +
247I LEU 3.1 1.4 + - - -
248I ALA* 2.9 27.7 + - - +
255I LEU* 3.5 28.8 - - + +
256I CYS 4.1 11.9 + - - -
257I GLY* 5.1 0.6 - - - -
270I TRP* 3.5 33.5 - + - -
274I THR* 3.9 17.0 - - + -
276I ILE* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I LEU 2.9 10.6 + - - +
242I ILE* 3.5 16.8 - - + +
244I HIS* 1.3 76.8 - - - +
246I LYS* 1.3 82.3 + - - +
248I ALA* 4.0 1.6 - - - +
249I ALA* 3.3 27.1 + - - +
273I LYS* 3.1 28.2 - - + +
274I THR* 3.2 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I TRP* 3.5 55.8 - - + +
242I ILE* 3.0 33.2 + - + +
243I GLY 3.9 1.6 - - - +
245I GLN* 1.3 92.1 - - - +
247I LEU* 1.3 60.4 + - - +
249I ALA* 3.5 5.5 + - - +
250I ALA* 3.3 14.9 + - - +
271J LEU 5.8 0.6 + - - -
275J GLY* 4.9 21.5 + - - -
276J ILE 5.0 4.6 + - - -
277J SER* 5.9 1.2 + - - +
302J HIS* 3.1 32.3 + - - +
303J ASN 5.4 0.2 + - - -
304J ALA* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I TRP* 3.7 11.1 - - + +
217I ALA* 3.9 6.7 - - + +
218I ARG* 3.8 32.5 - - + +
221I PHE* 5.5 2.7 - - + -
235I CYS* 3.6 31.4 - - + -
236I LEU* 3.8 18.6 - - + -
243I GLY 3.1 16.3 + - - +
244I HIS* 3.1 3.8 + - + +
246I LYS* 1.3 73.0 - - - +
248I ALA* 1.3 65.4 + - - +
249I ALA 3.1 1.8 - - - -
250I ALA* 3.0 1.8 + - + -
251I ILE* 3.0 52.5 + - + +
255I LEU* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I HIS 2.9 15.9 + - - +
245I GLN 4.0 1.1 - - - +
247I LEU* 1.3 73.9 - - - +
249I ALA* 1.3 59.5 + - - +
250I ALA 3.5 0.2 + - - -
251I ILE* 3.7 21.6 + - - +
253I THR 4.8 3.1 - - - +
255I LEU* 3.8 22.2 - - + +
274I THR 3.5 24.7 - - - +
275I GLY* 4.3 13.7 - - - +
276I ILE 4.7 0.2 - - - +
218N ARG* 5.4 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I GLN* 3.3 20.9 + - - +
246I LYS* 3.7 6.3 - - - +
247I LEU 3.1 1.0 - - - -
248I ALA* 1.3 79.5 - - - +
250I ALA* 1.3 60.2 + - - +
251I ILE 4.3 3.1 - - - +
218N ARG* 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I TRP* 4.0 10.8 - - + -
218I ARG* 3.8 38.2 + - + +
225I GLU* 5.1 4.2 - - - +
246I LYS 3.3 14.1 + - - +
247I LEU* 3.0 5.2 + - + +
249I ALA* 1.3 79.2 - - - +
251I ILE* 1.3 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I ARG* 5.3 4.9 - - + +
221I PHE* 4.4 22.0 - - + +
225I GLU* 5.3 4.0 - - - -
232I ILE* 4.0 23.8 - - + -
247I LEU* 3.0 39.2 + - + +
248I ALA* 3.7 12.6 - - - +
249I ALA 4.3 2.6 - - - +
250I ALA* 1.3 81.5 - - + +
252I ASN* 1.3 61.9 + - - +
253I THR* 3.5 25.4 - - - +
254I ARG 4.4 1.1 - - - +
255I LEU* 4.3 26.5 - - + -
218N ARG* 3.5 13.2 + - - -
----------------------------------------------------------
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