Contacts of the helix formed by residues 252 - 260 (chain B) in PDB entry 1MPX
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 SER 252 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 4.7 1.6 - - - -
247B PHE* 5.1 1.5 - - - +
250B ALA* 4.9 0.2 - - - +
251B GLY* 1.3 77.5 + - - +
253B ALA* 1.3 63.7 + - - +
255B ASP* 3.1 28.5 + - - +
256B PHE* 3.2 21.5 + - - +
597B ASP* 6.0 0.7 - - - -
607B ILE 4.1 5.8 - - - -
608B PHE 3.0 21.3 + - - -
609B PHE* 4.4 1.7 - - - -
610B ALA 3.6 17.3 + - - -
615B TYR* 3.2 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 4.0 19.1 - - + -
217B GLN* 3.4 25.4 + - - +
220B PHE* 3.5 8.9 - - + -
252B SER* 1.3 74.9 - - - +
254B GLY* 1.3 56.5 + - - +
256B PHE* 3.4 3.0 + - - +
257B ALA* 3.0 29.3 + - - +
268B TRP* 4.4 1.3 - - - -
597B ASP* 3.9 25.4 + - + +
607B ILE 5.0 0.4 + - - -
608B PHE* 4.0 12.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER* 3.8 0.4 - - - -
253B ALA* 1.3 76.8 - - - +
255B ASP* 1.3 59.0 + - - +
257B ALA* 3.8 0.7 - - - +
258B LYS* 2.9 31.5 + - - +
268B TRP* 4.0 17.1 + - - -
608B PHE* 2.9 24.7 + - - +
609B PHE* 4.4 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ALA* 3.1 26.7 - - - +
251B GLY* 3.8 2.6 - - - -
252B SER* 3.1 35.3 + - - +
254B GLY* 1.3 75.7 - - - +
256B PHE* 1.3 63.0 + - - +
258B LYS* 3.5 4.5 + - - +
259B ALA* 3.1 24.9 + - - +
609B PHE* 6.0 0.3 - - - -
610B ALA 4.3 7.3 - - - +
612B PRO* 5.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 3.7 27.1 - + + -
236B ILE* 4.3 21.8 - - + -
237B ALA 5.7 0.9 - - - -
238B ARG* 4.0 29.6 - - - -
246B ASN* 4.4 10.8 - - + -
247B PHE* 3.4 54.3 - + + -
250B ALA* 4.0 24.4 - - + +
252B SER 3.2 9.5 + - - +
253B ALA* 3.7 7.9 - - - +
255B ASP* 1.3 81.2 - - - +
257B ALA* 1.3 63.2 + - - +
259B ALA* 3.4 4.7 + - - +
260B ALA* 3.1 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 3.8 11.4 - - + -
253B ALA 3.0 10.1 + - - +
254B GLY 3.8 1.6 - - - +
255B ASP 3.3 0.2 - - - -
256B PHE* 1.3 80.4 - - - +
258B LYS* 1.3 61.5 + - - +
260B ALA 3.2 6.4 + - - -
262B LEU* 3.0 41.6 + - + +
268B TRP* 3.3 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLY 2.9 19.0 + - - +
255B ASP* 3.9 6.3 - - - +
257B ALA* 1.3 75.7 - - - +
259B ALA* 1.3 64.3 + - - +
261B GLY* 3.1 14.0 + - - -
262B LEU 4.9 0.4 - - - +
263B GLU* 3.8 43.4 - - + +
268B TRP* 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ALA* 6.1 2.7 - - + -
255B ASP 3.1 15.8 + - - +
256B PHE* 3.8 5.6 - - - +
258B LYS* 1.3 80.9 - - - +
260B ALA* 1.3 56.7 + - - +
261B GLY 3.2 0.7 - - - -
39D ALA* 2.9 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 3.6 35.5 - - + +
256B PHE* 3.1 20.5 + - + +
257B ALA* 3.2 5.1 + - - +
259B ALA* 1.3 75.2 - - - +
261B GLY* 1.3 60.6 + - - +
262B LEU* 3.7 13.2 + - + +
36D PHE* 3.8 15.6 - - - -
38D ALA* 5.0 0.2 - - - -
39D ALA* 4.1 15.1 + - - -
----------------------------------------------------------
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