Contacts of the helix formed by residues 265 - 274 (chain C) 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 LEU 265 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 4.4 4.7 - - - +
32A THR* 5.9 2.7 - - + +
36A PHE* 3.8 29.6 - - + -
223C PHE* 4.1 31.6 - - + +
224C THR* 4.6 2.0 - - + +
227C LEU* 3.9 35.9 - - + +
228C SER* 4.9 0.4 - - - +
262C LEU* 3.0 34.8 + - + +
264C GLN* 1.3 80.4 - - - +
266C PRO* 1.3 70.1 - - + +
267C TRP* 4.3 2.5 - - + +
268C TRP* 3.1 22.8 + - + +
269C HIS* 3.4 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 4.1 5.7 - - + +
28A THR* 3.8 24.9 - - + -
29A PRO 3.4 20.0 - - - +
30A ASP* 3.7 20.6 - - - +
32A THR* 3.7 18.4 - - + -
264C GLN 3.4 9.4 - - - +
265C LEU* 1.3 82.9 - - - +
267C TRP* 1.3 62.6 + - - +
269C HIS* 3.0 14.3 + - + +
270C LYS* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.0 22.8 + - - +
131C MSE 3.6 45.5 - - + +
132C THR* 4.4 5.2 - - - -
209C TRP* 3.4 40.0 - + - -
223C PHE* 3.4 42.1 - + - -
227C LEU* 3.5 20.4 - - + -
265C LEU* 3.1 1.9 - - + -
266C PRO* 1.3 77.3 - - - +
268C TRP* 1.3 63.2 + - - +
270C LYS* 3.1 25.4 + - + +
271C LEU* 3.1 42.9 + - + +
280C PHE* 4.4 11.9 - + - -
281C TRP* 4.0 15.5 - + - -
284C GLN* 4.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PHE* 3.7 16.2 - + - -
220C PHE* 3.5 31.9 - + - -
223C PHE* 4.3 8.5 - + + -
253C ALA 4.3 0.9 - - - -
254C GLY* 4.0 16.8 + - - -
257C ALA* 3.4 26.0 - - + +
262C LEU* 3.3 40.2 - - + +
263C GLU* 4.1 21.9 + - + +
265C LEU* 3.1 9.7 + - + +
267C TRP* 1.3 80.1 - - - +
269C HIS* 1.3 67.1 + + - +
271C LEU* 3.3 17.0 + - + +
272C THR* 3.2 41.3 + - + +
608C PHE* 3.6 27.1 - + - -
609C PHE* 5.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.5 19.7 + - - +
263C GLU* 2.7 50.9 + - + +
265C LEU 3.4 19.2 + - - -
266C PRO* 3.0 11.5 + - + +
268C TRP* 1.3 80.6 - + + +
270C LYS* 1.3 57.1 + - - +
272C THR* 3.3 7.4 + - - -
273C GLU* 3.0 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 4.0 19.1 - - + +
25A SER 3.6 20.2 - - - +
26A PRO* 3.0 22.4 + - + +
28A THR 3.1 13.6 + - - -
30A ASP* 2.9 36.5 + - - -
130C VAL* 4.4 1.0 - - - +
266C PRO* 3.0 17.0 + - - +
267C TRP* 3.1 25.0 + - + +
269C HIS* 1.3 77.3 - - - +
271C LEU* 1.3 62.1 + - - +
273C GLU* 4.6 2.7 - - - -
274C HIS* 3.2 35.6 + - + +
280C PHE* 4.0 30.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C TRP* 4.2 7.0 - - + -
210C PHE* 3.9 15.4 - - + -
215C PHE* 4.0 11.9 - - + -
223C PHE* 3.5 37.9 - - + -
267C TRP* 3.1 34.1 + - + +
268C TRP* 3.3 23.1 + - + +
270C LYS* 1.3 77.4 - - - +
272C THR* 1.3 61.2 + - - +
274C HIS 3.3 22.2 - - - +
275C ALA 3.5 1.2 + - - -
281C TRP* 3.7 33.0 - - + -
608C PHE* 3.7 15.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C TRP* 3.2 51.8 + - + +
269C HIS* 3.3 12.3 + - - -
271C LEU* 1.3 77.1 - - - +
273C GLU* 1.3 64.3 + - - +
274C HIS 3.2 0.4 + - - -
275C ALA 4.1 3.5 + - - -
606C ASN* 2.8 26.0 + - - -
608C PHE* 3.8 22.7 - - + -
609C PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.0 50.5 + - - +
269C HIS* 3.0 34.8 + - - +
270C LYS* 4.1 4.0 - - - +
271C LEU 3.3 0.2 - - - -
272C THR* 1.3 78.4 - - - +
274C HIS* 1.3 78.6 + - + +
275C ALA 3.7 1.1 + - - -
278C ASP* 4.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR 5.0 7.5 + - - -
26A PRO* 6.1 0.8 - - - +
204C TRP* 4.2 0.7 + - - -
210C PHE* 4.3 2.3 - - - -
270C LYS* 3.2 31.2 + - + +
271C LEU 3.3 7.4 - - - +
273C GLU* 1.3 96.3 + - + +
275C ALA* 1.3 61.7 + - - +
276C ALA 3.2 4.2 - - - +
278C ASP* 2.5 38.0 + - - +
280C PHE* 3.5 37.6 - + + +
281C TRP* 2.8 32.0 + - - +
----------------------------------------------------------
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