Contacts of the helix formed by residues 381 - 391 (chain M) in PDB entry 1MVW
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 GLU 381 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379M GLY* 3.6 4.5 - - - -
380M THR* 1.3 77.5 - - - +
382M VAL* 1.3 73.9 + - + +
384M ASP* 3.4 11.3 - - - +
385M MLY 2.9 56.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 382 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360M HIS* 3.4 47.8 - - + +
363M ASN* 4.1 22.7 - - + +
364M LEU* 3.6 12.1 - - + +
379M GLY 5.2 0.6 + - - -
381M GLU* 1.3 91.0 - - + +
383M ALA* 1.3 68.9 + - - +
384M ASP 2.9 2.0 - - - -
385M MLY 3.0 12.0 + - + +
386M ALA* 2.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364M LEU* 3.9 16.0 - - + +
379M GLY 4.6 3.5 + - - +
380M THR* 4.5 9.0 - - - -
381M GLU 3.5 0.8 - - - +
382M VAL* 1.3 79.1 - - - +
384M ASP* 1.3 54.1 + - - +
386M ALA* 3.1 3.8 + - - +
387M ALA* 2.6 38.2 + - - +
394M SER* 3.6 8.3 - - - +
397M LEU* 4.6 3.3 - - + +
398M LEU* 3.6 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380M THR* 2.4 33.9 + - - +
381M GLU* 3.4 11.9 - - - +
383M ALA* 1.3 82.6 - - - +
385M MLY 1.3 58.6 + - + +
387M ALA* 3.5 1.9 + - - +
388M TYR* 3.0 29.5 + - - +
394M SER* 2.3 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 385 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304M LEU* 4.1 48.0 - - + -
305M ILE* 6.2 0.2 - - - -
360M HIS* 4.1 27.1 - - + +
381M GLU* 2.9 56.0 - - - +
382M VAL* 3.0 13.4 + - + +
384M ASP* 1.3 75.9 + - + -
386M ALA* 1.3 66.8 + - - +
387M ALA 3.1 0.2 - - - -
388M TYR* 3.2 2.7 + - - +
389M LEU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357M ALA* 4.5 4.7 - - - +
360M HIS* 4.2 13.8 - - + +
361M TYR* 3.6 34.3 - - + -
364M LEU* 4.6 4.3 - - + -
382M VAL 2.9 15.5 + - - +
383M ALA* 3.6 6.7 - - - +
385M MLY 1.3 79.0 + - - +
387M ALA* 1.3 64.0 + - - +
389M LEU* 3.3 4.5 + - - +
390M MET* 3.1 27.9 + - - +
397M LEU* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383M ALA 2.6 21.9 + - - +
384M ASP 3.6 4.7 - - - +
386M ALA* 1.3 75.0 - - - +
388M TYR* 1.3 57.8 + - - +
391M GLY 3.1 2.9 + - - -
392M LEU* 2.6 48.4 + - + +
393M ASN 3.9 2.7 - - - +
394M SER* 3.5 34.1 - - - +
397M LEU* 4.6 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 388 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M MET 4.8 3.6 - - - -
304M LEU* 3.9 20.9 - - + -
353M MLY 3.1 40.2 - - - -
384M ASP 3.0 18.7 + - - +
385M MLY 3.2 2.0 + - - +
387M ALA* 1.3 74.3 - - - +
389M LEU* 1.3 88.4 + - + +
391M GLY* 3.1 12.6 + - - -
392M LEU 4.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M MET 3.6 22.7 - - - +
303M LEU* 3.1 25.6 - - - +
304M LEU* 4.0 4.3 - - + -
353M MLY 3.4 64.5 - - + +
354M LEU* 4.4 4.2 - - - +
356M GLY 4.7 0.9 - - - -
357M ALA* 4.4 9.9 - - + +
360M HIS* 3.9 18.4 - - + +
385M MLY 2.9 19.0 + - - +
386M ALA 3.7 3.8 - - - +
388M TYR* 1.3 98.6 - - + +
390M MET* 1.3 60.1 + - - +
616M VAL* 4.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 390 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354M LEU* 4.1 17.0 - - + +
357M ALA* 3.7 22.4 - - + -
358M VAL* 5.3 2.9 - - + -
361M TYR* 2.8 43.3 - - + +
386M ALA 3.1 14.9 + - - +
387M ALA 4.1 0.2 - - - +
388M TYR 3.1 0.6 - - - -
389M LEU* 1.3 77.2 - - - +
391M GLY* 1.3 51.0 + - - +
392M LEU* 4.1 14.3 - - + +
433M VAL* 4.2 26.2 - - + -
611M TYR* 4.2 19.5 - - + +
614M SER* 2.4 28.4 + - - -
616M VAL* 3.4 11.6 - - - +
619M LEU* 3.6 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 391 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353M MLY 4.9 1.1 - - - -
387M ALA 3.7 0.9 - - - -
388M TYR* 3.1 13.8 + - - -
389M LEU 3.5 0.2 - - - -
390M MET* 1.3 79.3 - - - +
392M LEU* 1.3 59.6 + - - +
613M MLY 4.9 0.5 - - - +
614M SER* 3.2 7.7 + - - -
615M SER* 2.7 40.0 + - - -
616M VAL* 3.6 11.1 - - - +
----------------------------------------------------------
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