Contacts of the strand formed by residues 402 - 407 (chain M) in PDB entry 2JA7
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 ALA 402 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391M LEU* 3.9 13.6 + - + -
392M VAL 4.5 4.9 - - - +
395M GLY 3.1 26.8 + - - +
396M PRO* 3.4 1.4 - - - +
401M GLY* 1.3 74.0 - - - +
403M LYS* 1.3 63.3 + - - +
404M TYR 3.9 0.7 - - - -
415M LEU* 3.7 11.8 - - + +
432M VAL* 4.3 13.7 - - + -
433M GLU 3.1 16.2 - - - +
434M ARG* 3.2 18.8 - - + +
435M HIS* 3.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372M LYS 3.6 20.7 + - - -
373M THR* 3.1 30.7 + - - +
375M THR* 4.6 19.9 - - + +
396M PRO* 3.4 22.2 - - + -
402M ALA* 1.3 76.4 - - - +
404M TYR* 1.3 97.7 + - + +
414M ASP* 4.6 1.6 - - - +
415M LEU* 3.7 16.4 + - - +
416M ARG* 5.2 12.5 + - - +
433M GLU 3.2 3.0 + - - -
434M ARG 5.7 0.4 - - - -
435M HIS* 4.6 8.5 - - + +
1107N ALA* 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375M THR* 5.8 0.4 - - + -
403M LYS* 1.3 104.4 - - + +
405M VAL* 1.3 63.4 + - - +
406M ILE* 4.2 2.9 - - + -
412M ARG* 4.2 22.4 + - + +
413M ILE 3.5 17.0 - - - -
414M ASP* 3.5 38.5 + - + -
415M LEU* 3.3 7.6 - - - +
416M ARG* 4.2 13.7 + - - -
432M VAL* 3.3 4.0 - - - +
433M GLU* 2.8 66.9 + - + +
1108N ARG* 4.1 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 405 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392M VAL* 4.0 24.9 - - + -
404M TYR* 1.3 73.3 - - - +
406M ILE* 1.3 63.0 + - - +
413M ILE* 2.9 57.4 + - + +
415M LEU* 4.1 7.3 - - + +
424M ILE* 4.8 3.8 - - + -
426M LEU* 4.1 10.5 - - + -
430M TRP* 3.8 30.1 - - + -
431M LYS 3.5 7.0 - - - +
432M VAL* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 406 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377M PRO* 5.6 2.0 - - + -
404M TYR* 5.0 5.4 - - + +
405M VAL* 1.3 75.1 - - - +
407M ARG* 1.3 62.9 + - - +
410M GLY* 6.1 0.4 - - - -
411M ASP 3.5 19.3 - - - +
412M ARG* 3.6 37.9 - - + +
430M TRP* 3.6 2.6 - - - +
431M LYS* 2.7 81.0 + - + +
433M GLU* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406M ILE* 1.3 77.0 - - - +
408M ASP* 1.3 73.6 + - - +
409M SER* 2.8 23.4 + - - +
410M GLY* 2.9 15.4 + - - -
411M ASP* 3.3 34.4 + - - +
413M ILE* 3.7 30.1 - - + +
430M TRP* 3.1 54.1 - - + +
----------------------------------------------------------
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