Contacts of the helix formed by residues 406 - 411 (chain A) in PDB entry 2JG0
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 406 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ALA* 3.2 19.0 + - - +
404A ALA 3.1 2.0 - - - -
405A ALA* 1.3 79.0 - - + +
407A PHE* 1.3 64.9 + - - +
408A PRO 3.3 1.3 - - - -
409A LEU* 3.0 40.5 + - + +
410A TYR* 3.0 11.3 + - - +
422A MET* 4.1 17.3 - - + -
426A THR* 3.7 27.1 - - - +
430A LEU* 4.4 17.3 - - + -
436A LEU* 4.9 3.6 - - + -
459A VAL* 4.4 4.3 - - + +
460A ALA* 3.9 35.4 - - + +
463A GLY* 5.9 0.2 - - - -
464A LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 4.6 15.5 - + - -
210A PHE* 4.2 4.9 - + - -
336A ASP* 3.5 38.6 - - + -
339A SER* 3.4 14.4 - - - +
340A LEU* 4.0 30.7 - - + -
403A ALA 4.3 2.0 - - - -
404A ALA* 3.0 26.0 + - - +
406A LEU* 1.3 77.8 - - - +
408A PRO* 1.3 66.1 - - + +
410A TYR* 3.1 21.7 + + - +
411A VAL* 3.1 16.6 + - - +
456A LEU* 4.0 24.5 - - + -
459A VAL* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 3.6 21.1 - - + -
339A SER* 3.3 17.9 - - - +
375A ILE* 4.3 10.3 - - + -
387A TYR* 3.7 37.5 - - + -
404A ALA 3.9 2.5 - - - +
405A ALA 3.4 16.6 - - - +
406A LEU 3.5 0.2 - - - -
407A PHE* 1.3 91.0 - - + +
409A LEU* 1.3 58.1 + - - +
411A VAL* 4.1 4.3 - - + -
412A ASN 3.4 1.0 + - - -
413A ALA* 2.9 30.7 + - + -
414A ALA* 3.1 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR* 4.2 4.7 - - + -
405A ALA 4.3 4.9 - - - +
406A LEU* 3.0 18.6 + - + +
408A PRO* 1.3 75.5 - - - +
410A TYR* 1.3 67.7 + - - +
411A VAL 3.1 0.2 - - - -
412A ASN 3.1 8.0 + - - -
414A ALA* 4.0 13.9 - - + -
419A ALA* 3.8 34.5 - - + +
422A MET* 3.7 30.7 - - + -
463A GLY* 3.5 24.0 - - - +
464A LEU* 3.9 25.8 - - + -
466A ASN* 3.0 14.0 + - - -
467A TYR* 3.4 17.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR* 3.4 31.9 + - - -
163A PHE* 4.9 0.3 - - - -
210A PHE* 3.9 13.2 - + - -
213A LEU* 3.6 25.9 - - + +
340A LEU* 4.6 2.2 - - + -
343A LYS* 5.1 3.8 + - - -
406A LEU 3.0 5.3 + - - +
407A PHE* 3.4 14.6 - + - +
409A LEU* 1.3 78.4 - - - +
411A VAL* 1.3 68.7 + - + +
412A ASN* 4.3 0.3 - - - +
458A TRP* 4.5 7.7 + + - -
459A VAL* 3.6 56.9 - - + +
462A GLU* 3.9 24.5 - - + -
463A GLY* 3.5 9.8 - - - -
466A ASN* 3.0 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 3.4 40.8 - - - +
340A LEU* 4.4 5.4 - - + +
342A PHE* 3.4 25.4 - - + -
343A LYS* 3.8 37.2 + - + +
407A PHE* 3.1 20.0 + - + +
408A PRO* 3.8 7.0 - - + +
410A TYR* 1.3 93.5 - - + +
412A ASN* 1.3 68.0 + - - +
413A ALA* 3.3 8.3 + - + -
----------------------------------------------------------
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