Contacts of the helix formed by residues 341 - 345 (chain D) in PDB entry 1JLH
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 ASP 341 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASN* 4.6 0.9 - - - -
187C ASP* 3.3 10.9 - - - +
189C THR* 5.3 2.4 - - - +
339D PRO 2.9 6.8 + - - -
340D TYR* 1.3 76.2 - - - +
342D GLN* 1.3 62.4 + - - +
343D TYR* 3.1 22.1 - - - +
344D LEU* 3.0 70.2 + - + +
382D PRO* 3.6 12.4 - - - +
383D GLY* 4.2 3.4 + - - +
407D ILE* 5.6 0.4 - - - -
408D PRO* 3.6 25.6 - - + +
412D GLN* 6.0 1.6 - - - +
421D HIS* 6.0 0.2 - - - -
424D LEU* 6.0 0.2 - - - +
481D LEU* 4.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASN* 3.1 27.9 + - - +
187C ASP* 2.8 16.1 + - + +
189C THR* 3.4 19.7 - - - +
190C HIS* 4.0 37.2 + - + +
193C LYS* 4.4 12.6 - - - +
341D ASP* 1.3 67.5 - - - +
343D TYR* 1.3 59.9 + - - +
344D LEU 3.0 2.2 - - - -
345D HIS* 3.0 51.1 + - - +
382D PRO* 4.6 2.0 - - - +
385D ASN* 3.1 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C THR* 3.8 20.6 + - + -
193C LYS* 3.7 33.1 - - + +
165D MET 4.7 0.3 - - - +
168D GLU* 3.4 19.5 - - - +
169D ALA* 3.1 43.3 + - + +
171D LYS* 3.6 20.4 - - + +
172D PRO* 3.3 30.0 - - + +
341D ASP* 3.1 15.8 + - - +
342D GLN* 1.3 79.9 - - - +
344D LEU* 1.3 56.1 + - + +
345D HIS* 3.2 9.1 + - - -
346D ARG 4.8 0.2 + - - -
412D GLN* 4.0 11.9 - - + -
413D HIS* 2.6 40.7 + + - -
481D LEU* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D MET* 5.6 1.6 - - - -
169D ALA* 3.5 26.9 - - + -
339D PRO* 3.8 30.2 - - + +
341D ASP* 3.0 36.7 + - + +
343D TYR* 1.3 75.8 - - - +
345D HIS* 1.3 62.9 + - - -
346D ARG 3.1 3.4 - - - -
347D PHE* 2.9 40.2 + - + +
348D ALA 4.6 0.2 + - - -
382D PRO* 4.4 0.8 - - - +
406D LEU* 5.6 2.5 - - + -
478D PHE* 4.6 14.6 - - + -
481D LEU* 4.0 28.5 - - + -
486D LEU* 4.6 7.0 - - + -
489D LEU* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LYS* 6.6 0.4 - - - -
168D GLU* 2.6 39.3 + - + +
341D ASP 3.6 0.6 + - - -
342D GLN* 3.0 39.4 + - - +
343D TYR* 3.2 12.9 - - - -
344D LEU* 1.3 76.9 - - - +
346D ARG* 1.3 91.9 + - + +
347D PHE 3.5 0.7 + - - -
348D ALA* 5.1 2.8 + - - +
349D ALA* 5.4 0.7 + - - +
381D GLU* 4.1 6.7 - - - +
382D PRO* 3.5 36.9 - - + +
----------------------------------------------------------
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