Contacts of the helix formed by residues 319 - 324 (chain B) in PDB entry 4R95
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 PRO 319 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LYS 4.6 1.3 - - - +
318B PHE* 1.3 93.9 - - + +
320B ASP* 1.3 65.6 + - - +
321B GLY 4.3 3.1 - - - +
322B PHE* 3.0 24.7 + - + +
323B TRP* 3.6 5.8 - - - -
327B GLN* 3.3 32.1 - - - +
328B LEU 5.6 2.0 - - - +
329B VAL* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LYS* 5.1 8.4 + - - +
318B PHE 4.9 1.9 - - - +
319B PRO* 1.3 72.2 - - - +
321B GLY* 1.3 57.7 + - - +
323B TRP* 3.2 12.7 + - - +
324B LEU* 3.0 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PRO* 3.2 3.6 - - - +
320B ASP* 1.3 74.8 - - - +
322B PHE* 1.4 61.0 - - - +
324B LEU* 3.4 11.0 + - - +
325B GLY 3.4 2.4 + - - -
326B GLU* 3.0 38.7 + - - +
327B GLN* 3.1 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 3.6 30.5 - + + -
319B PRO* 3.0 21.1 + - + +
321B GLY* 1.4 76.8 - - - +
323B TRP* 1.4 94.3 + + - +
325B GLY* 3.0 17.0 + - - -
327B GLN* 3.7 24.0 - - + +
328B LEU 5.3 1.6 - - - +
329B VAL* 3.4 37.7 - - + -
341B PHE* 4.6 7.9 - + - -
367B LEU* 4.0 19.5 - - + -
381B TYR 4.4 2.0 - - - -
382B LYS 4.4 1.1 - - - -
383B PHE* 3.3 47.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.9 14.9 - - - -
306B VAL* 4.1 13.9 - - + -
309B ILE* 3.6 34.5 - - + -
310B LYS* 3.5 48.4 - - + +
313B SER* 3.9 13.7 - - - -
318B PHE* 3.7 41.3 + + - +
319B PRO 3.6 20.6 - - - -
320B ASP* 3.2 10.3 + - - +
322B PHE* 1.4 94.0 - + - +
324B LEU* 1.3 59.8 + - + +
325B GLY 3.2 1.1 + - - -
341B PHE* 4.3 6.7 - + - -
383B PHE* 3.4 47.3 - + - -
385B ILE 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 5.6 9.0 - - + -
320B ASP* 3.0 30.1 + - + +
321B GLY* 3.8 4.5 - - - +
322B PHE 3.2 0.6 - - - -
323B TRP* 1.3 76.3 - - + +
325B GLY* 1.3 61.6 + - - +
326B GLU* 3.2 38.5 + - - +
385B ILE 5.6 1.6 - - - -
386B SER* 5.7 4.5 - - - -
----------------------------------------------------------
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