Contacts of the helix formed by residues 354 - 361 (chain B) in PDB entry 2PO5
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 GLN 354 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 5.0 6.1 - - - +
349B ASP* 3.1 18.2 - - - +
350B ILE* 3.1 35.4 + - - +
353B SER* 1.3 78.0 - - - +
355B VAL* 1.3 70.2 + - + +
358B LYS* 3.2 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 6.2 0.2 - - - +
350B ILE* 3.1 23.2 + - + +
351B GLU* 3.4 11.4 - - + +
354B GLN* 1.3 76.6 - - + +
356B LEU* 1.3 69.6 + - - +
358B LYS* 3.0 15.5 + - - +
359B GLU* 3.2 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASP* 3.3 46.7 - - + +
319B ILE* 4.1 16.8 - - + -
320B LYS* 4.6 11.9 - - + -
351B GLU 3.0 12.5 + - - +
352B TYR* 3.4 15.7 - - + +
355B VAL* 1.3 81.2 - - - +
357B ALA* 1.3 64.3 + - - +
359B GLU* 3.2 7.9 + - + +
360B CYS* 3.1 45.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE* 5.1 2.7 - - + -
352B TYR 2.9 15.7 + - - +
353B SER 3.0 28.0 - - - +
355B VAL 3.2 0.4 - - - -
356B LEU* 1.3 75.4 - - - +
358B LYS* 1.3 61.9 + - - +
360B CYS* 3.2 1.7 + - - -
361B GLY 3.1 18.0 + - - -
362B VAL* 3.2 46.3 + - + +
365B ILE* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B GLN 3.2 19.5 + - - +
355B VAL* 3.0 5.2 + - - +
357B ALA* 1.3 78.3 - - - +
359B GLU* 1.3 62.7 + - - +
360B CYS 3.2 0.9 + - - -
361B GLY* 3.3 11.7 + - - -
362B VAL* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B VAL* 3.2 11.0 + - + +
356B LEU* 3.2 12.8 + - + +
358B LYS* 1.3 78.2 - - - +
360B CYS* 1.3 62.1 + - - +
361B GLY 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE* 5.3 0.9 - - + -
320B LYS* 3.9 32.5 - - - -
323B CYS* 3.8 32.3 - - + +
324B GLU* 6.4 0.7 - - + -
328B LYS* 3.8 6.6 + - - -
356B LEU* 3.1 40.6 + - - +
357B ALA* 3.2 4.7 + - - +
358B LYS 3.1 0.4 - - - -
359B GLU* 1.3 81.9 - - - +
361B GLY* 1.3 61.5 + - - +
362B VAL* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 3.3 24.9 + - - +
357B ALA 3.1 4.0 + - - -
358B LYS* 3.3 10.9 + - - -
359B GLU 3.5 0.2 - - - -
360B CYS* 1.3 80.4 - - - +
362B VAL* 1.3 67.4 + - - +
363B GLU* 4.6 1.2 - - - +
----------------------------------------------------------
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