Contacts of the helix formed by residues 354 - 363 (chain A) in PDB entry 3APO
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 SER 354 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 1.3 75.7 - - - +
355A ALA* 1.3 64.4 + - - +
356A ASN* 3.5 7.6 + - - +
357A GLN* 3.0 37.6 + - - +
358A LEU* 2.9 21.8 + - - +
401A PHE* 3.7 1.6 - - - -
405A SER* 5.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A SER* 1.3 71.8 - - - +
356A ASN* 1.3 66.7 - - - +
358A LEU* 3.3 2.8 + - - +
359A GLU* 3.0 33.3 + - - +
401A PHE* 3.5 16.2 - - + -
405A SER* 5.1 2.4 + - - -
406A ALA* 4.0 17.0 - - + -
409A ILE* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A SER* 3.3 6.3 + - - +
355A ALA* 1.3 83.3 - - - +
357A GLN* 1.3 65.4 + - + +
358A LEU 3.2 0.2 + - - -
359A GLU* 3.3 11.3 + - - +
360A ASP* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLU* 4.5 6.7 + - - -
352A LEU 3.8 5.4 + - - +
353A LEU* 3.5 19.2 - - + +
354A SER* 3.0 40.3 + - - +
356A ASN* 1.3 75.9 - - + +
358A LEU* 1.3 57.0 + - - +
360A ASP* 3.4 3.1 - - - +
361A ARG* 3.1 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 4.0 24.5 - - + -
354A SER 2.9 16.5 + - - +
355A ALA 3.7 2.9 - - - +
356A ASN 3.2 0.2 - - - -
357A GLN* 1.3 72.1 - - - +
359A GLU* 1.3 65.0 + - + +
361A ARG* 3.2 1.7 + - + +
362A LEU* 2.7 71.1 + - + +
369A VAL* 4.3 21.3 - - + -
371A PHE* 4.5 9.6 - - + -
399A VAL* 4.7 0.7 - - + -
401A PHE* 4.0 27.1 - - + -
409A ILE* 4.0 26.5 - - + -
413A LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA* 3.0 21.7 + - - +
356A ASN* 3.9 10.8 - - - +
358A LEU* 1.3 81.7 - - + +
360A ASP* 1.3 64.9 + - - +
362A LEU* 4.1 6.4 - - + +
363A ALA* 3.5 19.4 + - - +
409A ILE* 4.4 26.5 - - + +
428A THR* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASN 3.0 18.0 + - - +
357A GLN* 3.4 9.2 - - - +
359A GLU* 1.3 78.5 - - - +
361A ARG* 1.3 70.1 + - - +
363A ALA* 3.5 14.1 + - - +
364A HIS 4.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLU* 4.6 9.5 + - - -
353A LEU* 3.6 31.4 - - + +
357A GLN* 3.1 56.3 + - - +
358A LEU* 3.2 4.0 + - - +
360A ASP* 1.3 85.8 + - + +
362A LEU* 1.3 63.3 + - + +
363A ALA 3.1 6.2 + - - -
364A HIS 3.7 0.7 + - - -
365A HIS* 3.5 16.5 + - - +
367A TRP* 2.9 56.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LEU* 2.7 55.7 + - + +
359A GLU* 4.3 5.8 - - + +
361A ARG* 1.3 71.8 - - - +
363A ALA* 1.3 63.2 + - - +
364A HIS 3.2 1.5 + - - -
365A HIS 4.0 4.2 - - - +
367A TRP* 3.7 28.5 - - + -
369A VAL* 4.4 0.4 - - + -
413A LEU* 6.1 0.9 - - + -
423A PHE* 3.7 52.1 - - + +
425A GLY* 4.0 2.1 + - - -
426A GLN 3.9 4.7 + - - -
427A GLY* 2.9 30.3 + - - +
428A THR* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLU 3.5 10.2 + - - +
360A ASP* 3.7 13.5 - - - +
361A ARG 3.1 2.0 - - - -
362A LEU* 1.3 80.0 - - - +
364A HIS* 1.3 88.1 + - + +
425A GLY 3.1 10.0 - - - +
426A GLN* 3.7 2.8 - - - -
427A GLY* 3.4 15.6 + - - +
----------------------------------------------------------
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