Contacts of the helix formed by residues 401 - 409 (chain A) in PDB entry 3F9C
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 401 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS* 5.7 0.7 - - - -
400A LYS* 1.3 76.2 - - - +
402A PHE* 1.3 75.7 + - - +
403A ASP* 3.1 13.5 + - - +
404A GLN* 2.9 43.4 + - - +
405A TRP* 4.6 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS* 3.6 47.8 - + + -
172A PHE* 4.0 4.0 - + - -
389A LEU* 3.4 49.1 - - + +
390A ALA* 3.4 15.2 - - - +
393A GLN* 3.1 24.5 + - + +
398A LEU* 3.8 22.0 - - + -
400A LYS* 3.7 23.1 - - + -
401A ASP* 1.3 86.1 - - - +
403A ASP* 1.3 55.9 + - - +
404A GLN 3.0 10.4 + - - -
405A TRP* 3.2 32.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA* 5.0 0.7 - - - +
393A GLN* 3.6 23.6 + - + +
400A LYS 4.0 1.1 - - - +
401A ASP* 3.5 14.6 - - - -
402A PHE* 1.3 74.5 - - - +
404A GLN* 1.3 60.7 + - - +
405A TRP 3.1 5.6 - - - -
406A ASP* 3.2 41.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ASP* 2.9 44.8 + - + +
402A PHE 3.0 0.8 - - - -
403A ASP* 1.3 79.7 + - - +
405A TRP* 1.3 103.7 + - + +
406A ASP 3.4 1.6 - - - -
407A CYS* 4.9 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS* 4.2 18.6 - + - -
386A LYS* 3.6 66.8 - - + +
389A LEU* 3.9 16.6 - - + -
390A ALA* 3.7 9.3 - - - +
401A ASP* 4.6 2.5 - - - -
402A PHE* 3.2 44.3 + + - +
403A ASP 3.1 1.0 - - - -
404A GLN* 1.3 117.0 + - + +
406A ASP* 1.3 56.2 + - - +
407A CYS* 3.1 4.9 - - - +
408A LEU* 2.7 46.3 + - + +
409A ILE 3.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA* 3.7 18.2 - - - +
394A LYS* 5.4 6.2 - - - +
403A ASP* 3.2 41.7 + - - +
404A GLN 3.4 0.8 - - - -
405A TRP* 1.3 77.7 - - - +
407A CYS* 1.3 61.2 + - - +
409A ILE* 3.1 31.7 + - + +
410A GLU* 3.8 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN 4.9 4.9 + - - -
405A TRP* 3.1 7.1 - - - -
406A ASP* 1.3 77.9 - - - +
408A LEU* 1.3 81.3 + - - +
410A GLU* 3.3 14.0 + - - +
412A ASP* 3.0 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 3.4 14.7 - - - +
383A LEU* 4.0 22.0 - - + +
386A LYS* 3.6 37.9 - - + -
387A ALA* 3.9 16.2 - - + +
405A TRP* 2.7 27.2 + - + +
407A CYS* 1.3 89.4 - - - +
409A ILE* 1.3 61.6 + - - +
410A GLU 3.1 1.8 - - - -
411A GLY 3.2 8.5 + - - -
412A ASP 4.3 6.1 - - - +
413A ASP* 4.2 24.2 - - + +
416A LEU* 3.5 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 4.1 16.2 - - + -
342A LYS* 3.6 46.7 - - + +
343A MET 4.5 2.4 - - - +
344A ILE* 3.3 14.0 - - - +
387A ALA 3.9 17.5 - - - +
390A ALA* 3.7 16.8 - - + +
391A PHE* 3.7 32.5 - - + +
394A LYS* 5.3 11.0 - - + -
406A ASP* 3.1 23.5 + - - +
408A LEU* 1.3 76.2 - - - +
410A GLU* 1.3 61.1 + - - +
411A GLY 3.3 1.3 - - - -
----------------------------------------------------------
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