Contacts of the helix formed by residues 402 - 413 (chain A) in PDB entry 2QPA
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 THR 402 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 5.3 9.2 - - + -
319A LEU* 3.9 4.3 - - - -
400A ASP 3.9 6.9 + - - +
401A LEU* 1.3 77.7 - - - +
403A ILE* 1.3 69.2 + - - +
404A LYS* 3.9 8.5 - - + +
405A ASP* 2.8 45.7 + - - +
406A PHE* 3.2 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 6.0 3.3 - - + +
319A LEU* 3.7 22.9 - - + +
323A ASP* 3.6 30.7 - - + +
327A LEU* 5.5 9.0 - - + -
402A THR* 1.3 74.7 - - - +
404A LYS* 1.3 66.5 + - - +
406A PHE* 3.0 14.0 + - - +
407A LEU* 3.1 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A THR* 3.9 10.2 - - + +
403A ILE* 1.3 78.7 - - - +
405A ASP* 1.3 55.1 + - - +
407A LEU* 2.7 38.0 + - + +
408A LYS* 2.8 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA* 3.8 11.1 - - + +
349A GLN* 2.9 44.4 - - + +
350A PRO* 4.1 3.1 - - - +
400A ASP 4.6 1.0 - - - +
401A LEU* 3.8 11.7 - - + +
402A THR* 2.8 44.6 + - - +
404A LYS* 1.3 78.6 - - - +
406A PHE* 1.3 60.1 + - + -
408A LYS* 3.9 6.1 - - - +
409A ALA* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 4.2 15.0 - + - -
312A VAL* 3.9 16.6 - - + -
319A LEU* 3.8 28.7 - - + -
324A TYR* 4.9 1.3 - + - -
327A LEU* 3.3 29.6 - - + -
342A VAL* 4.5 4.0 - - + +
343A VAL* 4.1 17.0 - - + -
346A ALA* 3.5 23.3 - - + -
401A LEU* 3.6 43.1 - - + -
402A THR 3.2 11.9 + - - -
403A ILE 3.0 7.0 + - - +
404A LYS 2.9 0.2 + - - -
405A ASP* 1.3 75.9 - - + +
407A LEU* 1.3 55.6 + - - +
409A ALA* 3.2 3.2 + - - +
410A ILE* 2.5 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 5.6 5.2 - - + -
330A MET* 3.3 30.7 - - + -
403A ILE* 3.1 35.1 + - + +
404A LYS* 2.7 22.7 + - + +
406A PHE* 1.3 69.7 - - + +
408A LYS* 1.3 57.9 + - - +
410A ILE* 2.9 7.7 + - + +
411A LYS* 2.8 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASP* 5.8 0.2 - - - +
349A GLN* 5.6 9.0 - - - +
404A LYS 2.8 14.6 + - - +
405A ASP* 3.9 7.9 - - - +
407A LEU* 1.3 74.3 - - - +
409A ALA* 1.3 60.2 + - - +
411A LYS* 3.9 7.3 - - - +
412A SER* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 3.4 26.8 - - + +
345A ASP* 3.0 29.5 + - - +
346A ALA* 3.9 6.7 - - + -
349A GLN* 5.7 0.2 - - - +
405A ASP 3.3 16.6 + - - +
406A PHE 3.2 4.0 + - - +
407A LEU 3.2 0.6 - - - -
408A LYS* 1.3 79.0 - - - +
410A ILE* 1.3 66.0 + - - +
412A SER* 3.4 10.5 + - - -
413A THR* 3.4 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 4.4 1.1 - - + -
327A LEU* 4.1 33.0 - - + -
330A MET* 3.3 42.6 - - + +
331A THR* 4.1 23.8 - - + -
334A TYR* 3.3 12.9 + - + +
342A VAL* 3.7 22.4 - - + -
406A PHE 2.5 29.8 + - - +
407A LEU 2.9 3.3 + - - +
409A ALA* 1.3 72.2 - - - +
411A LYS* 1.3 57.7 + - + +
413A THR* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A MET* 4.7 9.9 - - + -
407A LEU* 2.8 43.8 + - - +
408A LYS* 3.9 5.4 - - - +
410A ILE* 1.3 75.7 - - + +
412A SER* 1.3 62.9 + - - +
413A THR* 2.9 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASP* 5.0 7.4 - - - -
408A LYS 2.9 19.9 + - - -
409A ALA* 3.5 11.4 - - - -
410A ILE 3.1 0.2 - - - -
411A LYS* 1.3 76.1 - - - +
413A THR* 1.3 60.7 + - - +
414A ARG 4.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TYR* 2.4 35.7 + - + -
338A ASP* 5.0 9.4 - - + +
341A VAL* 4.4 21.6 - - + +
342A VAL* 4.2 18.3 - - + +
345A ASP* 5.9 1.6 - - - +
409A ALA 3.4 10.4 + - - -
410A ILE 2.8 15.5 + - - +
411A LYS* 2.9 5.7 + - - +
412A SER* 1.3 83.1 + - - +
414A ARG* 1.3 69.9 + - - +
415A PRO* 4.3 0.3 - - - +
----------------------------------------------------------
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