Contacts of the helix formed by residues 403 - 416 (chain R) in PDB entry 6QX2
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 403 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401R SER* 3.8 3.3 - - - -
402R ASP* 1.3 84.2 - - + +
404R ASP* 1.3 64.2 + - - +
405R LYS* 3.5 10.3 + - - +
406R VAL* 3.3 28.8 + - + +
407R ALA* 3.2 21.3 + - - +
434T THR* 4.3 6.9 - - - +
436T LEU* 4.0 24.5 - - + -
437T GLU* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 404 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403R THR* 1.3 71.8 - - - +
405R LYS* 1.3 56.8 + - - +
407R ALA* 3.3 8.8 + - - +
408R MET* 2.9 35.9 + - + +
423R GLN* 6.2 0.4 - - - +
426R LEU* 4.0 4.8 - - + +
431T ARG* 3.3 32.3 - - + +
434T THR* 4.6 10.0 + - + +
437T GLU* 5.5 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403R THR* 3.3 9.1 + - - +
404R ASP* 1.3 77.0 - - - +
406R VAL* 1.3 61.3 + - + +
408R MET* 3.4 10.7 - - - +
409R GLU* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401R SER* 3.9 20.6 - - - +
402R ASP* 4.4 14.4 - - + +
403R THR* 3.3 27.6 + - + +
405R LYS* 1.3 74.1 - - + +
407R ALA* 1.3 53.9 - - - +
409R GLU* 3.2 12.5 + - - +
410R SER* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397R THR 5.0 0.9 - - - -
398R ILE* 4.3 11.9 - - + -
401R SER* 3.2 27.4 + - - +
403R THR 3.2 7.9 + - - +
404R ASP* 3.5 10.5 - - - +
406R VAL* 1.3 77.8 - - - +
408R MET* 1.3 56.1 + - - +
410R SER* 3.4 2.3 + - - -
411R LEU* 2.9 37.9 + - - +
426R LEU* 4.2 20.9 - - + -
434T THR* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 408 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404R ASP* 2.9 21.8 + - + +
405R LYS* 3.4 12.3 - - - +
406R VAL 3.3 0.2 - - - -
407R ALA* 1.3 76.5 - - - +
409R GLU* 1.3 61.2 + - - +
411R LEU* 3.9 1.8 - - - +
412R GLN* 3.1 40.4 + - - +
419R GLU* 3.4 47.8 - - + +
422R ALA* 3.7 8.1 - - + +
423R GLN* 3.4 45.3 - - + +
426R LEU* 3.6 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 409 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405R LYS 3.2 9.0 + - - +
406R VAL* 3.2 15.8 + - - +
408R MET* 1.3 77.0 - - - +
410R SER* 1.3 60.5 + - - +
412R GLN* 3.3 11.9 + - - +
413R GLN* 2.9 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 410 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397R THR* 3.6 22.9 - - - -
400R GLU* 5.7 2.2 - - - -
401R SER* 3.9 8.3 + - - -
406R VAL* 2.8 29.2 + - - +
407R ALA 3.7 2.5 - - - -
409R GLU* 1.3 79.3 + - - +
411R LEU* 1.3 55.9 + - - +
413R GLN* 4.0 5.9 - - - +
414R ARG* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394R ILE* 3.9 35.9 - - + +
397R THR* 3.9 22.9 - - + -
398R ILE* 4.1 19.5 - - + -
407R ALA 2.9 24.8 + - - +
408R MET 3.9 4.0 - - - +
410R SER* 1.3 72.1 - - - +
412R GLN* 1.3 63.7 + - - +
415R PHE* 3.1 36.1 + - + +
417R LEU* 3.6 15.2 - - + +
422R ALA* 4.2 16.8 - - + +
425R ILE* 4.5 8.5 - - + -
426R LEU* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 412 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408R MET* 3.1 41.2 + - - +
409R GLU* 3.5 9.3 - - + +
411R LEU* 1.3 77.2 - - - +
413R GLN* 1.3 58.6 + - + +
416R LYS* 3.0 30.3 + - - -
417R LEU* 3.2 26.3 + - - +
418R SER* 3.7 10.4 - - - +
419R GLU* 3.6 39.6 + - - +
422R ALA* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 413 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409R GLU* 2.9 52.2 + - + +
410R SER* 4.0 5.5 - - - +
412R GLN* 1.3 80.3 - - + +
414R ARG* 1.3 63.2 + - - +
415R PHE 3.5 0.2 + - - -
416R LYS* 3.9 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397R THR* 5.2 4.9 - - + +
410R SER* 2.9 19.4 + - - +
413R GLN* 1.3 78.0 - - - +
415R PHE* 1.3 82.3 + - + +
416R LYS 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 415 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386R ILE* 4.4 16.3 - - + +
390R HIS* 4.0 33.9 - + + -
393R GLU* 3.9 30.1 - - + -
394R ILE* 3.7 33.4 - - + -
397R THR* 3.8 15.9 - - - -
411R LEU* 3.1 27.1 + - + +
414R ARG* 1.3 95.3 - - + +
416R LYS* 1.3 71.1 + - - +
417R LEU* 3.3 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 416 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386R ILE* 5.8 1.7 - - - +
412R GLN 3.0 14.2 + - - -
413R GLN* 3.9 17.9 + - - +
414R ARG 3.7 1.8 - - - -
415R PHE* 1.3 80.6 - - - +
417R LEU* 1.3 60.5 + - - +
421R GLN* 4.8 1.6 - - - +
----------------------------------------------------------
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