Contacts of the helix formed by residues 406 - 422 (chain W) in PDB entry 5O9G
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 GLY 406 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380W GLN* 5.1 2.6 - - - +
404W GLY 3.1 8.9 + - - -
405W LEU* 1.3 78.1 - - - +
407W LYS* 1.3 64.2 + - - +
408W THR 3.2 2.7 - - - -
409W VAL* 3.4 4.1 + - - +
410W GLN* 3.1 30.0 + - - +
1501W ADP 3.5 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 407 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399W LEU* 3.7 29.2 - - + +
401W ASP* 4.4 16.2 - - + +
402W GLU 3.7 14.9 + - - +
403W MET* 3.4 25.5 - - - +
404W GLY 3.7 2.4 - - - +
405W LEU* 4.9 2.7 - - + +
406W GLY* 1.3 78.4 - - - +
408W THR* 1.3 58.8 + - - +
410W GLN* 3.8 10.7 + - - +
411W THR* 3.0 25.8 + - - -
440W TRP* 5.3 0.4 - - - -
513W ASP* 4.8 8.3 - - - +
514W GLU* 5.3 2.2 - - - -
540W ILE* 3.7 31.5 - - + +
541W THR* 5.3 6.1 - - - +
1501W ADP 3.0 34.0 + - - +
1502W BEF 3.5 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 408 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406W GLY 3.2 0.6 - - - -
407W LYS* 1.3 78.1 - - - +
409W VAL* 1.3 65.4 + - - +
411W THR* 3.2 4.3 + - - -
412W VAL* 3.1 27.5 + - + +
440W TRP* 3.2 59.8 + - + +
443W THR* 4.7 16.6 - - + +
513W ASP* 4.9 0.5 + - - -
1501W ADP 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371W ILE* 5.7 0.2 - - + -
376W LEU* 4.9 10.3 - - + -
380W GLN* 6.3 1.3 - - + -
406W GLY* 3.4 5.3 + - - +
408W THR* 1.3 77.4 - - - +
410W GLN* 1.3 58.9 + - + +
412W VAL* 3.3 6.5 + - + +
413W ALA* 2.9 31.6 + - + +
443W THR* 4.5 12.3 - - + -
447W TRP* 3.9 52.7 - - + +
1501W ADP 3.3 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 410 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376W LEU* 5.7 1.6 - - + -
379W PHE* 4.3 0.9 - - - -
380W GLN* 3.3 50.3 + - + +
383W GLY* 4.6 7.9 - - - -
384W ILE* 4.3 11.3 - - + +
387W MET* 4.7 5.8 - - - +
399W LEU* 3.6 27.9 - - + +
401W ASP* 4.3 1.4 + - - -
405W LEU 3.8 7.8 - - - +
406W GLY 3.1 17.8 + - - +
407W LYS* 4.1 7.6 - - - +
408W THR 3.3 0.2 - - - -
409W VAL* 1.3 76.3 - - + +
411W THR* 1.3 57.6 + - - +
413W ALA* 4.1 5.3 - - - +
414W PHE* 2.9 31.4 + - - +
597W ARG* 3.5 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 411 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387W MET* 5.2 6.4 - - - +
399W LEU* 5.4 1.7 - - - +
407W LYS 3.0 14.5 + - - -
408W THR* 3.2 12.0 + - - -
410W GLN* 1.3 76.4 - - - +
412W VAL* 1.3 60.9 + - + +
414W PHE* 3.3 5.0 + - + +
415W ILE* 2.9 53.2 + - + +
430W ILE* 5.2 1.1 - - + -
440W TRP* 4.6 17.9 - - + -
509W PHE* 4.9 4.7 - - + -
511W ALA* 4.1 22.2 - - + -
538W MET* 6.4 0.2 - - + -
540W ILE* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 412 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408W THR* 3.1 26.1 + - + +
409W VAL* 3.3 6.5 + - + +
411W THR* 1.3 76.8 - - + +
413W ALA* 1.3 57.9 + - - +
415W ILE* 3.4 6.0 + - + +
416W SER* 2.9 29.6 + - - -
440W TRP* 5.0 7.6 - - + +
443W THR* 5.5 4.0 - - + +
444W PHE* 3.6 49.8 - - + +
447W TRP* 4.9 10.5 - - + -
448W ALA* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368W PRO* 5.7 5.3 - - + +
371W ILE* 5.1 16.2 - - + -
376W LEU* 5.2 3.4 - - + -
384W ILE* 3.7 25.7 - - + +
409W VAL* 2.9 21.9 + - + +
410W GLN 4.1 0.4 - - - +
412W VAL* 1.3 77.2 - - - +
414W PHE* 1.3 57.5 + - - +
416W SER* 4.0 4.7 - - - -
417W TRP* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384W ILE* 4.2 17.4 - - + +
387W MET* 3.5 46.9 - - + -
388W ALA* 3.3 35.9 - - + -
391W TRP* 4.2 15.0 - + + -
410W GLN 2.9 19.9 + - - +
411W THR* 3.8 3.1 - - - +
413W ALA* 1.3 75.2 - - - +
415W ILE* 1.3 64.2 + - + +
417W TRP* 3.9 7.7 - + - +
418W LEU* 2.9 54.7 + - + +
509W PHE* 3.8 31.9 - + - -
538W MET* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411W THR* 2.9 32.9 + - + +
412W VAL* 3.9 5.8 - - + +
414W PHE* 1.3 77.9 - - + +
416W SER* 1.3 60.8 + - - +
418W LEU* 3.3 7.6 + - + +
419W ILE* 2.9 54.2 + - + +
428W HIS* 4.3 11.7 - - + -
430W ILE* 3.7 34.5 - - + -
444W PHE* 5.6 7.9 - - + -
451W LEU* 5.1 3.4 - - + -
487W VAL* 4.5 13.5 - - + -
509W PHE* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 416 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370W PHE* 4.0 21.0 - - - +
412W VAL* 2.9 19.0 + - - -
413W ALA* 4.0 5.2 - - - -
415W ILE* 1.3 78.3 - - - +
417W TRP* 1.3 57.0 + - - +
419W ILE* 3.3 2.4 + - - -
420W PHE* 2.9 55.1 + - - +
448W ALA* 5.0 9.4 - - - +
451W LEU* 4.2 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 417 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361W PHE* 4.2 10.8 - + - -
362W GLU 5.6 0.4 - - - -
364W LEU* 3.8 32.5 - - + +
368W PRO* 4.0 34.5 - - + +
370W PHE* 4.8 10.7 - + + -
384W ILE* 5.3 11.4 - - + -
388W ALA* 3.7 25.4 - - + -
391W TRP* 6.1 0.7 - + - -
413W ALA 2.9 20.3 + - - +
414W PHE* 4.1 9.4 - + - +
416W SER* 1.3 76.6 - - - +
418W LEU* 1.3 65.1 + - + +
421W ALA* 2.5 49.8 + - + +
422W ARG* 3.4 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388W ALA* 6.4 0.2 - - + -
391W TRP* 3.6 56.1 - - + +
414W PHE* 2.9 42.5 + - + +
415W ILE* 3.7 6.7 - - + +
416W SER 3.2 0.2 - - - -
417W TRP* 1.3 86.0 - - + +
419W ILE* 1.3 64.1 + - + +
422W ARG* 3.3 27.2 + - + +
424W GLN* 3.4 23.5 + - + +
428W HIS* 5.2 11.2 - - + +
509W PHE* 5.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346W ILE* 5.1 4.3 - - + -
415W ILE* 2.9 30.3 + - + +
416W SER 3.8 2.9 - - - +
418W LEU* 1.3 77.8 - - + +
420W PHE* 1.3 75.3 + - + +
423W ARG* 3.3 10.7 - - - +
424W GLN 3.2 33.7 + - - +
425W ASN* 3.3 37.9 + - - +
426W GLY 4.9 0.7 - - - +
428W HIS* 3.8 24.9 - - + +
451W LEU* 4.0 18.2 - - + -
486W ASN* 4.8 11.4 - - - +
487W VAL* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 420 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344W SER* 6.5 1.8 - - - -
346W ILE* 4.8 20.4 - - + -
370W PHE* 3.6 36.4 - + + -
416W SER* 2.9 34.8 + - - +
419W ILE* 1.3 85.9 - - + +
421W ALA* 1.3 58.3 + - - +
423W ARG* 4.5 3.5 - - - +
425W ASN* 5.5 1.6 - - - -
450W ASP* 4.9 13.7 - - + -
451W LEU* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370W PHE* 6.2 0.7 - - + -
417W TRP* 2.5 54.0 + - + +
420W PHE* 1.3 79.4 - - - +
422W ARG* 1.3 71.9 + - - +
423W ARG* 3.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352W SER* 2.7 27.5 + - - -
354W TYR* 3.6 10.1 - - + -
359W PRO* 4.1 25.9 - - - +
360W ARG 4.9 4.0 + - - -
361W PHE* 3.3 40.2 - - - +
362W GLU* 4.3 12.1 + - - +
391W TRP* 3.8 19.0 - - + -
392W SER* 5.1 1.2 + - - -
417W TRP* 3.4 33.8 - - + -
418W LEU* 3.3 34.6 + - + +
421W ALA* 1.3 90.7 + - - +
423W ARG* 1.3 57.6 + - - +
424W GLN* 3.4 7.8 - - + +
----------------------------------------------------------
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