Contacts of the helix formed by residues 413 - 435 (chain B) in PDB entry 5DO7
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 413 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 3.4 19.9 + - - +
409B ASN* 2.8 8.8 + - - +
410B ASP* 3.4 22.2 - - - +
411B PHE 4.1 0.9 - - - -
412B ARG* 1.3 74.6 - - - +
414B LEU* 1.3 58.3 + - - +
415B PRO* 3.2 23.7 - - - +
416B THR* 2.8 34.6 + - + +
417B LEU* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PHE 5.3 3.4 - - - +
412B ARG 3.3 7.6 + - - +
413B ASP* 1.3 74.1 - - - +
415B PRO* 1.3 78.6 - - + +
416B THR 3.3 0.2 - - - -
417B LEU* 2.8 24.5 + - + +
418B LEU* 2.8 36.6 + - + +
438D HIS* 3.8 26.9 - - + +
517D TRP* 4.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 3.2 14.6 - - - +
414B LEU* 1.3 95.5 - - + +
416B THR* 1.3 63.3 + - - +
418B LEU* 3.3 2.5 + - + +
419B ILE* 3.1 27.5 + - - +
436D PHE* 4.2 11.4 - - + -
438D HIS* 3.5 31.6 - - + +
439D GLY* 4.3 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ASP* 4.3 13.2 - - - +
413B ASP* 2.8 31.5 + - + +
414B LEU 3.3 0.8 - - - -
415B PRO* 1.3 77.5 - - - +
417B LEU* 1.3 70.3 + - + +
419B ILE* 2.8 30.9 + - - +
420B HIS* 2.8 43.9 + - + +
470B LYS* 5.9 1.8 - - - -
503B GLU* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ASP* 4.2 17.3 - - - +
411B PHE* 4.0 36.8 - - + +
413B ASP 3.3 15.7 - - - +
414B LEU* 2.8 22.6 + - + +
416B THR* 1.3 86.8 - - + +
418B LEU* 1.3 58.4 + - - +
420B HIS* 3.6 4.9 + - + +
421B GLY* 3.4 17.5 + - - -
503B GLU* 4.0 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 2.8 35.6 + - + +
415B PRO 3.8 4.3 - - - +
417B LEU* 1.3 69.8 - - - +
419B ILE* 1.3 63.7 + - + +
421B GLY* 3.5 2.0 + - - -
422B ALA* 2.8 29.6 + - - +
433D PHE* 5.1 0.2 - - - -
436D PHE* 4.1 6.1 - - + -
438D HIS* 3.5 35.2 - - + +
514D PRO* 6.5 0.4 - - + -
517D TRP* 4.1 30.7 - - + +
518D LEU* 4.0 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO 3.1 21.1 - - - +
416B THR* 2.8 9.8 + - - +
418B LEU* 1.3 75.8 - - - +
420B HIS* 1.3 57.2 + - + +
422B ALA* 2.7 7.0 + - - +
423B GLU* 2.4 59.6 + - + +
433D PHE* 4.0 23.8 - - + -
436D PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B THR* 2.8 52.1 + - + +
417B LEU* 4.1 6.3 + - - +
419B ILE* 1.3 71.1 - - + +
421B GLY* 1.3 64.8 + - - +
423B GLU* 2.8 23.7 + - - +
424B ALA* 2.8 24.9 + - - +
466B ASP* 2.3 47.7 + - - -
470B LYS* 4.2 10.1 - - - -
503B GLU* 3.5 25.6 + - + +
507B TYR* 4.0 20.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU 3.4 10.6 + - - -
418B LEU* 3.7 3.4 - - - -
419B ILE 3.2 0.8 - - - -
420B HIS* 1.3 76.5 - - - +
422B ALA* 1.3 51.3 + - - +
424B ALA* 3.7 2.0 - - - -
425B CYS* 2.6 41.1 + - - +
507B TYR* 5.3 3.5 - - - +
510B ILE* 3.6 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU 2.8 13.3 + - - +
419B ILE* 2.7 12.3 + - + +
421B GLY* 1.3 69.2 - - - -
423B GLU* 1.3 54.4 + - - +
425B CYS* 2.8 26.8 + - - -
426B LEU* 2.8 33.7 + - + +
429D MET* 4.2 12.1 - - - -
433D PHE* 3.4 35.4 - - + -
518D LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 2.4 39.3 + - + +
420B HIS* 2.8 36.0 + - - +
422B ALA* 1.3 70.9 - - - +
424B ALA* 1.3 60.0 + - - +
426B LEU* 4.9 4.8 - - - +
427B MET* 3.9 24.7 + - + +
462B ASN* 1.9 53.2 + - - +
466B ASP* 4.5 4.0 - - - +
507B TYR* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B HIS 2.8 14.1 + - - +
421B GLY 3.8 2.2 - - - +
423B GLU* 1.3 73.0 - - - +
425B CYS* 1.3 71.3 + - - +
426B LEU 2.7 4.0 + - - -
427B MET* 2.8 17.4 + - - +
428B SER 3.2 6.4 + - - -
507B TYR* 3.7 47.3 + - + +
510B ILE* 4.3 4.9 - - + -
511B TYR* 3.9 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY 2.6 24.0 + - - +
422B ALA* 2.8 8.4 + - - +
424B ALA* 1.3 73.2 - - - +
426B LEU* 1.3 60.2 + - - +
428B SER* 2.8 19.8 + - - -
429B MET* 3.0 40.0 + - - +
510B ILE* 3.4 24.4 - - + +
514B PRO* 5.6 0.2 - - - +
425D CYS* 4.4 1.8 - - - -
429D MET* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ALA* 2.8 32.1 + - + +
423B GLU* 4.9 4.0 - - - +
424B ALA 2.7 4.0 + - - -
425B CYS* 1.3 70.9 - - - +
427B MET* 1.3 66.2 + - - +
429B MET* 2.8 8.4 + - + +
430B THR* 2.8 30.0 + - + +
426D LEU* 3.5 32.5 - - + -
429D MET* 3.7 33.0 - - + -
433D PHE* 5.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 4.3 23.8 - - + -
423B GLU* 3.9 18.9 + - + +
424B ALA* 2.8 12.9 + - - +
426B LEU* 1.3 72.8 - - - +
428B SER* 1.3 63.4 + - - +
430B THR* 2.8 8.8 + - - +
431B ILE* 2.8 29.0 + - - +
458B LEU* 3.7 28.3 - - + +
459B ILE* 4.6 16.2 - - - -
461B PHE* 5.1 3.8 - - + -
462B ASN* 3.7 30.3 - - + +
511B TYR* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ALA 3.2 2.0 + - - -
425B CYS 2.8 14.7 + - - -
427B MET* 1.3 73.3 - - - +
429B MET* 1.3 65.6 + - - +
431B ILE* 4.6 0.2 - - - -
432B GLY* 2.8 22.9 + - - -
510B ILE 3.8 13.2 - - - -
511B TYR* 3.0 27.4 + - - -
514B PRO* 3.2 10.7 - - - +
515B THR* 2.8 45.3 + - - -
518B LEU* 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B CYS* 3.0 40.2 + - - +
426B LEU* 2.8 12.7 + - + +
428B SER* 1.3 77.5 - - - +
430B THR* 1.3 60.2 + - + +
432B GLY* 3.5 1.0 - - - -
433B PHE* 2.8 41.3 + - + -
514B PRO* 5.3 6.5 - - + +
518B LEU* 3.5 15.7 - - - +
422D ALA* 4.2 21.5 - - - -
425D CYS* 3.6 21.1 - - - -
426D LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A PHE* 3.9 20.3 - - + -
426B LEU* 2.8 24.8 + - + +
427B MET* 2.8 16.2 + - - +
429B MET* 1.3 70.1 - - + +
431B ILE* 1.3 78.7 + - - +
433B PHE* 2.8 4.4 + - - +
434B LEU* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 5.7 5.4 - - + -
427B MET 2.8 16.5 + - - +
428B SER 3.8 2.2 - - - +
430B THR* 1.3 81.8 + - - +
432B GLY* 1.3 66.8 + - - +
434B LEU* 3.3 5.4 + - - +
435B TYR* 3.2 29.1 + - + +
451B LEU* 3.9 17.0 - - + +
454B MET* 4.3 6.1 - - + -
455B ILE* 4.1 15.5 - - + +
458B LEU* 3.8 31.2 - - + -
511B TYR* 3.8 24.2 - - + +
515B THR* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER 2.8 18.2 + - - -
429B MET 3.5 3.6 - - - -
430B THR 2.9 0.4 + - - -
431B ILE* 1.3 75.1 - - - +
433B PHE* 1.3 63.4 + - - -
435B TYR* 2.8 15.9 + - - +
436B PHE* 2.8 12.0 + - - -
515B THR* 4.2 9.2 + - - -
518B LEU* 3.6 26.3 - - - +
519B ALA* 4.4 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PRO* 3.4 10.0 - - + +
558A PRO* 5.5 9.0 - - + -
559A PHE* 3.3 24.5 - + + -
429B MET* 2.8 23.9 + - + +
430B THR* 2.8 7.4 + - - +
432B GLY* 1.3 69.3 - - - -
434B LEU* 1.3 58.1 + - - +
436B PHE* 2.7 39.3 + + - +
518B LEU* 3.3 33.2 - - + -
419D ILE* 4.1 24.9 - - + -
422D ALA* 3.4 33.4 - - + -
426D LEU* 5.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 3.5 22.7 - - + -
544A VAL* 3.1 37.5 - - + -
550A ARG* 3.1 39.3 + - + +
555A MET* 4.9 4.7 - - + -
556A PRO* 3.8 5.4 - - - +
559A PHE* 3.1 28.6 - - + -
430B THR* 2.8 16.6 + - - +
431B ILE* 3.5 6.1 - - - +
433B PHE* 1.3 75.8 - - - +
435B TYR* 1.3 87.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 4.1 10.2 - - + +
549A LEU* 3.2 36.1 + - - +
550A ARG* 4.1 18.8 - - + +
431B ILE* 3.2 22.5 + - + +
432B GLY 2.8 5.9 + - - -
434B LEU* 1.3 97.2 - - + +
436B PHE* 1.3 67.3 + - - +
437B GLY* 3.0 5.4 + - - -
443B LEU* 4.9 9.7 - - + +
447B ASP* 3.5 31.6 - - + -
448B THR* 5.0 1.6 - - - -
450B ALA* 3.6 11.8 - - - +
451B LEU* 3.3 47.0 + - + -
454B MET* 4.3 8.0 - - + +
519B ALA* 3.6 10.5 - - + +
----------------------------------------------------------
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