Contacts of the helix formed by residues 500 - 519 (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 GLU 500 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLN* 4.6 4.1 + - - +
410B ASP* 5.0 5.8 - - - +
467B VAL* 3.8 25.3 - - - +
470B LYS* 3.8 24.9 - - - +
496B LYS* 3.2 41.4 + - - +
497B ILE* 4.8 4.9 - - - +
499B GLY* 1.3 75.0 - - - +
501B LEU* 1.3 68.0 + - - +
503B GLU* 2.8 24.0 + - - +
504B HIS* 3.1 6.9 + - + -
543B ARG* 3.5 37.0 - - - +
547B LEU* 4.2 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ILE* 3.9 16.4 + - + +
498B LEU* 2.8 26.4 + - + +
500B GLU* 1.3 75.8 - - - +
502B PRO* 1.3 68.2 - - + +
504B HIS* 2.8 12.1 + - + +
505B CYS* 2.8 38.2 + - - -
536B TRP* 4.0 24.5 - - + -
540B PHE* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE* 4.1 20.2 - - + -
411B PHE* 4.1 21.2 - - + -
498B LEU 3.5 6.7 - - - +
499B GLY 3.7 6.3 - - - +
500B GLU 3.4 4.9 - - - +
501B LEU* 1.3 96.8 - - + +
503B GLU* 1.3 64.5 + - - +
505B CYS* 3.3 15.6 + - + +
506B ALA* 3.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ASP* 3.4 19.8 - - - +
411B PHE* 4.2 14.1 - - + -
416B THR* 5.5 0.2 - - - +
417B LEU* 4.0 21.6 - - + +
420B HIS* 3.5 31.5 + - + +
466B ASP* 4.1 0.7 - - - +
470B LYS* 2.7 31.5 + - - -
499B GLY 5.7 0.2 - - - +
500B GLU* 2.8 16.9 + - - +
502B PRO* 1.3 72.3 - - - +
504B HIS* 1.3 49.9 + - - +
506B ALA* 2.8 15.0 + - - +
507B TYR* 2.8 34.4 + - + +
543B ARG* 3.6 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLU* 3.1 6.9 + - + +
501B LEU* 2.8 20.3 + - + +
503B GLU* 1.3 76.8 - - - +
505B CYS* 1.3 57.3 + - - -
507B TYR* 3.4 9.6 - - - +
508B ILE* 2.8 57.8 + - + +
536B TRP* 3.6 30.6 - + - -
539B VAL* 3.9 8.2 - - + +
540B PHE* 3.5 41.1 - + + +
543B ARG* 3.1 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 2.8 35.4 + - - -
502B PRO* 3.5 9.6 - - + +
504B HIS* 1.3 72.1 - - - +
506B ALA* 1.3 61.6 + - - +
508B ILE* 3.3 2.8 + - - +
509B ILE* 2.8 32.1 + - - +
532B PHE* 4.9 3.4 - - + -
536B TRP* 3.7 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B PRO 3.3 6.2 + - - +
503B GLU* 2.8 12.5 + - - +
505B CYS* 1.3 75.0 - - - +
507B TYR* 1.3 67.7 + - - +
509B ILE* 2.9 13.3 + - + -
510B ILE* 2.8 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B HIS* 4.0 33.7 - + + -
421B GLY* 5.9 3.4 - - - -
424B ALA* 3.7 23.3 - - + +
427B MET* 5.4 0.2 - - - -
459B ILE* 3.6 32.1 - - + +
462B ASN* 2.5 31.2 + - - +
463B VAL* 4.4 9.8 + - + -
466B ASP* 3.5 20.2 - - - -
503B GLU* 2.8 17.3 + - + +
504B HIS* 3.4 15.3 - - - +
506B ALA* 1.3 77.0 - - - +
508B ILE* 1.3 69.4 + - + +
510B ILE* 3.9 4.2 - - - +
511B TYR* 3.4 15.9 + - + +
539B VAL* 5.5 4.9 - - + -
543B ARG* 3.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 5.9 1.3 - - + -
504B HIS* 2.8 55.9 + - + +
505B CYS 3.7 3.8 - - - +
507B TYR* 1.3 74.3 - - + +
509B ILE* 1.3 68.5 + - - +
511B TYR* 2.8 8.8 + - + +
512B GLY 2.8 20.9 + - - +
532B PHE* 3.5 26.9 - - + -
535B VAL* 4.1 17.9 - - + +
536B TRP* 3.2 35.4 - - + +
539B VAL* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B CYS 2.8 21.9 + - - +
506B ALA* 2.9 23.9 + - + +
508B ILE* 1.3 72.0 - - - +
510B ILE* 1.3 64.6 - - + +
513B MET* 2.8 69.4 + - + +
528B PHE* 6.3 1.1 - - + -
532B PHE* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY* 3.6 15.7 - - - +
424B ALA* 4.3 2.0 - - + -
425B CYS* 3.4 38.8 - - + +
428B SER* 3.8 4.3 - - - -
506B ALA* 2.8 32.5 + - + +
507B TYR* 3.9 5.8 - - - +
509B ILE* 1.3 82.0 - - + +
511B TYR* 1.3 56.9 + - - +
513B MET* 4.9 9.2 - - + -
514B PRO* 3.3 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ALA* 3.9 15.0 - - + -
427B MET* 3.8 30.5 - - + -
428B SER* 3.0 32.0 + - - -
431B ILE* 3.8 11.1 - - + +
454B MET 4.0 1.6 + - - -
455B ILE* 2.6 52.6 + - + -
458B LEU* 4.1 6.8 - - + +
459B ILE* 3.0 48.9 - - + +
507B TYR* 3.4 13.4 + - + +
508B ILE* 2.8 9.9 + - - +
510B ILE* 1.3 79.9 - - - +
512B GLY* 1.3 64.0 + - - +
515B THR* 3.4 9.3 + - - -
535B VAL* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ILE* 4.8 6.7 - - - -
508B ILE 2.8 13.7 + - - -
509B ILE* 3.9 0.9 - - - -
511B TYR* 1.3 86.1 - - - +
513B MET* 1.3 67.6 + - - +
515B THR* 4.2 2.1 - - - -
516B TYR* 3.7 15.6 + - - +
528B PHE* 5.2 1.0 - - - -
531B HIS* 4.3 12.8 + - - -
532B PHE* 5.0 11.0 - - - -
535B VAL* 5.2 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ILE* 2.8 60.0 + - + +
510B ILE* 4.9 9.9 - - + -
512B GLY* 1.3 70.1 - - - +
514B PRO* 1.3 79.4 - - + +
516B TYR* 2.8 23.7 + - - +
517B TRP* 3.4 11.6 + - + +
528B PHE* 3.8 31.4 - - + -
532B PHE* 5.1 1.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B CYS 5.6 0.4 - - - +
428B SER* 3.2 23.8 - - - +
429B MET* 5.3 7.2 - - + +
509B ILE 3.8 1.1 - - - +
510B ILE 3.3 22.2 - - - +
511B TYR 3.9 0.2 - - - -
512B GLY 3.5 1.1 - - - -
513B MET* 1.3 100.7 - - + +
515B THR* 1.3 65.1 + - - +
517B TRP* 2.8 12.4 + - + +
518B LEU* 2.8 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER* 2.8 48.7 + - - -
431B ILE* 3.8 25.3 - - + +
432B GLY* 4.3 6.1 - - - +
451B LEU* 4.3 15.0 - - + -
455B ILE* 3.6 28.8 - - + +
511B TYR* 3.4 12.1 + - - -
512B GLY 4.2 0.9 - - - -
514B PRO* 1.3 69.9 - - - +
516B TYR* 1.3 66.4 + - - +
518B LEU* 4.5 0.2 - - - -
519B ALA* 2.8 26.2 + - - +
531B HIS* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLY 3.7 9.5 + - - +
513B MET* 2.8 22.9 + - - +
515B THR* 1.3 78.6 - - - +
517B TRP* 1.3 75.8 + + - +
520B ASN 3.4 1.9 + - - -
521B LEU* 3.1 48.9 + - + +
522B ARG 2.5 30.9 + - - -
523B PRO 4.6 0.6 + - - -
527B PRO* 3.5 8.5 - - - +
528B PHE* 3.1 59.8 + + + +
531B HIS* 3.5 32.3 - + + +
607B GLN* 3.3 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B HIS* 3.5 12.8 - - - -
513B MET* 3.4 17.8 + - + +
514B PRO* 2.8 14.3 + - + +
516B TYR* 1.3 92.3 - + - +
518B LEU* 1.3 67.8 + - - +
520B ASN* 2.8 18.0 + - - +
521B LEU 5.1 4.5 - - - -
522B ARG 5.1 3.8 - - - -
523B PRO* 5.1 2.7 - - + -
524B GLY 3.9 28.0 - - - -
528B PHE* 3.7 32.2 - + + -
414D LEU* 4.9 16.4 - - + -
418D LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER 4.1 2.2 - - - +
429B MET* 3.5 38.1 - - + +
432B GLY* 3.6 20.0 - - - -
433B PHE* 3.3 32.3 - - + -
436B PHE* 3.6 23.6 - - + -
437B GLY* 2.8 19.8 + - - -
438B HIS* 4.1 6.2 - - - -
514B PRO* 2.8 30.2 + - + +
515B THR 3.7 0.2 - - - +
517B TRP* 1.3 75.5 - - - +
519B ALA* 1.3 58.5 + - - +
520B ASN 3.0 1.4 + - - -
418D LEU* 3.8 24.4 - - + +
422D ALA* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B GLY* 4.5 3.1 - - - +
435B TYR* 3.6 20.1 - - + +
437B GLY* 3.7 8.4 - - - -
443B LEU* 4.0 9.7 - - - +
451B LEU* 3.3 33.9 - - + -
515B THR 2.8 20.0 + - - +
518B LEU* 1.3 71.0 - - - +
520B ASN* 1.3 68.8 + - - +
521B LEU* 3.4 15.2 - - + +
----------------------------------------------------------
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