Contacts of the helix formed by residues 537 - 553 (chain A) in PDB entry 3OJW
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 ILE 537 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A THR* 4.9 0.9 - - + -
532A GLY 4.6 3.0 + - - +
533A PRO 4.3 0.4 + - - -
534A GLY 3.3 17.7 + - - +
535A THR* 2.8 3.7 + - - +
536A GLY* 1.3 77.8 - - - +
538A ALA* 1.3 68.9 + - - +
539A PRO* 3.5 0.7 - - - -
540A PHE* 2.8 30.3 + - + +
541A MET* 3.2 28.1 + - - +
562A LEU* 4.1 15.3 - - + -
564A TYR* 4.0 24.5 - - + -
574A LEU* 4.3 11.9 - - + +
575A TYR* 4.1 26.2 - - + -
579A LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A SER 3.8 16.4 - - - +
459A ALA* 3.1 28.4 - - + +
472A THR* 3.7 24.7 - - - +
535A THR 3.0 15.3 + - - +
536A GLY 3.2 0.6 - - - -
537A ILE* 1.3 77.7 - - - +
539A PRO* 1.3 71.6 - - + +
541A MET* 3.1 11.5 + - - +
677A TRP* 4.8 0.2 - - + -
752A FAD 4.1 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY* 4.6 10.0 + - - +
457A SER* 3.8 16.3 - - - -
458A ILE 3.7 14.2 - - - +
518A PHE* 4.0 27.6 - - + -
536A GLY 3.4 11.4 - - - +
538A ALA* 1.3 94.8 - - + +
540A PHE* 1.3 62.0 + - + +
542A GLY* 3.1 5.0 + - - -
543A PHE* 3.1 28.9 + - + -
630A CYS* 3.7 30.3 - - + -
675A ASP* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 3.9 11.4 - + - -
530A MET* 3.5 32.3 - - + -
531A VAL 3.5 29.8 - - - -
532A GLY* 3.9 1.1 - - - -
536A GLY 3.7 24.2 - - - -
537A ILE* 2.8 18.0 + - + +
539A PRO* 1.3 74.5 - - + +
541A MET* 1.3 58.5 + - - -
542A GLY 3.1 1.6 - - - -
543A PHE* 3.6 12.5 - + - +
544A ILE* 2.9 38.3 + - + +
562A LEU* 4.1 17.3 - - + -
628A TYR* 3.5 46.2 - - + -
630A CYS* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ALA* 3.5 17.7 - - + +
537A ILE* 3.2 27.0 + - + +
538A ALA* 3.1 6.8 + - - +
540A PHE* 1.3 77.8 - - - +
542A GLY* 1.3 56.3 + - - +
544A ILE* 4.1 3.8 - - - +
545A GLN* 2.9 40.3 + - - +
575A TYR* 3.7 50.7 - - + -
578A GLU* 3.9 20.2 - - + -
579A LEU* 3.8 26.7 - - + -
582A PHE* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER* 3.2 21.0 + - - -
458A ILE 5.1 0.9 - - - -
459A ALA* 3.6 3.4 + - - -
460A SER* 3.6 26.2 - - - -
461A SER* 3.4 1.8 - - - -
538A ALA 3.8 1.2 + - - -
539A PRO 3.1 7.4 + - - -
540A PHE 3.1 0.2 - - - -
541A MET* 1.3 78.2 - - - +
543A PHE* 1.3 64.3 + - - +
545A GLN* 3.2 3.0 + - - +
546A GLU* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER* 3.5 37.7 - - - -
317A GLY* 3.8 4.0 - - - -
518A PHE* 3.5 36.3 - + - -
520A LEU* 3.6 33.0 - - + -
528A VAL* 4.8 0.7 - - + -
530A MET* 3.9 17.7 - - + -
539A PRO 3.1 16.7 + - - +
540A PHE* 3.6 22.0 - + - +
542A GLY* 1.3 75.9 - - - +
544A ILE* 1.3 58.0 + - - +
546A GLU* 3.2 2.6 + - - +
547A ARG* 2.9 36.1 + - + +
628A TYR* 3.6 38.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A MET* 3.7 30.3 - - + -
540A PHE* 2.9 24.8 + - + +
541A MET* 4.1 5.2 - - - +
543A PHE* 1.3 73.2 - - - +
545A GLN* 1.3 66.2 + - - +
547A ARG* 3.9 6.0 - - + +
548A ALA* 2.9 24.4 + - - +
560A THR* 4.5 5.6 - - + -
562A LEU* 4.2 8.5 - - + -
579A LEU* 4.1 20.0 - - + -
582A PHE* 3.6 38.4 - - + -
587A ALA* 4.8 6.7 - - + +
588A LEU* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ALA 3.8 12.7 + - - -
460A SER* 3.4 4.3 - - - +
461A SER* 3.1 25.8 + - - -
464A VAL* 3.8 12.8 - - + +
465A HIS* 3.2 32.0 + - + -
470A HIS* 4.6 7.1 + - - -
541A MET* 2.9 31.7 + - - +
542A GLY 3.4 4.7 - - - +
544A ILE* 1.3 77.2 - - - +
546A GLU* 1.3 56.2 + - - +
548A ALA* 3.5 2.8 + - - +
549A TRP* 3.0 27.2 + - - +
582A PHE* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 4.3 3.6 - - - +
316A SER* 3.2 20.1 + - - -
461A SER* 2.8 27.2 + - - +
462A SER 4.6 0.7 + - - -
463A LYS* 3.4 38.6 + - + +
464A VAL* 4.8 0.2 - - - -
520A LEU* 3.5 27.3 - - + +
542A GLY 2.9 14.5 + - - +
543A PHE 3.6 4.3 - - - +
545A GLN* 1.3 74.9 - - - +
547A ARG* 1.3 59.8 + - - +
549A TRP* 3.1 8.7 + - + +
550A LEU* 2.9 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 3.9 21.0 - - + +
521A PRO* 4.3 8.5 + - - +
523A LYS 4.6 0.2 + - - -
524A SER* 3.2 24.5 + - - +
526A THR 3.0 23.8 + - - -
528A VAL* 3.5 18.9 - - + +
543A PHE* 2.9 27.7 + - + +
544A ILE* 3.9 4.9 - - - +
546A GLU* 1.3 71.8 - - - +
548A ALA* 1.3 64.0 + - - +
550A LEU* 3.2 15.9 + - - +
551A ARG* 3.1 26.9 + - - +
557A VAL* 3.4 17.1 - - + +
558A GLY 3.3 15.4 + - - +
559A GLU 3.2 24.7 + - - -
560A THR* 3.0 27.3 + - + +
587A ALA 4.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE 2.9 17.9 + - - +
545A GLN 3.7 4.5 - - - +
547A ARG* 1.3 77.1 - - - +
549A TRP* 1.3 63.5 + - - +
551A ARG* 3.2 8.0 + - - +
552A GLU* 3.1 32.6 + - - +
581A ARG* 5.4 2.7 - - - +
582A PHE* 4.0 16.8 - - + -
587A ALA* 3.4 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LYS* 3.7 58.5 + - + -
464A VAL* 3.8 18.6 - - + -
545A GLN 3.0 15.4 + - - +
546A GLU* 3.1 9.6 + - - +
548A ALA* 1.3 77.2 - - - +
550A LEU* 1.3 92.6 + - + +
552A GLU* 3.1 21.7 + - - +
553A GLN* 2.9 67.0 + - + +
555A LYS* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LYS* 6.1 1.3 - - - -
520A LEU* 5.7 2.5 - - + -
524A SER* 4.2 21.8 - - - -
546A GLU* 2.9 29.6 + - + +
547A ARG* 3.2 24.2 + - - +
549A TRP* 1.3 99.5 - - + +
551A ARG* 1.3 63.7 + - - +
553A GLN* 3.2 9.2 + - - +
554A GLY 3.4 0.2 + - - -
555A LYS* 3.0 47.6 + - + +
557A VAL* 3.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ARG 3.1 19.9 + - - +
548A ALA* 3.2 8.0 + - - +
550A LEU* 1.3 75.0 - - - +
552A GLU* 1.3 65.0 + - + +
554A GLY* 2.9 15.8 + - - -
555A LYS 4.1 9.7 + - - +
557A VAL* 3.7 28.6 + - + +
585A ASP* 3.0 25.3 + - - +
586A GLY* 3.3 21.5 + - - -
587A ALA* 3.5 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ALA* 3.1 19.2 + - - +
549A TRP* 3.1 23.7 + - - +
551A ARG* 1.3 75.5 - - + +
553A GLN* 1.3 65.9 + - - +
554A GLY* 3.0 5.1 + - - -
581A ARG* 4.5 14.6 + - - -
585A ASP* 5.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A TRP* 2.9 62.5 + - + +
550A LEU* 3.5 10.3 - - - +
551A ARG 3.1 0.8 - - - -
552A GLU* 1.3 82.7 - - - +
554A GLY* 1.3 60.2 + - - +
555A LYS* 3.5 23.6 - - + +
----------------------------------------------------------
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