Contacts of the helix formed by residues 537 - 553 (chain A) in PDB entry 5J3V
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 ASN 537 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LYS* 3.0 31.3 + - - +
497A GLN* 3.3 26.4 + - - +
498A GLU* 3.6 15.3 - - + +
533A TYR* 3.4 28.0 - - + -
534A GLN* 3.5 10.3 + - - +
536A LYS* 1.3 107.3 + - - +
538A LEU* 1.3 64.8 + - - +
539A LEU 3.1 2.7 - - - -
540A ILE* 3.2 11.9 + - + +
541A LEU 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A PHE* 3.7 32.5 - - + +
533A TYR* 4.1 14.3 - - + +
534A GLN 3.0 18.5 + - - +
535A HIS* 4.0 18.2 - - + +
536A LYS 3.4 0.6 - - - -
537A ASN* 1.3 76.4 - - - +
539A LEU* 1.3 59.9 + - + +
541A LEU* 3.4 18.4 + - + +
542A TYR* 3.0 50.0 + - + +
572A LYS* 3.9 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A HIS 3.7 17.9 - - - +
536A LYS* 3.9 13.9 - - - +
537A ASN 3.1 0.2 - - - -
538A LEU* 1.3 78.4 - - + +
540A ILE* 1.3 66.0 + - + +
542A TYR* 3.3 12.2 + - + +
543A ASP* 3.1 17.3 + - - +
582A ASP* 5.7 4.3 - - - +
585A PRO* 3.6 32.9 - - + +
21C ALA* 5.1 14.6 - - + -
22C THR* 3.4 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLU* 3.9 28.7 - - + +
501A CYS* 3.7 14.7 - - + +
502A SER* 3.6 39.0 - - - +
505A ALA* 6.0 0.2 - - + -
536A LYS 4.2 6.1 - - - +
537A ASN* 3.2 21.5 + - - +
539A LEU* 1.3 75.4 - - + +
541A LEU* 1.3 58.1 + - - +
543A ASP* 3.2 3.9 + - + +
544A ALA* 3.0 26.3 + - - +
22C THR* 3.6 31.4 - - + +
25C ALA* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 5.4 0.2 - - + -
501A CYS* 3.7 13.0 - - - -
526A LEU* 3.8 38.6 - - + +
529A ALA* 3.8 32.3 - - + +
530A PHE* 3.6 32.8 - - + -
533A TYR* 4.2 8.7 - - + -
537A ASN 3.1 12.6 + - - +
538A LEU* 3.6 17.5 - - + +
539A LEU 3.2 0.2 - - - -
540A ILE* 1.3 74.3 - - - +
542A TYR* 1.3 59.3 + - - +
544A ALA* 3.2 0.7 + - - +
545A ILE* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A PHE* 3.4 29.8 - + - -
538A LEU* 3.0 37.8 + - + +
539A LEU* 3.3 11.0 + - + +
541A LEU* 1.3 75.4 - - - +
543A ASP* 1.3 56.5 + - - +
545A ILE* 4.7 0.2 - - - -
546A GLY* 3.0 24.3 + - - -
569A LEU* 4.1 2.5 - - + -
572A LYS* 3.5 29.2 - - - +
576A LEU* 5.9 0.3 - - - +
582A ASP 5.1 3.8 + - - -
585A PRO* 3.5 40.6 - - + +
586A LEU* 3.4 39.0 - - + +
589A CYS* 3.6 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ALA* 3.8 5.7 - - - +
539A LEU 3.1 7.0 + - - +
540A ILE* 3.4 8.9 - - - +
542A TYR* 1.3 76.0 - - - +
544A ALA* 1.3 55.3 + - - +
546A GLY* 5.1 0.2 - - - -
547A THR* 2.6 51.5 + - - -
22C THR* 3.4 28.4 - - + +
23C LYS* 3.9 16.3 - - - +
26C ARG* 2.6 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A CYS* 3.9 30.1 - - - +
504A PHE* 4.9 4.5 - - + -
505A ALA* 3.9 9.8 - - + +
508A GLU* 2.8 32.6 - - - +
526A LEU* 4.5 15.4 - - + +
540A ILE 3.0 16.0 + - - +
541A LEU* 3.2 4.5 + - - +
543A ASP* 1.3 77.1 - - - +
545A ILE* 1.3 58.1 + - - +
548A LEU* 3.1 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LEU* 5.9 1.8 - - + -
526A LEU* 4.2 24.9 - - + +
527A VAL* 5.6 1.1 - - + +
530A PHE* 3.6 35.7 - - + -
541A LEU* 2.9 30.2 + - + +
542A TYR* 5.2 0.2 - - - -
544A ALA* 1.3 75.3 - - - +
546A GLY* 1.3 66.0 + - - +
548A LEU* 3.1 17.6 + - + +
549A ALA* 3.2 12.6 + - - +
556A LEU* 5.9 0.7 - - - +
565A LEU* 3.9 33.4 - - + -
569A LEU* 5.1 2.7 - - + -
589A CYS* 3.7 21.3 - - - -
593A VAL* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A TYR 3.0 17.2 + - - -
543A ASP* 3.8 0.9 - - - -
545A ILE* 1.3 76.6 - - - +
547A THR* 1.3 61.2 + - - +
549A ALA* 3.5 2.4 + - - -
550A ASP* 3.2 29.3 + - - +
589A CYS* 3.9 13.6 - - - -
592A SER* 3.3 21.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ALA* 3.4 24.7 - - - +
508A GLU* 3.6 17.3 - - + +
509A GLU* 3.6 24.5 + - + +
543A ASP* 2.6 41.8 + - - -
544A ALA* 4.4 0.7 - - - -
546A GLY* 1.3 70.5 - - - +
548A LEU* 1.3 61.8 + - - +
550A ASP* 3.2 10.4 + - + +
551A SER* 2.8 33.1 + - - +
23C LYS* 5.8 0.3 - - - +
26C ARG* 3.3 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLU* 3.3 29.3 + - + +
515A LEU* 4.7 3.6 - - + -
519A LEU* 3.8 19.3 - - + -
522A ILE* 3.9 29.2 - - + -
523A LEU* 3.9 28.3 - - + -
526A LEU* 4.1 7.2 - - + -
544A ALA 3.1 9.1 + - - +
545A ILE* 3.1 12.3 + - + +
547A THR* 1.3 76.3 - - - +
549A ALA* 1.3 57.3 + - - +
551A SER* 3.1 3.9 + - - -
552A VAL* 2.9 53.7 + - + +
556A LEU* 4.7 5.4 - - + -
565A LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ILE 3.2 8.6 + - - +
546A GLY 3.8 8.1 - - - +
547A THR 3.3 0.2 - - - -
548A LEU* 1.3 78.5 - - - +
550A ASP* 1.3 57.5 + - - +
552A VAL* 4.2 2.2 - - - -
553A GLY* 3.0 28.4 + - - -
556A LEU* 4.0 16.8 - - + +
592A SER* 3.4 27.4 - - - +
593A VAL* 4.0 10.1 - - + +
596A ALA* 3.6 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLY 3.2 16.9 + - - +
547A THR* 3.6 11.7 - - + +
548A LEU 3.2 0.6 - - - -
549A ALA* 1.3 77.9 - - - +
551A SER* 1.3 62.8 + - - +
553A GLY* 4.2 3.7 + - - -
592A SER* 3.2 30.0 + - - +
595A THR* 5.7 2.1 - - - +
17C ARG* 4.3 7.3 + - - -
23C LYS* 5.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLU* 2.9 34.7 + - - -
509A GLU* 4.0 4.5 + - - +
512A CYS* 3.7 37.1 - - - +
513A THR* 3.9 6.2 + - - +
515A LEU* 5.5 0.7 - - - -
547A THR* 2.8 24.1 + - - +
548A LEU* 3.6 7.0 - - - -
550A ASP* 1.3 77.4 - - - +
552A VAL* 1.3 65.3 + - - +
553A GLY* 3.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A CYS 4.1 15.3 - - - +
513A THR* 4.7 1.9 - - - +
515A LEU* 4.6 2.2 - - + -
516A VAL* 4.3 23.8 - - + +
519A LEU* 3.7 28.9 - - + -
548A LEU* 2.9 37.7 + - + +
549A ALA* 4.2 1.8 - - - +
551A SER* 1.3 74.4 - - - +
553A GLY* 1.3 69.5 + - - +
555A HIS* 2.8 34.1 + - + -
556A LEU* 3.9 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ALA 3.0 16.9 + - - +
550A ASP 4.7 3.4 - - - -
551A SER 3.2 3.4 - - - -
552A VAL* 1.3 78.0 - - - +
554A HIS* 1.3 59.0 + - - -
555A HIS 3.2 3.8 + - - -
556A LEU* 3.4 11.1 + - - +
596A ALA* 3.3 25.2 - - - +
----------------------------------------------------------
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