Contacts of the helix formed by residues 536 - 550 (chain A) in PDB entry 3M6L
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 536 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 3.0 27.2 + - - -
532A ALA* 3.9 2.5 - - + -
533A SER 3.1 6.3 + - - +
534A GLY 3.1 0.2 + - - -
535A SER* 1.3 99.0 + - - +
537A VAL* 1.3 64.2 + - - +
538A TRP 3.3 1.6 - - - -
539A LEU* 3.4 11.5 + - + +
540A CYS* 3.2 23.0 + - - -
584A VAL* 3.6 25.8 - - + +
585A GLU* 3.7 5.3 - - - -
586A ALA* 2.9 41.0 + - - +
615A PHE* 4.0 11.4 - - - -
620A PHE* 4.1 18.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ALA* 3.8 10.3 - - + -
505A LEU* 3.8 14.8 - - + -
520A LEU* 3.4 32.8 - - + -
532A ALA* 3.7 30.1 - - + +
533A SER 3.8 7.6 - - - -
534A GLY 3.2 15.7 + - - +
536A GLU* 1.3 77.6 - - - +
538A TRP* 1.3 58.9 + - - +
540A CYS* 3.1 5.1 + - - +
541A LEU* 2.8 28.0 + - + +
556A VAL* 4.9 5.4 - - + -
558A SER* 3.7 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LYS* 3.3 64.6 - - + +
504A ALA 3.8 17.3 - - - -
505A LEU* 4.1 12.2 - - + +
506A ASN* 5.8 6.3 - - - -
534A GLY 4.9 0.6 + - - -
535A SER 4.3 6.8 + - - +
536A GLU 3.3 0.4 - - - -
537A VAL* 1.3 79.2 - - - +
539A LEU* 1.4 64.7 + - - +
541A LEU* 3.2 26.9 + - + +
542A GLU* 2.9 60.9 + - + +
----------------------------------------------------------
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 SER 4.7 2.3 + - - +
536A GLU* 3.4 17.3 + - + +
538A TRP* 1.4 79.7 - - - +
540A CYS* 1.3 57.4 + - - +
542A GLU* 3.4 4.4 + - - +
543A SER* 2.8 39.0 + - - +
584A VAL* 4.2 8.5 - - + -
600A TYR* 5.5 0.7 - - + -
620A PHE* 3.8 42.6 - - + +
621A SER* 3.4 34.5 - - - +
622A VAL* 3.5 9.6 - - + +
625A LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 3.5 32.9 - - + +
532A ALA* 3.6 20.6 - - + -
536A GLU 3.2 13.5 + - - +
537A VAL* 3.1 9.7 + - - +
539A LEU* 1.3 76.9 - - - +
541A LEU* 1.3 61.0 + - - +
543A SER* 4.3 0.4 - - - -
544A ALA* 2.9 31.4 + - - +
556A VAL* 4.0 13.2 - - + +
584A VAL* 3.7 30.7 - - - -
625A LEU* 4.4 1.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
505A LEU* 3.7 32.1 - - + -
506A ASN* 5.7 5.6 - - - +
520A LEU* 4.0 19.7 - - + +
521A LYS* 4.6 10.7 + - + -
537A VAL* 2.8 21.0 + - + +
538A TRP* 3.2 28.2 + - + +
540A CYS* 1.3 76.3 - - - +
542A GLU* 1.3 63.7 + - + +
544A ALA* 3.4 2.1 + - - +
545A ASN* 3.0 31.8 + - - +
556A VAL* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A TRP* 2.9 59.1 + - + +
539A LEU* 3.9 1.1 - - - +
541A LEU* 1.3 75.4 - - - +
543A SER* 1.4 57.9 + - - +
545A ASN* 3.3 17.7 + - - +
546A GLU* 3.0 26.0 + - - +
622A VAL* 3.4 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 3.8 15.0 - - - -
539A LEU* 2.8 27.6 + - - +
540A CYS 3.8 3.4 - - - -
542A GLU* 1.4 71.8 - - - +
544A ALA* 1.3 54.4 + - - +
546A GLU* 3.2 3.5 + - - +
547A LEU* 2.8 39.1 + - - +
622A VAL* 3.6 28.9 - - - +
625A LEU* 3.5 19.7 - - - +
626A VAL* 3.9 11.2 - - - +
629A ILE* 4.9 0.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
521A LYS* 3.8 10.8 - - + +
530A LEU* 4.1 4.2 - - + +
540A CYS 2.9 10.8 + - - +
541A LEU 3.8 3.8 - - - +
543A SER* 1.3 74.5 - - - +
545A ASN* 1.3 58.8 + - - +
547A LEU* 3.3 4.0 + - - +
548A GLU* 2.9 33.6 + - - +
554A CYS* 3.9 25.1 - - + -
556A VAL* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LYS* 2.9 25.7 - - - +
541A LEU* 3.0 21.4 + - - +
542A GLU* 3.5 21.6 - - - +
543A SER 3.2 0.4 - - - -
544A ALA* 1.3 77.6 - - - +
546A GLU* 1.3 61.8 + - - +
548A GLU* 3.3 4.7 + - - +
549A LYS* 3.0 36.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
542A GLU 3.0 13.1 + - - +
543A SER 3.2 7.6 + - - +
545A ASN* 1.3 77.8 - - - +
547A LEU* 1.3 56.5 + - - +
549A LYS* 3.2 26.0 + - - +
550A GLN* 2.7 62.0 + - - +
622A VAL* 4.0 16.6 - - + -
626A VAL* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A PHE* 4.4 4.3 - - + -
530A LEU* 4.3 6.1 - - + -
543A SER 2.8 27.2 + - - +
544A ALA 3.3 0.6 + - - +
546A GLU* 1.3 72.3 - - - +
548A GLU* 1.3 54.3 + - - +
550A GLN* 3.3 4.4 + - - +
551A GLY 3.1 6.1 + - - -
552A PHE* 2.7 42.3 + - + +
554A CYS* 3.7 29.6 - - - -
626A VAL* 4.0 13.7 - - + -
629A ILE* 3.8 39.5 - - + -
630A LEU* 3.8 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LYS* 3.7 20.7 - - - +
523A SER* 2.8 28.3 + - - -
544A ALA 2.9 21.0 + - - +
545A ASN* 3.8 6.3 - - - +
546A GLU 3.2 0.2 - - - -
547A LEU* 1.3 75.2 - - - +
549A LYS* 1.3 65.2 + - - +
551A GLY* 3.1 13.5 + - - -
552A PHE 3.4 18.4 + - - +
553A ALA* 3.5 8.7 - - - +
554A CYS* 3.0 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ASN* 3.0 26.9 + - - +
546A GLU* 3.2 29.4 + - - +
548A GLU* 1.3 76.9 - - - +
550A GLN* 1.3 60.4 + - + +
551A GLY 3.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLU* 2.7 50.7 + - - +
547A LEU* 3.3 6.7 + - - +
548A GLU 3.1 0.6 - - - -
549A LYS* 1.3 76.4 - - + +
551A GLY* 1.3 55.3 + - - +
552A PHE* 3.5 21.1 - - + -
626A VAL* 4.2 13.1 - - - +
630A LEU* 3.7 21.5 - - - +
----------------------------------------------------------
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