Contacts of the helix formed by residues 533 - 547 (chain A) in PDB entry 3T6A
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 533 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A PRO* 4.3 8.1 - - - +
528A GLU 4.1 2.9 - - - +
529A ASN* 3.2 16.2 - - - +
530A LYS* 2.9 60.1 + - + +
531A PRO 2.8 6.0 + - - -
532A LEU* 1.3 73.7 - - - +
534A THR* 1.3 62.1 + - + +
535A ALA* 3.4 5.7 - - + +
536A LEU* 3.3 33.5 + - + +
537A LEU* 2.9 29.0 + - - +
786A LEU* 4.5 2.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU 3.1 7.3 + - - +
533A GLU* 1.3 73.6 - - + +
535A ALA* 1.3 59.7 + - + +
537A LEU* 3.5 7.6 + - - +
538A LYS* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLU* 3.4 6.1 - - - +
534A THR* 1.3 82.6 + - + +
536A LEU* 1.3 61.7 + - + +
538A LYS* 3.1 13.3 - - + +
539A ARG* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A PHE 4.2 13.9 - - - +
525A LEU* 4.2 12.3 - - + -
526A PRO* 3.5 32.5 - - + -
529A ASN* 4.1 12.1 - - + +
533A GLU* 3.3 37.6 + - + +
535A ALA* 1.3 78.0 - - + +
537A LEU* 1.3 63.9 + - - +
538A LYS 3.1 0.9 - - - -
539A ARG* 3.4 11.5 + - + +
540A ALA* 3.1 23.2 + - - +
782A PHE* 5.6 2.5 - - + -
786A LEU* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 3.3 51.1 - - + +
533A GLU 2.9 17.3 + - - +
534A THR* 3.9 7.4 - - - +
536A LEU* 1.3 73.0 - - - +
538A LYS* 1.3 63.5 + - - +
540A ALA* 3.5 6.1 + - + +
541A LYS* 3.0 25.5 + - - +
611A VAL* 4.8 14.4 - - + -
615A GLY* 5.9 5.8 - - - +
616A CYS* 3.9 22.3 - - - -
786A LEU* 3.8 23.3 - - + +
787A LEU* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A THR* 3.0 15.7 + - - +
535A ALA* 3.1 15.9 - - + +
537A LEU* 1.3 78.6 - - - +
539A ARG* 1.3 64.1 + - - +
541A LYS* 3.3 4.1 + - - +
542A GLU* 3.1 44.6 + - + +
616A CYS* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ALA 3.0 15.1 + - - +
536A LEU* 3.4 14.8 + - + +
538A LYS* 1.3 76.5 - - - +
540A ALA* 1.3 65.2 + - - +
542A GLU* 3.4 38.9 + - - +
543A LEU* 3.1 37.6 + - + +
546A ASN* 5.2 4.2 - - - +
773A GLU* 3.0 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU 3.1 17.4 + - - +
537A LEU* 3.8 8.7 - - + +
539A ARG* 1.3 72.5 - - - +
541A LYS* 1.3 68.0 + - - +
543A LEU* 2.9 17.9 + - - +
544A PHE* 3.2 11.9 + - - +
616A CYS* 5.9 2.0 - - - -
777A ILE* 3.3 33.2 - - + +
786A LEU* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A LEU 3.0 15.8 + - - +
538A LYS* 3.6 5.4 - - - +
540A ALA* 1.3 78.6 - - - +
542A GLU* 1.3 53.7 + - + +
544A PHE* 3.1 24.9 + - + +
545A THR* 2.7 61.8 + - - +
612A ASP* 2.7 30.7 + - - +
616A CYS* 3.1 35.6 - - + +
617A THR* 3.7 7.4 - - - -
622A ASP* 4.9 4.6 + - - -
626A THR* 3.2 27.4 + - - +
----------------------------------------------------------
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 LYS* 3.1 40.3 + - + +
539A ARG* 3.5 33.9 + - - +
541A LYS* 1.3 78.9 - - + +
543A LEU* 1.3 56.9 + - - +
545A THR* 4.1 6.5 - - - -
546A ASN* 2.8 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ARG* 3.1 34.3 + - + +
540A ALA* 2.9 11.0 + - - +
542A GLU* 1.3 78.9 - - - +
544A PHE* 1.3 62.2 + - - +
546A ASN* 5.1 1.1 - - - +
547A ASN* 2.8 49.3 + - - +
771A ASP* 5.0 3.8 - - - +
773A GLU* 3.3 39.7 - - + +
774A MET* 4.3 14.6 - - + +
777A ILE* 4.2 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ALA 3.2 5.5 + - - +
541A LYS* 3.1 27.2 + - + +
543A LEU* 1.3 79.5 - - - +
545A THR* 1.3 67.0 + - - +
547A ASN 3.4 15.8 - - - +
552A ILE* 3.5 31.5 - - + +
609A ILE* 6.1 4.3 - - + -
612A ASP* 3.6 22.4 - - - +
626A THR* 4.2 4.7 - - + -
629A LYS* 3.1 44.7 + - + -
630A ILE* 3.9 24.5 - - + -
633A VAL* 4.2 15.5 - - + -
774A MET* 5.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LYS* 2.7 50.5 + - - +
542A GLU* 3.6 7.0 - - - -
544A PHE* 1.3 78.4 - - - +
546A ASN* 1.3 72.1 + - - +
547A ASN 4.7 0.2 - - - -
629A LYS* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ARG* 5.2 4.0 - - - +
542A GLU* 2.8 38.3 + - - +
543A LEU* 3.8 2.0 - - - +
545A THR* 1.3 87.8 - - - +
547A ASN* 1.3 66.4 + - - +
548A ASP 4.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 2.8 38.6 + - - +
544A PHE 3.4 2.8 + - - +
545A THR 3.3 0.6 - - - -
546A ASN* 1.3 85.2 - - - +
548A ASP* 1.3 65.3 + - - +
551A VAL* 4.0 14.7 - - + +
552A ILE* 3.6 14.4 - - + +
629A LYS* 3.2 24.4 + - - -
771A ASP* 6.0 2.1 - - - +
774A MET* 3.1 31.8 - - + +
----------------------------------------------------------
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