Contacts of the helix formed by residues 567 - 572 (chain A) in PDB entry 3MBK
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 SER 567 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLU* 3.6 12.2 + - - +
494A TRP* 3.5 34.7 - - - -
538A TYR* 2.8 23.2 + - - -
565A HIS* 4.0 2.1 - - - +
566A ALA* 1.3 78.6 - - - +
568A SER* 1.3 57.8 + - - +
569A LEU 3.3 0.4 + - - -
570A GLU* 3.7 2.0 + - - +
571A ALA* 3.0 27.4 + - - +
587A PHE* 3.5 19.8 - - - -
590A MET* 5.4 0.7 - - - -
591A VAL* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 3.7 9.2 - - - +
488A LEU* 3.9 8.1 + - - -
538A TYR* 4.0 8.8 + - - -
564A ALA* 3.2 20.7 - - - +
565A HIS* 2.9 32.1 + - - +
567A SER* 1.3 77.4 + - - +
569A LEU* 1.3 66.7 + - - +
571A ALA* 4.3 1.3 - - - -
572A CYS* 2.9 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 3.7 25.4 - - + +
378A CYS* 3.9 5.4 - - - -
379A ARG 3.8 20.9 - - - +
565A HIS 3.5 18.2 - - - +
566A ALA 3.8 9.6 - - - +
567A SER 3.3 0.8 - - - -
568A SER* 1.3 78.8 - - - +
570A GLU* 1.3 52.7 + - - +
573A THR* 2.7 35.2 + - - +
590A MET* 6.3 0.9 - - - -
594A ILE* 4.1 26.0 - - + -
598A GLY* 3.6 22.7 - - - +
599A PHE 4.2 1.3 - - - +
600A CYS* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ILE* 6.0 0.4 - - + -
566A ALA 4.8 0.6 + - - -
567A SER 3.7 2.0 + - - -
569A LEU* 1.3 77.8 - - - +
571A ALA* 1.3 67.8 + - - +
572A CYS 3.2 2.0 - - - -
573A THR* 3.1 5.1 + - - -
574A CYS* 2.9 41.4 + - + +
581A PRO* 5.6 0.2 - - - +
582A GLN* 2.8 42.5 + - - +
587A PHE* 3.4 18.0 - - + -
590A MET* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A TYR* 3.6 21.8 - - + +
539A ILE* 3.9 25.1 - - + +
542A SER* 3.3 33.7 - - - +
543A PHE* 4.0 8.0 + - - +
567A SER 3.0 22.0 + - - +
568A SER* 4.3 2.0 - - - -
570A GLU* 1.3 77.5 - - - +
572A CYS* 1.3 60.7 + - - +
573A THR 3.5 0.2 + - - -
574A CYS* 4.2 5.2 + - - +
575A GLN* 5.0 1.6 + - - +
587A PHE* 4.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 4.5 15.0 - - + -
488A LEU* 3.9 24.2 - - - -
538A TYR* 6.0 0.2 - - - -
542A SER* 4.3 12.3 - - - +
543A PHE* 5.0 2.7 - - - -
546A THR* 3.4 45.9 + - + +
562A ILE* 4.4 8.5 - - + -
568A SER* 2.9 34.4 + - - +
571A ALA* 1.3 79.5 - - - +
573A THR* 1.3 60.6 + - + +
576A LEU* 3.9 9.0 + - - +
----------------------------------------------------------
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