Contacts of the helix formed by residues 574 - 586 (chain B) in PDB entry 1Z6T
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 574 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ASN* 3.4 35.2 + - - +
546B GLU* 4.9 3.3 + - - -
570B GLU* 4.1 17.3 + - - +
571B PRO* 2.8 25.0 + - - -
573B THR* 1.3 79.7 + - - +
575B GLU* 1.3 63.2 + - - +
576B VAL* 3.6 14.9 + - - +
577B TYR* 3.2 3.7 + - - +
578B GLN* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PHE* 5.1 1.9 - - - +
540B VAL* 4.1 24.4 - - + +
543B ASN* 3.5 10.8 + - - +
544B PHE* 4.1 16.2 - - + -
573B THR 3.7 2.6 + - - -
574B SER* 1.3 69.3 + - - +
576B VAL* 1.3 60.3 + - - +
578B GLN* 3.8 18.5 - - + +
579B GLN* 2.9 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 4.1 8.6 - - + +
543B ASN* 3.9 5.4 - - + +
544B PHE* 3.7 51.6 - - + +
547B PHE* 3.6 39.3 - - + -
567B GLY* 3.9 10.3 - - - -
570B GLU* 3.8 9.0 - - + -
574B SER* 3.7 13.7 - - - +
575B GLU* 1.3 75.8 - - - +
577B TYR* 1.3 58.8 + - - +
579B GLN* 3.3 4.3 + - - +
580B ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B GLY 3.3 17.0 + - - +
568B LEU* 3.4 33.0 - - + +
570B GLU* 3.3 20.4 - - + +
571B PRO 3.2 20.6 - - - +
572B GLU* 3.2 40.7 - - + +
574B SER* 3.2 4.9 + - - +
576B VAL* 1.3 80.4 - - - +
578B GLN* 1.3 65.0 + - - +
580B ALA* 3.1 3.1 + - - +
581B LYS* 2.8 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B GLU* 2.4 45.2 + - - +
573B THR 5.0 2.5 - - - +
574B SER 3.1 16.4 + - - +
575B GLU* 3.8 17.7 - - + +
576B VAL 3.3 0.2 - - - -
577B TYR* 1.3 86.1 - - - +
579B GLN* 1.3 62.6 - - - +
581B LYS* 3.4 9.2 + - - +
582B LEU* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PHE* 2.6 28.3 + - - +
506B SER* 3.6 2.3 - - - -
507B LEU* 3.3 37.5 + - + +
544B PHE* 3.6 10.0 - - - -
575B GLU* 2.9 44.2 + - - +
576B VAL 3.6 4.3 - - - +
578B GLN* 1.3 76.4 - - - +
580B ALA* 1.3 61.4 + - - +
582B LEU* 3.2 13.2 + - + +
583B GLN* 3.1 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 3.6 15.2 - - + +
564B VAL* 3.4 35.6 - - - +
567B GLY* 3.6 19.3 - - - -
568B LEU* 3.7 5.4 - - + +
576B VAL 2.8 21.0 + - - +
577B TYR 3.5 4.7 - - - +
579B GLN* 1.3 72.6 - - - +
581B LYS* 1.3 56.9 + - - +
583B GLN* 3.5 1.8 + - - +
584B ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 3.7 21.7 - - + +
577B TYR* 2.8 47.4 + - + +
578B GLN* 3.6 12.1 - - - +
579B GLN 3.2 0.2 - - - -
580B ALA* 1.3 75.4 - - - +
582B LEU* 1.3 64.5 + - + +
584B ALA* 3.5 14.5 + - - +
585B LYS* 3.3 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B GLN* 3.2 13.8 + - + +
579B GLN* 3.2 14.8 + - + +
581B LYS* 1.3 77.2 - - + +
583B GLN* 1.3 59.7 + - + +
585B LYS* 3.4 8.4 + - + +
586B GLN* 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 3.7 25.2 - - + +
508B ASP* 3.6 25.2 + - - +
564B VAL* 3.4 28.4 - - + +
579B GLN* 3.1 14.2 + - + +
580B ALA 3.7 7.0 - - - +
582B LEU* 1.3 75.7 - - + +
584B ALA* 1.3 66.3 + - - +
586B GLN* 3.3 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B VAL* 4.1 13.4 - - + +
568B LEU* 4.4 13.9 - - + -
580B ALA 3.1 17.6 + - - +
581B LYS* 3.6 17.7 - - - +
583B GLN* 1.3 77.6 - - - +
585B LYS* 1.3 63.2 + - - +
586B GLN 4.3 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LYS* 3.3 21.4 + - + +
582B LEU* 3.6 11.9 - - + +
584B ALA* 1.3 81.1 - - - +
586B GLN* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LEU* 2.9 33.5 + - - +
583B GLN* 3.3 36.6 + - + +
584B ALA 4.3 1.8 - - - -
585B LYS* 1.3 77.9 - - - +
----------------------------------------------------------
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