Contacts of the helix formed by residues 534 - 551 (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 ASP 534 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B HIS* 5.7 8.0 - - + +
532B ILE 4.1 1.0 + - - -
533B LEU* 1.3 76.7 - - - +
535B GLU* 1.3 59.8 + - - +
536B LYS* 3.3 11.2 + - - +
537B ASP* 2.9 38.0 + - - +
538B CYS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASP* 1.3 76.2 - - - +
536B LYS* 1.3 62.8 + - - +
538B CYS* 3.5 9.0 - - - +
539B ALA* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASP* 3.3 11.4 + - - +
535B GLU* 1.3 80.3 - - - +
537B ASP* 1.3 64.7 + - - +
539B ALA* 3.4 15.1 + - - +
540B VAL* 3.4 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B HIS* 4.8 12.5 - - - +
498B LYS* 5.9 1.0 - - - +
501B CYS* 3.6 32.4 - - - +
505B PHE* 3.4 13.8 - - - -
533B LEU* 4.0 14.4 - - + +
534B ASP* 2.9 24.5 + - - +
536B LYS* 1.3 77.6 - - - +
538B CYS* 1.3 60.6 + - - +
540B VAL* 3.2 5.4 + - - +
541B SER* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ARG* 3.6 28.9 - - - -
533B LEU* 3.9 12.5 - - + +
534B ASP 2.9 20.8 + - - +
535B GLU* 3.5 13.0 - - - +
537B ASP* 1.3 76.5 - - - +
539B ALA* 1.3 60.0 + - - +
541B SER* 3.3 10.6 - - - -
542B GLU* 3.1 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLU 3.3 10.5 + - - +
536B LYS* 3.6 10.3 - - - +
537B ASP 3.3 0.2 - - - -
538B CYS* 1.3 75.3 - - - +
540B VAL* 1.3 65.5 + - + +
542B GLU* 3.1 17.9 + - - +
543B ASN* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PHE* 3.3 31.2 - - + -
536B LYS* 3.4 14.3 + - + +
537B ASP* 3.2 12.9 + - - +
539B ALA* 1.3 73.3 - - + +
541B SER* 1.3 67.7 + - - +
543B ASN* 3.1 11.7 + - - +
544B PHE* 3.0 40.7 + - + -
575B GLU* 4.1 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PHE* 3.5 15.8 - - - -
526B PHE* 3.7 20.5 + - - -
530B ARG* 3.0 29.6 + - - +
533B LEU* 3.9 18.6 - - - +
537B ASP 2.8 17.4 + - - -
538B CYS 3.3 11.2 - - - -
540B VAL* 1.3 72.5 - - - +
542B GLU* 1.3 57.2 + - - +
544B PHE* 3.3 2.8 + - - +
545B GLN* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ARG* 3.6 27.9 + - - +
538B CYS* 3.1 34.7 + - - +
539B ALA* 3.1 17.3 + - - +
541B SER* 1.3 72.3 - - - +
543B ASN* 1.3 66.2 + - - +
545B GLN* 3.8 4.7 - - - +
546B GLU* 3.1 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ALA* 3.0 21.3 + - - +
540B VAL* 3.3 15.3 - - - +
542B GLU* 1.3 76.7 - - - +
544B PHE* 1.3 62.2 - - + +
546B GLU* 3.2 22.1 + - - +
547B PHE* 3.1 22.7 + - - +
570B GLU* 4.5 0.3 - - - +
573B THR 4.5 2.6 - - - +
574B SER* 3.4 25.9 + - - +
575B GLU* 3.5 20.7 + - + +
576B VAL* 3.9 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B MET 4.2 4.9 - - - -
505B PHE* 3.6 26.0 - + + -
506B SER 3.6 18.6 - - - -
507B LEU* 4.5 8.1 - - + -
510B ILE* 3.5 26.9 - - + -
526B PHE* 3.6 25.6 - + + -
540B VAL* 3.0 43.5 + - + -
541B SER 3.8 1.3 - - - +
543B ASN* 1.3 79.0 - - + +
545B GLN* 1.3 62.7 + - - +
547B PHE* 3.3 4.8 + + - +
548B LEU* 3.1 28.0 + - - +
575B GLU* 4.1 9.6 - - + -
576B VAL* 3.7 28.7 - - + -
579B GLN* 3.6 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ILE* 4.1 18.7 - - + +
526B PHE* 4.2 13.2 - - + -
527B VAL* 2.8 30.5 - - - +
530B ARG* 2.7 47.4 + - - +
541B SER 2.9 7.8 + - - +
542B GLU* 3.8 5.7 - - - +
543B ASN 3.3 0.6 - - - -
544B PHE* 1.3 77.1 - - - +
546B GLU* 1.3 60.8 + - + +
548B LEU* 3.4 7.7 + - - +
549B SER* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B GLU* 3.1 22.0 + - - +
543B ASN* 3.2 30.8 + - - +
545B GLN* 1.3 76.9 - - + +
547B PHE* 1.3 58.1 + - - +
549B SER* 3.9 6.5 - - - -
550B LEU* 3.0 33.3 + - - +
570B GLU* 4.3 13.3 - - - +
571B PRO* 5.1 9.9 - - - +
574B SER* 4.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 4.1 13.2 - - + -
510B ILE* 4.3 28.7 - - + -
543B ASN 3.1 13.8 + - - +
544B PHE 3.3 12.1 - - - +
546B GLU* 1.3 78.0 - - - +
548B LEU* 1.3 65.2 + - + +
550B LEU* 3.8 0.6 - - - +
551B ASN* 3.0 52.7 + - + +
555B LEU* 5.8 2.9 - - + -
563B ILE* 4.1 15.3 - - + -
566B LEU* 3.7 29.4 - - + -
567B GLY* 3.7 12.8 - - - -
570B GLU* 3.6 28.9 - - + +
576B VAL* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ILE* 3.7 38.4 - - + -
514B THR* 4.7 2.7 - - + -
519B PRO* 5.1 2.2 - - + -
522B LEU* 3.9 17.7 - - + -
523B ILE* 3.7 26.6 - - + +
526B PHE* 3.5 38.6 - - + -
544B PHE 3.1 17.2 + - - +
545B GLN* 3.8 3.1 - - - +
547B PHE* 1.3 76.8 - - + +
549B SER* 1.3 61.3 + - - +
551B ASN 3.4 0.7 + - - -
552B GLY* 2.9 31.0 + - - -
555B LEU* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ILE* 4.2 18.4 - - - +
545B GLN* 2.8 32.6 + - - +
546B GLU* 3.9 7.1 - - - -
547B PHE 3.4 0.2 - - - -
548B LEU* 1.3 73.2 - - - +
550B LEU* 1.3 67.5 + - - +
552B GLY* 3.4 9.8 + - - -
553B HIS* 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B GLU 3.0 19.1 + - - +
547B PHE 3.8 4.0 - - - +
549B SER* 1.3 78.6 - - - +
551B ASN* 1.3 80.3 + - - +
552B GLY 3.3 0.2 - - - -
553B HIS* 3.3 21.8 + - - +
569B CYS 6.1 0.2 - - - +
570B GLU* 3.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B PHE* 3.0 48.5 + - + +
548B LEU 3.5 2.2 - - - -
549B SER 3.2 0.2 - - - -
550B LEU* 1.3 98.4 - - - +
552B GLY* 1.3 57.4 + - - +
553B HIS* 3.2 6.9 + - - -
554B LEU* 2.9 30.7 + - + +
555B LEU* 3.3 20.3 + - + +
566B LEU* 3.6 39.1 + - + +
570B GLU* 4.5 3.0 + - - -
----------------------------------------------------------
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