Contacts of the helix formed by residues 534 - 551 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D HIS* 5.4 9.8 + - + -
532D ILE 4.1 0.6 + - - -
533D LEU* 1.3 80.5 - - - +
535D GLU* 1.3 67.3 + - - +
536D LYS* 3.0 13.1 + - - +
537D ASP* 2.8 36.9 + - - +
538D CYS* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ASP* 1.3 82.4 - - - +
536D LYS* 1.3 62.5 + - - +
538D CYS* 3.6 7.7 + - - +
539D ALA* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ASP* 3.0 11.3 + - - +
535D GLU* 1.3 80.0 - - - +
537D ASP* 1.3 65.2 + - - +
539D ALA* 3.4 8.7 + - - +
540D VAL* 3.3 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D HIS* 4.8 10.0 - - - +
498D LYS* 6.1 0.2 - - - -
501D CYS* 3.6 33.0 - - - +
505D PHE* 3.3 17.4 - - + -
533D LEU* 4.0 15.1 - - + +
534D ASP* 2.8 28.4 + - - +
536D LYS* 1.3 76.5 - - - +
538D CYS* 1.3 55.4 + - - +
540D VAL* 3.2 4.5 + - - +
541D SER* 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D ARG* 3.7 22.4 + - + +
533D LEU* 4.0 11.6 - - + +
534D ASP 2.9 21.6 + - - +
535D GLU* 3.6 8.5 - - - +
536D LYS 3.3 0.2 - - - -
537D ASP* 1.3 77.1 - - - +
539D ALA* 1.3 60.5 + - - +
541D SER* 3.3 10.0 - - - -
542D GLU* 3.2 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D GLU 3.3 9.6 + - - +
536D LYS* 3.6 10.8 - - - +
537D ASP 3.2 0.4 - - - -
538D CYS* 1.3 75.8 - - - +
540D VAL* 1.3 61.2 + - + +
542D GLU* 2.8 31.4 + - - +
543D ASN* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D PHE* 3.3 36.8 - - + -
536D LYS* 3.3 12.9 + - + +
537D ASP* 3.2 10.6 + - - +
539D ALA* 1.3 76.8 - - + +
541D SER* 1.3 63.9 + - - +
543D ASN* 3.0 22.0 + - - +
544D PHE* 3.1 26.9 + - + -
575D GLU* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D PHE* 3.4 21.1 - - - -
526D PHE* 3.5 23.6 + - - -
530D ARG* 3.1 22.6 + - - +
533D LEU* 4.0 12.3 - - - +
537D ASP 2.7 17.3 + - - -
538D CYS* 3.3 12.8 - - - -
540D VAL* 1.3 74.3 - - - +
542D GLU* 1.3 56.3 + - - +
544D PHE* 3.2 1.6 + - - -
545D GLN* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D ARG* 3.4 29.2 - - - +
538D CYS* 3.2 30.5 + - - +
539D ALA* 2.8 20.5 + - - +
541D SER* 1.3 72.1 - - - +
543D ASN* 1.3 65.8 + - - +
545D GLN* 3.3 3.0 + - - +
546D GLU* 3.0 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D ALA* 3.0 14.7 + - - +
540D VAL* 3.1 15.1 - - + +
542D GLU* 1.3 76.0 - - - +
544D PHE* 1.3 67.8 + - + +
546D GLU* 3.3 17.0 + - - +
547D PHE* 3.1 23.4 + - - +
570D GLU* 4.9 0.5 - - - +
573D THR 4.5 1.6 - - - +
574D SER* 3.4 26.0 + - - +
575D GLU* 3.1 28.2 + - - +
576D VAL* 4.2 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D MET 3.9 4.7 - - - -
505D PHE* 3.4 30.1 - + + -
506D SER 3.4 18.8 - - - -
507D LEU* 4.4 7.2 - - + -
510D ILE* 3.4 28.5 - - + -
526D PHE* 3.4 25.1 - + + -
540D VAL* 3.1 32.5 + - + -
541D SER 3.8 0.9 - - - +
543D ASN* 1.3 80.1 - - + +
545D GLN* 1.3 63.1 + - - +
547D PHE* 3.4 3.6 + + - +
548D LEU* 3.1 29.3 + - - +
575D GLU* 4.2 10.5 - - + -
576D VAL* 3.7 30.7 - - + -
579D GLN* 3.6 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D ILE* 3.4 30.9 + - - +
526D PHE* 4.3 9.5 - - + -
527D VAL* 3.1 32.5 - - - +
530D ARG* 2.9 41.3 + - - +
541D SER 2.9 8.2 + - - +
542D GLU* 3.5 4.7 - - - +
543D ASN 3.3 0.2 - - - -
544D PHE* 1.3 77.9 - - - +
546D GLU* 1.3 62.1 + - + +
548D LEU* 3.4 11.4 + - - +
549D SER* 3.0 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D GLU* 3.0 23.5 + - - +
543D ASN* 3.3 20.8 + - - +
545D GLN* 1.3 78.5 - - + +
547D PHE* 1.3 63.4 + - - +
549D SER* 3.0 9.1 + - - +
550D LEU* 2.9 34.7 + - + +
570D GLU* 4.5 11.9 - - - +
571D PRO* 4.7 12.5 - - - +
574D SER* 5.5 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D LEU* 4.2 10.8 - - + -
510D ILE* 4.2 33.0 - - + -
543D ASN 3.1 14.4 + - - +
544D PHE 3.4 8.1 - - - +
546D GLU* 1.3 78.3 - - - +
548D LEU* 1.3 64.9 + - + +
550D LEU* 4.6 0.2 - - - -
551D ASN* 2.9 55.7 + - + +
555D LEU* 5.6 4.3 - - + -
563D ILE* 4.0 24.9 - - + -
566D LEU* 3.7 9.2 - - + -
567D GLY* 3.6 24.9 - - - -
570D GLU* 3.6 31.6 - - + -
576D VAL* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510D ILE* 3.7 32.8 - - + -
514D THR* 4.5 7.0 - - + -
519D PRO* 4.8 2.7 - - + -
522D LEU* 4.2 12.8 - - + -
523D ILE* 3.4 29.2 - - + +
526D PHE* 3.5 38.4 - - + -
544D PHE 3.1 15.4 + - - +
545D GLN* 3.6 3.1 - - - +
546D GLU 3.2 0.2 - - - -
547D PHE* 1.3 81.2 - - + +
549D SER* 1.3 59.1 + - - +
551D ASN 3.5 0.7 - - - -
552D GLY* 2.8 30.8 + - - -
555D LEU* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D ILE* 3.9 15.9 - - - -
545D GLN* 3.0 17.1 + - - +
546D GLU* 3.0 17.5 + - - +
548D LEU* 1.3 76.8 - - - +
550D LEU* 1.3 73.4 + - - +
552D GLY* 3.3 11.0 + - - -
553D HIS* 5.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 4.1 21.2 - - - +
211B SER* 5.5 9.9 - - - -
546D GLU* 2.9 15.9 + - + +
547D PHE 3.9 4.3 - - - +
549D SER* 1.3 84.6 + - - +
551D ASN* 1.3 80.4 + - - +
552D GLY 3.4 0.2 - - - -
553D HIS* 3.2 20.9 + - + -
569D CYS* 5.8 3.1 - - + +
570D GLU* 3.8 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D PHE* 2.9 47.6 + - + +
548D LEU 3.5 1.8 - - - -
549D SER 3.2 0.6 - - - -
550D LEU* 1.3 100.1 - - - +
552D GLY* 1.3 57.6 + - - +
553D HIS* 3.3 9.8 - - - -
554D LEU* 3.0 27.7 + - + +
555D LEU* 3.3 20.9 + - + +
566D LEU* 3.5 40.4 + - + +
570D GLU* 3.8 5.3 + - - -
----------------------------------------------------------
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