Contacts of the helix formed by residues 574 - 586 (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 SER 574 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543D ASN* 3.4 31.3 + - - +
546D GLU* 5.5 2.4 + - - +
570D GLU* 4.1 12.4 + - - +
571D PRO* 2.8 26.9 + - - +
573D THR* 1.3 83.4 + - - +
575D GLU* 1.3 59.7 + - - +
576D VAL* 3.6 14.2 + - - +
577D TYR* 3.3 9.8 + - - +
578D GLN* 3.1 26.5 + - - +
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Residues in contact with GLU 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D PHE* 4.7 2.4 - - - +
540D VAL* 4.0 35.6 - - + +
543D ASN* 3.1 13.0 + - - +
544D PHE* 4.2 7.0 - - + -
573D THR 3.6 2.4 + - - -
574D SER* 1.3 69.1 - - - +
576D VAL* 1.3 59.7 + - - +
578D GLN* 3.7 16.0 - - - +
579D GLN* 2.9 60.4 + - - +
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Residues in contact with VAL 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LEU* 4.0 11.9 - - + +
543D ASN* 4.2 0.9 - - + +
544D PHE* 3.7 51.8 - - + +
547D PHE* 3.7 38.8 - - + -
567D GLY* 3.8 14.6 - - - -
570D GLU* 4.0 4.9 - - + -
574D SER* 3.2 12.5 - - - +
575D GLU* 1.3 78.4 - - - +
577D TYR* 1.3 53.1 + - - +
579D GLN* 3.3 4.2 + - - +
580D ALA* 2.8 33.8 + - - +
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Residues in contact with TYR 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D GLY 3.2 17.6 + - - +
568D LEU* 3.5 34.5 - - + +
570D GLU* 3.4 19.9 - - + +
571D PRO 3.3 20.2 - - - +
572D GLU* 3.4 35.4 + - + +
574D SER* 3.3 5.4 + - - +
576D VAL* 1.3 80.4 - - - +
578D GLN* 1.3 76.4 + - - +
580D ALA* 3.7 0.9 - - - +
581D LYS* 2.8 56.5 + - + +
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Residues in contact with GLN 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D GLU* 2.6 36.4 + - - +
573D THR 4.8 2.9 - - - +
574D SER 3.1 16.7 + - - +
575D GLU* 4.0 15.9 - - + +
576D VAL 3.3 0.2 - - - -
577D TYR* 1.3 91.3 - - - +
579D GLN* 1.3 63.5 + - - +
581D LYS* 3.4 12.2 + - - +
582D LEU* 3.2 28.2 + - + +
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Residues in contact with GLN 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D PHE* 2.6 29.2 + - - +
506D SER* 3.5 2.9 - - - -
507D LEU* 3.1 38.9 + - + +
544D PHE* 3.6 8.6 - - - -
575D GLU* 2.9 40.8 + - - +
576D VAL* 3.7 3.8 - - - +
578D GLN* 1.3 77.0 - - - +
580D ALA* 1.3 62.6 + - - +
582D LEU* 3.2 13.8 + - + +
583D GLN* 3.1 23.2 + - - +
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Residues in contact with ALA 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LEU* 3.6 13.4 - - + +
564D VAL* 3.6 23.2 - - - +
567D GLY* 3.5 30.7 - - - -
568D LEU* 3.6 5.4 - - + +
576D VAL 2.8 22.3 + - - +
577D TYR 3.7 2.7 - - - +
579D GLN* 1.3 71.2 - - - +
581D LYS* 1.3 63.0 + - - +
583D GLN* 3.4 1.9 + - - -
584D ALA* 3.0 23.6 + - - +
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Residues in contact with LYS 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D LEU* 3.7 12.7 - - + +
572D GLU* 5.1 8.3 + - - -
577D TYR* 2.8 47.6 + - + +
578D GLN* 3.6 14.1 + - - +
579D GLN 3.2 0.2 - - - -
580D ALA* 1.3 77.8 - - - +
582D LEU* 1.3 61.3 + - + +
584D ALA* 3.6 4.0 + - + +
585D LYS* 3.3 51.1 + - + +
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Residues in contact with LEU 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D GLN* 3.2 16.5 + - + +
579D GLN* 3.2 15.4 + - + +
581D LYS* 1.3 76.9 - - + +
583D GLN* 1.3 60.8 + - - +
585D LYS* 3.4 11.3 + - + +
586D GLN* 2.9 34.3 + - - +
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Residues in contact with GLN 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LEU* 4.1 15.6 - - - +
508D ASP* 4.0 18.4 + - - +
511D LYS* 6.1 3.4 - - - +
564D VAL* 3.2 33.9 - - + +
579D GLN 3.1 12.8 + - - +
580D ALA* 3.9 1.3 - - - +
582D LEU* 1.3 77.3 - - - +
584D ALA* 1.3 64.8 + - - +
586D GLN* 3.3 28.2 + - + +
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Residues in contact with ALA 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG* 4.0 25.2 + - - +
564D VAL* 4.1 11.1 - - + +
568D LEU* 4.4 10.3 - - + -
580D ALA 3.0 17.4 + - - +
581D LYS* 3.7 8.1 - - + +
582D LEU 3.3 0.2 - - - -
583D GLN* 1.3 76.8 - - - +
585D LYS* 1.3 65.1 + - + +
586D GLN 4.4 1.7 - - - -
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Residues in contact with LYS 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D LYS* 3.3 39.2 + - + +
582D LEU* 3.7 13.7 - - + +
584D ALA* 1.3 82.7 - - + +
586D GLN* 1.3 62.7 + - - +
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Residues in contact with GLN 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LEU* 2.9 23.8 + - - +
583D GLN* 3.3 23.8 + - + +
584D ALA 4.4 1.8 - - - -
585D LYS* 1.3 78.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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