Contacts of the helix formed by residues 519 - 529 (chain A) 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 PRO 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A LEU* 4.8 12.8 - - + +
514A THR* 4.0 8.3 - - + -
517A VAL 4.8 0.2 - - - +
518A GLY* 1.3 84.0 - - - +
520A ALA* 1.3 67.8 + - + +
521A HIS 3.5 1.6 - - - -
522A LEU* 3.3 6.7 + - + +
523A ILE* 3.0 39.8 + - + +
548A LEU* 4.6 2.5 - - + +
552A GLY* 3.3 28.9 - - - +
555A LEU* 3.6 37.0 - - + +
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Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A SER* 4.8 6.0 - - - -
196A LEU* 3.9 24.7 - - + -
218A LEU 4.0 10.3 - - - +
219A ASN* 5.5 3.4 - - + -
517A VAL 5.0 0.8 + - - +
518A GLY 3.6 2.4 - - - -
519A PRO* 1.3 82.1 - - + +
521A HIS* 1.3 63.5 + - - +
523A ILE* 3.4 9.7 + - - +
524A HIS* 3.1 21.7 + - - +
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Residues in contact with HIS 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 3.7 31.1 + - - +
196A LEU* 5.2 3.8 - - + +
197A MET* 4.0 32.1 - - + +
485A ASN* 3.1 31.8 + - - -
486A PHE* 5.9 0.2 - + - -
513A LYS* 3.0 23.0 + - - +
517A VAL* 5.5 7.7 + - + -
518A GLY 5.0 1.4 + - - +
519A PRO 3.5 0.2 - - - -
520A ALA* 1.3 77.7 - - - +
522A LEU* 1.3 57.1 + - - +
524A HIS* 3.1 9.6 + + - +
525A GLU* 2.8 50.0 + - + +
529A TYR* 5.1 3.6 + - - -
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A MET* 3.9 15.0 - - + -
509A TRP* 3.9 20.9 - - + +
510A ILE* 4.1 26.7 - - + -
513A LYS* 3.8 22.8 - - + +
514A THR* 3.8 27.6 - - + -
518A GLY 5.1 1.9 + - - +
519A PRO* 3.3 10.7 + - + +
520A ALA 3.3 0.2 - - - -
521A HIS* 1.3 79.0 - - - +
523A ILE* 1.3 62.6 + - - +
525A GLU* 3.2 20.6 + - - +
526A PHE* 3.0 38.5 + - + -
548A LEU* 4.2 10.1 - - + -
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Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A PRO* 3.0 29.5 + - + +
520A ALA* 3.6 8.1 - - - +
522A LEU* 1.3 77.9 - - - +
524A HIS* 1.3 62.5 + - - +
526A PHE* 3.3 10.5 + - - +
527A VAL* 3.3 23.1 + - + +
545A GLN* 4.2 23.6 - - + +
548A LEU* 3.5 47.1 - - + +
549A SER* 4.0 11.9 - - - +
552A GLY* 5.2 1.3 - - - -
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Residues in contact with HIS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASP* 3.5 25.1 + - + -
193A SER* 3.3 26.6 + - - +
520A ALA 3.1 11.7 + - - +
521A HIS* 3.1 18.7 + + - +
523A ILE* 1.3 75.1 - - + +
525A GLU* 1.3 62.7 + - + +
527A VAL* 3.2 10.9 + - + +
528A GLU* 2.8 62.7 + - + +
529A TYR* 5.9 2.0 - - - -
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Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A TYR 4.4 1.6 - - - +
485A ASN 4.0 5.7 - - - +
488A ALA* 3.3 25.2 + - - +
489A TYR 4.6 0.5 + - - -
504A MET* 3.5 11.9 - - + +
509A TRP* 5.2 1.2 + - - -
513A LYS* 2.9 31.5 + - - -
521A HIS* 2.8 39.6 + - + +
522A LEU* 3.2 25.9 + - - +
524A HIS* 1.3 74.5 - - + +
526A PHE* 1.3 62.1 + - - +
528A GLU* 4.4 2.9 - - - -
529A TYR* 3.1 54.0 + - + +
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Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A MET* 3.5 43.1 - - + -
505A PHE* 3.9 23.3 - + - -
510A ILE* 5.0 2.2 - - + -
522A LEU* 3.0 32.6 + - + -
523A ILE* 3.6 8.1 - - - +
524A HIS 3.3 0.2 - - - -
525A GLU* 1.3 79.3 - - - +
527A VAL* 1.3 61.0 + - - +
529A TYR 4.4 0.2 - - - -
530A ARG* 3.3 25.7 + - - +
541A SER* 3.4 32.1 + - - +
544A PHE* 3.5 25.8 - + + -
545A GLN* 4.1 18.4 - - + +
548A LEU* 3.4 30.3 - - + -
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Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A ILE* 3.3 10.3 + - + +
524A HIS* 3.2 13.1 + - - +
526A PHE* 1.3 78.4 - - - +
528A GLU* 1.3 68.9 + - - +
529A TYR 3.4 0.5 + - - -
530A ARG* 3.6 23.2 + - - +
531A HIS 4.9 0.9 + - - -
545A GLN* 3.1 37.2 - - - +
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Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A HIS* 2.8 49.9 + - + +
525A GLU* 4.1 2.0 - - - +
527A VAL* 1.3 78.6 - - - +
529A TYR* 1.3 81.7 + - + +
531A HIS* 3.1 26.3 + - + -
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A ALA* 3.8 23.8 - - + -
489A TYR* 3.3 37.4 + + - +
492A ALA* 3.7 23.6 - - + -
500A LEU* 4.0 19.9 - - + +
504A MET* 4.5 3.1 - - - -
521A HIS* 5.1 4.0 + - - -
524A HIS* 5.9 1.7 - + - -
525A GLU* 3.1 48.5 + - + +
526A PHE 4.4 0.2 - - - -
528A GLU* 1.3 100.6 - - + +
530A ARG* 1.3 64.4 + - - +
531A HIS* 3.1 11.0 - + - -
532A ILE* 3.2 23.6 - - - +
533A LEU* 4.0 5.1 - - - +
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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