Contacts of the helix formed by residues 574 - 586 (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 SER 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543A ASN* 3.2 31.4 + - - +
546A GLU* 5.0 2.3 + - - -
570A GLU* 4.0 14.0 + - - +
571A PRO* 2.8 24.6 + - - -
572A GLU 4.1 0.2 - - - +
573A THR* 1.3 83.2 + - - +
575A GLU* 1.3 59.9 + - - +
576A VAL* 3.5 14.6 + - - +
577A TYR* 3.3 9.6 + - - +
578A GLN* 3.1 26.2 + - - +
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Residues in contact with GLU 575 (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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505A PHE* 5.4 1.4 - - - +
540A VAL* 4.0 37.7 - - + +
543A ASN* 3.0 11.7 + - - +
544A PHE* 4.3 5.8 - - + -
573A THR 3.6 2.4 + - - -
574A SER* 1.3 68.6 - - - +
576A VAL* 1.3 60.8 + - - +
578A GLN* 3.7 18.2 - - + +
579A GLN* 2.9 61.9 + - - +
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Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LEU* 4.0 12.1 - - + +
543A ASN* 4.1 4.9 - - + +
544A PHE* 3.8 51.8 - - + +
547A PHE* 3.7 35.7 - - + -
567A GLY* 3.9 13.9 - - - -
570A GLU* 3.9 4.9 - - + -
574A SER* 3.2 13.0 - - - +
575A GLU* 1.3 78.4 - - - +
577A TYR* 1.3 57.8 + - - +
579A GLN* 3.3 4.7 + - - +
580A ALA* 2.8 28.2 + - - +
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Residues in contact with TYR 577 (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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567A GLY 3.2 14.5 + - - +
568A LEU* 3.5 38.3 - - + +
570A GLU* 3.5 19.4 - - + +
571A PRO 3.3 20.2 - - - +
572A GLU* 3.3 32.2 + - + +
574A SER* 3.3 5.6 + - - +
576A VAL* 1.3 79.7 - - - +
578A GLN* 1.3 78.4 + - - +
580A ALA* 3.2 0.9 + - - +
581A LYS* 2.7 64.0 + - + +
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Residues in contact with GLN 578 (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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572A GLU* 2.6 40.1 + - - +
573A THR 4.8 2.5 - - - +
574A SER 3.1 15.5 + - - +
575A GLU* 3.8 19.1 - - + +
576A VAL 3.3 0.2 - - - -
577A TYR* 1.3 94.7 - - - +
579A GLN* 1.3 63.7 + - - +
581A LYS* 3.4 7.5 + - - +
582A LEU* 3.2 27.0 + - - +
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Residues in contact with GLN 579 (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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505A PHE* 2.7 27.4 + - - +
506A SER* 3.6 3.3 - - - -
507A LEU* 3.2 38.1 + - + +
544A PHE* 3.8 9.0 - - - -
575A GLU* 2.9 40.5 + - - +
576A VAL* 3.7 4.0 - - - +
578A GLN* 1.3 77.5 - - - +
580A ALA* 1.3 61.1 + - - +
582A LEU* 3.3 14.3 + - + +
583A GLN* 3.1 28.7 + - - +
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Residues in contact with ALA 580 (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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507A LEU* 3.6 16.1 - - + +
564A VAL* 3.5 31.6 - - - +
567A GLY* 3.5 21.3 - - - -
568A LEU* 3.7 5.4 - - + +
576A VAL 2.8 21.3 + - - +
577A TYR 3.6 2.2 - - - +
579A GLN* 1.3 71.8 - - - +
581A LYS* 1.3 63.9 + - - +
583A GLN* 3.4 1.7 + - - -
584A ALA* 3.0 23.9 + - - +
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Residues in contact with LYS 581 (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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568A LEU* 3.7 15.2 - - + +
577A TYR* 2.7 56.4 + - + +
578A GLN* 3.6 11.0 - - - +
580A ALA* 1.3 73.4 - - - +
582A LEU* 1.3 60.6 + - + +
584A ALA* 3.5 7.0 + - - +
585A LYS* 3.3 36.7 + - + +
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Residues in contact with LEU 582 (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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578A GLN* 3.2 15.0 + - + +
579A GLN* 3.3 15.6 + - + +
581A LYS* 1.3 76.4 - - + +
583A GLN* 1.3 62.2 + - + +
585A LYS* 3.4 8.6 + - + +
586A GLN* 2.9 38.7 + - - +
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Residues in contact with GLN 583 (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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507A LEU* 3.8 24.4 - - + +
508A ASP* 3.6 25.7 + - - +
564A VAL* 3.4 31.2 - - + +
579A GLN* 3.1 13.7 + - - +
580A ALA* 3.4 4.0 + - - +
582A LEU* 1.3 78.3 - - + +
584A ALA* 1.3 64.9 + - - +
586A GLN* 3.3 41.3 + - + +
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Residues in contact with ALA 584 (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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564A VAL* 4.1 15.6 - - + +
568A LEU* 4.3 15.7 - - + -
580A ALA 3.0 17.6 + - - +
581A LYS* 3.7 11.4 - - - +
582A LEU 3.3 0.2 - - - -
583A GLN* 1.3 78.1 - - - +
585A LYS* 1.3 63.8 + - - +
586A GLN 4.4 1.6 - - - -
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Residues in contact with LYS 585 (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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581A LYS* 3.3 23.3 + - + +
582A LEU* 3.6 11.7 - - + +
584A ALA* 1.3 81.6 - - + +
586A GLN* 1.3 62.4 + - - +
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Residues in contact with GLN 586 (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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582A LEU* 2.9 26.5 + - - +
583A GLN* 3.3 40.0 + - + +
584A ALA 4.4 1.8 - - - -
585A LYS* 1.3 78.5 - - - +
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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