Contacts of the helix formed by residues 574 - 586 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543C ASN* 3.4 35.6 + - - +
546C GLU* 5.0 2.2 + - - -
570C GLU* 4.1 17.3 + - - +
571C PRO* 2.8 26.6 + - - +
573C THR* 1.3 79.5 + - - +
575C GLU* 1.3 63.4 + - - +
576C VAL* 3.1 14.5 + - - +
577C TYR* 3.3 3.7 + - - +
578C GLN* 3.1 24.7 + - - +
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Residues in contact with GLU 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C VAL* 4.1 35.4 - - + -
543C ASN* 3.5 10.7 + - + +
544C PHE* 4.2 8.1 - - + -
573C THR 3.6 2.7 + - - +
574C SER* 1.3 69.7 + - - +
576C VAL* 1.3 60.4 + - - +
578C GLN* 3.5 23.0 - - - +
579C GLN* 2.9 46.6 + - - +
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Residues in contact with VAL 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C LEU* 4.1 8.7 - - + +
543C ASN* 3.8 18.8 - - + +
544C PHE* 3.8 42.6 - - + +
547C PHE* 3.6 40.6 - - + -
567C GLY* 4.0 8.5 - - - -
570C GLU* 3.8 8.7 - - + -
574C SER* 3.7 11.2 - - - +
575C GLU* 1.3 76.6 - - - +
577C TYR* 1.3 52.8 + - - +
579C GLN* 3.3 4.9 + - - +
580C ALA* 2.8 34.5 + - - +
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Residues in contact with TYR 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C GLY 3.4 16.1 + - - +
568C LEU* 3.3 32.8 - - + -
570C GLU* 3.2 21.8 - - + +
571C PRO 3.2 22.0 - - - +
572C GLU* 3.3 38.5 - - + +
574C SER* 3.3 4.9 + - - +
576C VAL* 1.3 77.6 - - - +
578C GLN* 1.3 70.6 + - - +
580C ALA* 3.2 2.4 + - - +
581C LYS* 2.8 61.6 + - + +
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Residues in contact with GLN 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C GLU* 2.5 39.3 + - - +
573C THR 4.9 2.9 - - - +
574C SER 3.1 15.8 + - - +
575C GLU* 3.5 24.7 - - - +
576C VAL 3.3 0.2 - - - -
577C TYR* 1.3 87.2 - - - +
579C GLN* 1.3 61.4 - - - +
581C LYS* 3.4 8.3 + - - +
582C LEU* 3.2 27.3 + - - +
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Residues in contact with GLN 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C PHE* 2.6 29.9 + - - +
506C SER* 3.5 2.1 + - - -
507C LEU* 3.3 39.5 + - + +
544C PHE* 3.8 12.6 - - - -
575C GLU* 2.9 31.8 + - - +
576C VAL* 3.6 4.3 - - - +
578C GLN* 1.3 73.7 - - - +
580C ALA* 1.3 63.4 + - - +
582C LEU* 3.3 12.2 + - + +
583C GLN* 3.1 27.2 + - + +
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Residues in contact with ALA 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C LEU* 3.7 14.1 - - + +
564C VAL* 3.5 34.7 - - - +
567C GLY* 3.6 19.5 - - - -
568C LEU* 3.7 6.5 - - + +
576C VAL 2.8 20.6 + - - +
577C TYR 3.5 4.5 - - - +
579C GLN* 1.3 72.2 - - - +
581C LYS* 1.3 57.1 + - - +
583C GLN* 3.5 1.8 + - - +
584C ALA* 3.1 25.3 + - - +
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Residues in contact with LYS 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C LEU* 3.7 20.6 - - + +
577C TYR* 2.8 51.0 + - + +
578C GLN* 3.6 11.4 - - - +
580C ALA* 1.3 74.5 - - - +
582C LEU* 1.3 64.0 + - - +
584C ALA* 3.5 9.3 + - - +
585C LYS* 3.3 29.4 + - + +
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Residues in contact with LEU 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C GLN 3.2 14.0 + - - +
579C GLN* 3.3 13.9 + - + +
581C LYS* 1.3 78.1 - - + +
583C GLN* 1.3 58.3 + - + +
585C LYS* 3.3 10.3 + - + +
586C GLN* 2.9 40.8 + - + +
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Residues in contact with GLN 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C LEU* 3.9 21.6 - - - +
508C ASP* 3.2 28.7 + - - +
564C VAL* 3.0 33.3 - - + +
579C GLN* 3.1 16.5 + - + +
580C ALA 3.8 1.3 - - - +
582C LEU* 1.3 76.7 - - + +
584C ALA* 1.3 67.1 + - - +
586C GLN* 3.4 37.9 + - + +
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Residues in contact with ALA 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C VAL* 4.2 14.1 - - + +
568C LEU* 4.6 13.0 - - + -
580C ALA 3.1 18.2 + - - +
581C LYS* 3.7 14.6 - - - +
582C LEU 3.3 0.2 - - - -
583C GLN* 1.3 77.1 - - - +
585C LYS* 1.3 64.6 + - + +
586C GLN 4.3 2.1 - - - -
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Residues in contact with LYS 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C LYS* 3.3 17.6 + - + +
582C LEU* 3.3 13.2 + - + +
584C ALA* 1.3 81.5 - - - +
586C GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C LEU* 2.9 30.3 + - + +
583C GLN* 3.4 37.5 + - + +
584C ALA 4.3 2.0 - - - -
585C 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