Contacts of the helix formed by residues 573 - 587 (chain C) in PDB entry 1Z5S
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 CYS 573 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C ASN* 3.0 29.2 - - - -
535C LEU 4.7 1.8 - - - -
536C TYR* 3.8 18.2 - - + -
539C LEU* 4.5 10.5 - - + -
569C ALA 3.8 5.6 + - - +
570C LEU 5.2 0.7 - - - -
571C GLU* 2.8 2.9 + - - +
572C SER* 1.3 94.1 - - - +
574C SER* 1.3 68.2 + - - +
575C PHE* 2.7 7.1 + - - -
576C ALA* 3.0 24.8 + - + +
577C ARG* 3.2 11.0 + - - +
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Residues in contact with SER 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C GLU* 3.4 15.6 + - - +
572C SER 3.9 0.2 - - - -
573C CYS* 1.3 74.3 - - - +
575C PHE* 1.3 56.4 + - - +
577C ARG* 3.7 6.2 - - - +
578C HIS* 2.9 33.5 + - - +
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Residues in contact with PHE 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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482C ASP* 5.6 4.5 - - - -
536C TYR* 4.5 12.8 - + + -
540C MET* 4.1 25.1 - - + -
573C CYS 2.7 5.7 + - - +
574C SER* 1.3 75.8 - - - +
576C ALA* 1.3 72.7 + - - +
577C ARG 2.9 1.9 + - - -
578C HIS* 3.0 4.8 + - + +
579C SER* 2.7 33.5 + - - -
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Residues in contact with ALA 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C TYR* 3.4 32.5 - - + -
539C LEU* 3.7 28.8 - - + +
540C MET* 4.1 14.1 - - + +
573C CYS* 3.0 15.0 + - + +
575C PHE* 1.3 78.0 - - - +
577C ARG* 1.3 61.6 + - - +
579C SER* 3.3 8.6 - - - -
580C LEU* 3.1 22.0 + - - +
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Residues in contact with ARG 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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539C LEU* 4.2 15.8 - - + +
563C VAL* 2.7 38.2 + - + -
564C THR* 2.8 35.0 + - - +
565C LYS 4.2 5.1 + - - -
566C PRO* 4.4 2.4 - - - +
567C ASN 4.8 1.4 + - - +
570C LEU* 2.9 34.0 + - + +
571C GLU* 3.6 22.0 - - - +
573C CYS 3.2 8.1 + - - +
574C SER* 3.7 8.5 - - - +
575C PHE 2.9 1.6 + - - -
576C ALA* 1.3 75.5 - - - +
578C HIS* 1.3 68.9 + - - +
579C SER 2.8 2.2 + - - -
580C LEU* 2.8 3.7 + - - +
581C LEU* 2.7 39.8 + - + +
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Residues in contact with HIS 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C SER 2.9 22.1 + - - +
575C PHE* 3.8 5.1 - - + +
577C ARG* 1.3 72.4 - - - +
579C SER* 1.3 52.2 + - - +
581C LEU* 3.5 13.9 - - + +
582C GLN* 2.7 59.7 + - + +
585C TYR* 5.8 2.0 - + - -
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Residues in contact with SER 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C MET* 4.9 3.3 - - - +
543C ASN* 4.2 18.4 - - - -
575C PHE* 2.7 39.0 + - - -
576C ALA* 3.3 11.7 - - - -
577C ARG 2.8 0.4 + - - -
578C HIS* 1.3 76.2 - - - +
580C LEU* 1.3 51.1 + - - -
582C GLN* 2.8 11.2 + - - +
583C THR* 2.6 38.2 + - - -
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Residues in contact with LEU 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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539C LEU* 3.4 37.7 - - + +
542C LEU* 3.9 23.6 - - + -
543C ASN* 4.1 14.0 + - - +
546C VAL* 4.3 14.6 - - + -
559C LEU* 4.7 1.8 - - + -
563C VAL* 4.0 17.7 - - + -
576C ALA 3.1 8.8 + - - +
577C ARG* 2.8 10.1 + - - +
579C SER* 1.3 76.2 - - - +
581C LEU* 1.3 53.6 + - - +
583C THR* 4.0 7.9 - - - -
584C LEU* 2.7 63.4 + - + +
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Residues in contact with LEU 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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560C LEU* 3.9 14.4 - - + -
563C VAL* 3.9 23.6 - - + -
564C THR* 3.4 30.1 - - + -
577C ARG* 2.7 46.2 + - + +
578C HIS* 3.5 12.6 - - + +
580C LEU* 1.3 71.7 - - - +
582C GLN* 1.3 58.4 + - - +
584C LEU* 3.6 4.6 - - + +
585C TYR* 2.7 60.7 + - + +
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Residues in contact with GLN 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 HIS* 2.7 46.1 + - + +
579C SER* 2.8 10.5 + - - +
581C LEU* 1.3 70.8 - - - +
583C THR* 1.3 68.1 + - - +
585C TYR* 3.0 36.1 + - - +
586C LYS* 3.3 10.4 + - - +
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Residues in contact with THR 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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543C ASN* 2.7 43.3 + - - +
546C VAL* 4.1 17.7 - - + -
547C GLN* 3.6 22.2 + - + -
579C SER 2.6 14.4 + - - -
580C LEU* 3.4 10.5 - - + -
582C GLN* 1.3 74.5 - - - +
584C LEU* 1.3 61.2 + - - +
586C LYS* 3.3 7.6 + - - +
587C VAL* 3.3 21.4 + - + +
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Residues in contact with LEU 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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546C VAL* 3.3 35.4 - - + -
551C PHE* 5.8 0.4 - - + -
556C ALA* 4.3 14.4 - - - +
559C LEU* 4.2 12.6 - - + +
560C LEU* 3.8 44.6 - - + +
563C VAL* 4.5 6.3 - - + -
580C LEU* 2.7 43.7 + - + +
581C LEU* 3.7 6.7 - - - +
583C THR* 1.3 69.8 - - - +
585C TYR* 1.3 62.9 + - - +
586C LYS 2.9 6.8 + - - -
587C VAL* 3.0 30.3 + - + +
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Residues in contact with TYR 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C LEU* 3.5 34.5 - - + -
564C THR* 4.0 8.2 - - + +
578C HIS* 5.8 2.0 - + - -
581C LEU* 2.7 60.5 + - + +
582C GLN* 3.0 32.5 + - + +
584C LEU* 1.3 72.2 - - - +
586C LYS* 1.3 58.8 + - - +
587C VAL* 4.8 1.2 - - - +
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Residues in contact with LYS 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582C GLN 3.3 6.8 + - - +
583C THR* 3.3 11.6 + - - +
584C LEU 2.9 0.6 - - - -
585C TYR* 1.3 81.4 - - - +
587C VAL* 1.3 66.8 + - + +
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Residues in contact with VAL 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C VAL* 3.3 35.9 - - + +
547C GLN* 5.3 2.2 - - + -
551C PHE* 6.3 0.2 - - + -
553C LYS* 5.7 8.2 - - + +
556C ALA* 4.3 22.9 - - + +
583C THR* 3.4 14.1 - - + +
584C LEU* 3.0 44.2 - - + +
585C TYR 4.8 1.2 - - - +
586C LYS* 1.3 81.6 - - + +
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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