Contacts of the helix formed by residues 574 - 584 (chain C) in PDB entry 3HZJ
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 GLN 574 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572C SER* 2.8 10.8 + - - +
573C ALA* 1.3 87.5 - - + +
575C GLU* 1.3 53.4 + - - +
576C SER 3.2 3.5 + - - -
577C VAL* 3.2 26.9 + - + +
578C ILE* 2.8 45.7 + - + +
611C SER* 3.6 11.3 - - - +
617C ILE 4.9 3.2 + - - -
618C GLY* 3.8 6.3 - - - -
619C TYR* 2.9 48.3 + - - +
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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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571C ASP* 5.1 4.0 - - - +
572C SER* 3.4 29.6 + - - +
573C ALA 3.5 2.4 - - - +
574C GLN* 1.3 74.9 - - - +
576C SER* 1.3 59.0 + - - +
578C ILE* 3.4 6.1 + - - +
579C THR* 2.9 35.3 + - - -
604C TYR* 2.4 37.2 + - - -
608C LYS* 3.9 14.9 - - - -
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Residues in contact with SER 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ALA 5.2 0.8 + - - -
574C GLN 3.3 0.8 - - - -
575C GLU* 1.3 78.3 - - - +
577C VAL* 1.3 64.6 + - - +
579C THR* 3.3 6.5 + - - -
580C ARG* 3.0 38.3 + - - +
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Residues in contact with VAL 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ALA 5.4 1.1 - - - +
574C GLN* 3.4 32.8 - - + +
576C SER* 1.3 80.1 - - - +
578C ILE* 1.3 61.9 + - - +
580C ARG* 3.6 11.8 + - - +
581C ASP* 3.3 21.3 + - - +
619C TYR* 4.1 15.9 - - + +
621C GLN* 3.3 26.4 - - - +
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Residues in contact with ILE 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 SER* 4.2 2.5 - - - +
574C GLN* 2.8 28.0 + - + +
575C GLU* 3.7 6.1 - - - +
577C VAL* 1.3 72.3 - - - +
579C THR* 1.3 65.2 + - - +
581C ASP* 3.2 6.1 + - - +
582C ILE* 3.0 28.9 + - + +
604C TYR* 3.9 23.8 - - + +
607C CYS* 3.7 25.6 - - + +
608C LYS* 3.7 33.9 - - + +
611C SER* 4.0 14.6 - - - +
619C TYR* 3.7 29.4 - - + -
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Residues in contact with THR 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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575C GLU* 2.9 23.1 + - - -
576C SER* 3.7 6.3 - - - -
578C ILE* 1.3 75.1 - - - +
580C ARG* 1.3 65.8 + - - +
582C ILE* 3.2 8.5 + - + +
583C HIS* 3.2 48.8 + - + +
604C TYR* 4.0 16.4 - - - -
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Residues in contact with ARG 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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576C SER* 3.0 23.2 + - - +
577C VAL* 3.6 12.8 - - - +
579C THR* 1.3 78.7 - - - +
581C ASP* 1.3 64.1 + - - +
583C HIS* 3.5 13.4 + - - +
584C ARG* 3.6 16.0 + - - +
621C GLN* 5.9 4.8 - - - +
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Residues in contact with ASP 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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577C VAL 3.3 7.3 + - - +
578C ILE 3.2 8.3 + - - +
580C ARG* 1.3 81.4 - - - +
582C ILE* 1.3 55.6 + - - +
584C ARG* 2.7 47.8 + - - +
585C THR* 2.4 24.3 + - - -
619C TYR* 2.4 40.8 + - - +
621C GLN* 3.7 15.4 + - - -
622C GLY* 2.8 20.0 + - - -
624C SER* 3.4 7.4 + - - +
625C PHE* 4.8 0.3 - - - -
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Residues in contact with ILE 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 ILE* 3.0 27.3 + - + +
579C THR* 3.2 7.6 + - + +
581C ASP* 1.3 74.4 - - - +
583C HIS* 1.3 68.7 + - + +
585C THR* 3.4 22.0 + - - +
592C PHE* 5.9 0.2 - - - +
600C GLN* 3.7 41.4 + - + +
603C LEU* 3.7 22.7 - - + +
604C TYR* 3.1 50.9 - - + +
607C CYS* 5.0 0.2 - - - -
624C SER* 4.4 7.6 - - - -
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Residues in contact with HIS 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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579C THR* 3.2 35.7 + - + +
580C ARG* 3.9 8.1 - - - +
581C ASP 3.3 0.4 - - - -
582C ILE* 1.3 79.2 - - + +
584C ARG* 1.3 57.5 + - - +
585C THR 3.4 1.2 + - - -
587C PRO* 3.8 17.8 - - - +
595C THR* 4.1 18.4 + - - -
600C GLN* 3.5 29.5 + - - +
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Residues in contact with ARG 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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580C ARG 3.6 14.1 - - - +
581C ASP* 2.7 49.4 + - - +
583C HIS* 1.3 76.9 - - - +
585C THR* 1.3 58.7 + - - +
586C PHE 3.6 2.5 + - - -
587C PRO* 3.8 13.1 - - - +
621C GLN* 5.1 4.8 - - - +
622C GLY* 4.6 7.9 - - - +
625C PHE* 3.2 40.4 - - + -
698C GLN* 4.5 16.6 - - - +
706C ALA* 5.7 0.8 - - - +
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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