Contacts of the helix formed by residues 568 - 579 (chain E) in PDB entry 5ZRV
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 568 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562E LEU* 5.9 7.5 - - - +
566E VAL 4.7 1.5 - - - +
567E ASP* 1.3 69.1 - - - +
569E LYS* 1.3 62.3 + - - -
570E LYS 3.2 0.7 - - - -
571E LEU* 3.1 17.4 + - - +
572E ASP 3.6 7.4 + - - -
585E ALA* 6.1 0.9 - - - -
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Residues in contact with LYS 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567E ASP 2.8 3.4 + - - -
568E PRO* 1.3 75.5 - - - +
570E LYS* 1.3 60.7 + - - +
571E LEU 3.4 0.3 + - - -
572E ASP* 3.5 11.3 + - - -
573E SER 4.1 2.9 + - - -
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Residues in contact with LYS 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566E VAL 5.1 2.5 - - - -
567E ASP 2.7 18.2 + - - -
569E LYS* 1.3 71.1 - - - +
571E LEU* 1.3 56.5 + - - +
573E SER* 3.3 5.0 + - - -
574E LEU* 2.9 23.7 + - - -
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Residues in contact with LEU 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566E VAL 5.5 0.2 + - - -
567E ASP 4.0 0.6 + - - -
568E PRO* 3.1 17.5 + - - +
570E LYS* 1.3 73.5 - - - +
572E ASP* 1.3 60.8 + - - +
574E LEU* 4.2 3.8 - - - +
575E THR* 2.9 26.9 + - - -
584E ALA 5.4 3.8 + - - -
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Residues in contact with ASP 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568E PRO 3.6 6.0 + - - -
569E LYS 3.5 8.8 + - - -
570E LYS 3.2 1.0 - - - -
571E LEU* 1.3 74.9 - - - +
573E SER* 1.3 56.4 + - - +
576E THR* 2.9 27.4 + - - -
583E GLY* 4.6 20.3 - - - -
584E ALA 5.3 0.9 - - - +
585E ALA 6.0 1.5 - - - +
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Residues in contact with SER 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569E LYS 4.1 4.0 + - - -
570E LYS 3.3 6.6 + - - -
572E ASP* 1.3 74.6 - - - +
574E LEU* 1.3 57.4 + - - +
576E THR* 3.8 1.0 - - - +
577E SER* 2.9 27.9 + - - -
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Residues in contact with LEU 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570E LYS 2.9 14.9 + - - -
571E LEU* 3.2 6.7 + - - +
573E SER* 1.3 78.5 - - - +
575E THR* 1.3 56.6 + - - +
577E SER* 3.8 1.6 + - - -
578E PHE* 3.8 10.7 + - - -
670E ASP 5.7 0.7 - - - +
674E GLN* 6.1 0.7 - - - -
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Residues in contact with THR 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571E LEU 2.9 14.4 + - - -
572E ASP 4.1 0.2 - - - -
574E LEU* 1.3 75.1 - - - +
576E THR* 1.3 65.1 + - - +
577E SER 3.1 1.3 - - - -
578E PHE* 3.3 10.5 + - - +
579E GLY 3.3 8.1 + - - -
580E PHE* 3.4 9.8 + - - -
582E VAL 6.0 0.4 - - - -
583E GLY* 5.9 3.1 - - - -
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Residues in contact with THR 576 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295E LYS* 5.8 4.2 - - - -
572E ASP 2.9 16.7 + - - -
573E SER* 3.8 1.1 - - - +
575E THR* 1.3 73.3 - - - +
577E SER* 1.3 64.3 + - - +
579E GLY* 3.3 12.4 + - - -
580E PHE 3.3 19.2 - - - +
582E VAL 6.0 0.4 - - - -
583E GLY* 5.5 3.7 - - - -
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Residues in contact with SER 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E LEU* 6.0 2.3 - - - -
573E SER 2.9 18.1 + - - -
574E LEU 3.8 3.1 + - - -
575E THR 3.1 0.6 - - - -
576E THR* 1.3 76.0 - - - +
578E PHE* 1.3 60.7 + - - +
579E GLY* 3.5 0.7 + - - -
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Residues in contact with PHE 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574E LEU 3.8 6.6 + - - -
575E THR* 3.3 10.0 + - - +
577E SER* 1.3 76.6 - - - +
579E GLY* 1.3 56.9 + - - +
580E PHE 3.9 0.4 - - - -
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Residues in contact with GLY 579 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575E THR 3.3 2.8 + - - -
576E THR 3.3 8.0 + - - -
577E SER 3.2 2.5 - - - -
578E PHE* 1.3 82.0 - - - +
580E PHE* 1.3 68.7 + - - +
581E PRO* 3.3 3.6 - - - +
711E PRO* 4.0 18.8 - - - +
712E PRO 5.3 1.7 - - - +
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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