Contacts of the helix formed by residues 505 - 509 (chain P) in PDB entry 1ZD2
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 HIS 505 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360P PHE 5.7 0.2 - - - -
502P MET 4.9 3.0 + - - +
503P SER 3.1 1.4 + - - -
504P GLN* 1.3 112.2 + - + +
506P MET* 1.3 64.1 + - - +
507P GLU 3.4 2.7 - - - -
508P ASP* 3.2 36.1 + - - +
509P TRP* 4.2 6.6 - - + +
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Residues in contact with MET 506 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340P TRP* 3.6 28.0 - - + -
359P PRO* 3.7 0.9 - - + -
360P PHE* 3.3 46.0 - - + +
489P MET* 3.5 17.7 - - - +
502P MET 4.8 0.9 - - - +
503P SER* 3.0 43.0 + - - +
504P GLN 3.4 0.6 - - - -
505P HIS* 1.3 72.7 - - - +
507P GLU* 1.3 54.7 + - - +
508P ASP 2.8 16.8 + - - -
509P TRP* 2.9 17.6 + - - +
510P ILE* 2.9 28.6 + - + +
513P LEU* 3.7 20.2 - - + -
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Residues in contact with GLU 507 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503P SER 3.8 2.4 - - - +
504P GLN 3.9 13.5 - - - +
506P MET* 1.3 70.4 - - - +
508P ASP* 1.3 62.9 + - - +
510P ILE 3.6 13.2 - - - +
511P PRO* 3.0 34.7 - - + +
513P LEU* 4.0 21.3 - - - +
515P ARG* 2.9 43.0 + - - -
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Residues in contact with ASP 508 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482P LYS* 3.1 29.5 + - - +
504P GLN 5.3 0.2 - - - +
505P HIS* 3.2 33.1 - - - +
506P MET 2.8 5.7 + - - -
507P GLU* 1.3 81.3 + - - +
509P TRP* 1.3 69.6 + - + +
511P PRO* 4.1 1.6 - - - +
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Residues in contact with TRP 509 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344P LEU* 6.3 1.1 - - + -
360P PHE* 3.6 29.8 - + + -
362P PRO* 3.1 49.8 - - + +
478P SER 4.7 2.5 - - - -
479P LEU* 3.1 42.2 - - + -
481P ARG 3.9 18.4 - - - -
482P LYS* 3.4 12.5 - - + -
483P ILE 2.8 26.5 + - - -
505P HIS* 4.2 9.3 - - + +
506P MET* 2.9 8.4 + - - +
508P ASP* 1.3 90.8 - - + +
510P ILE* 1.3 59.3 + - - +
511P PRO* 3.3 7.7 - - - +
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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