Contacts of the helix formed by residues 525 - 531 (chain C) in PDB entry 3ZNS
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 ASP 525 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524C TYR* 1.3 93.6 - - - +
526C SER* 1.3 80.5 + - - +
527C VAL* 3.0 25.7 + - - +
528C MET* 3.4 23.7 + - - +
529C LEU 4.4 1.0 + - - -
548C ILE* 4.5 0.5 - - - +
568C ARG* 2.8 37.4 + - - +
640C TRP* 3.3 35.0 - - + +
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Residues in contact with SER 526 (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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516A LEU 5.1 13.6 + - - -
524C TYR* 4.4 5.7 - - - -
525C ASP* 1.3 75.2 + - - +
527C VAL* 1.3 59.3 + - - +
528C MET 3.0 2.9 - - - -
529C LEU* 2.7 52.1 + - - +
530C LYS* 3.8 10.8 + - - +
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Residues in contact with VAL 527 (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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525C ASP* 3.0 21.0 + - - +
526C SER* 1.3 77.2 + - - +
528C MET* 1.3 57.1 + - - +
530C LYS* 3.2 34.4 + - + +
633C HIS 5.2 0.7 - - - +
636C ASN* 3.9 36.3 - - + +
637C ALA* 4.2 6.6 + - - +
640C TRP* 4.0 37.2 - - + -
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Residues in contact with MET 528 (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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523C ILE* 5.0 1.3 - - + -
524C TYR* 4.3 2.5 - - - -
525C ASP 3.4 28.0 + - - +
526C SER 3.0 1.0 - - - -
527C VAL* 1.3 72.7 - - - +
529C LEU* 1.3 53.2 + - - +
530C LYS 3.2 0.6 + - - -
531C HIS* 3.8 4.8 + - - +
548C ILE* 3.8 14.1 - - + -
637C ALA* 3.9 9.6 - - - +
640C TRP* 3.9 35.9 - - + -
641C ALA 4.0 7.0 - - - -
663C VAL 3.5 22.9 - - - +
664C VAL* 3.5 20.2 - - + -
665C ARG* 2.7 69.3 + - - +
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Residues in contact with LEU 529 (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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524C TYR* 3.6 22.7 - - - +
526C SER* 2.7 36.9 + - - +
528C MET* 1.3 71.4 - - - +
530C LYS* 1.3 60.5 + - + +
531C HIS 3.3 1.8 + - - +
532C GLN* 2.9 21.3 - - - +
545C ALA* 3.2 43.5 - - + +
548C ILE* 3.5 21.8 - - + -
549C GLN* 4.2 14.8 - - + +
665C ARG* 3.7 1.8 + - - -
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Residues in contact with LYS 530 (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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526C SER* 4.2 10.8 - - - +
527C VAL* 3.2 21.3 + - - +
529C LEU* 1.3 76.7 - - + +
531C HIS* 1.3 58.8 + - - +
532C GLN* 2.9 19.3 + - - +
630C ASN* 4.0 5.7 + - - -
633C HIS* 3.4 58.5 - - + +
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Residues in contact with HIS 531 (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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528C MET 3.8 2.5 + - - +
529C LEU 3.3 1.4 - - - -
530C LYS* 1.3 72.3 - - - +
532C GLN* 1.3 61.6 + - - +
543C GLU* 3.5 26.0 + - - -
628C ILE* 3.6 23.3 + - + +
630C ASN* 4.9 0.4 + - - -
634C SER* 2.7 36.7 + - - +
637C ALA* 3.5 26.3 - - + +
665C ARG* 2.8 44.3 + - - +
666C PRO* 3.8 16.6 - - + +
679C PHE* 5.4 0.6 + - - -
681C PHE* 3.5 34.5 - + - -
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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