Contacts of the helix formed by residues 795 - 803 (chain C) in PDB entry 1ZYC
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 THR 795 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793C ASN* 3.6 25.8 - - - +
794C ARG* 1.3 82.1 - - - +
796C LEU* 1.3 61.7 + - - +
797C TYR* 2.5 37.8 + - - +
798C ASP* 3.4 22.0 + - - +
799C LEU 3.9 1.9 + - - -
838C PRO 3.3 4.1 + - - -
839C MET* 3.1 41.5 - - + +
841C ILE 3.5 10.1 - - - -
842C PHE* 3.8 10.5 - - + +
843C ILE* 4.1 3.2 - - - +
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Residues in contact with LEU 796 (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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795C THR* 1.3 72.2 + - - +
797C TYR* 1.3 64.9 + - - +
798C ASP 3.1 1.3 - - - -
799C LEU* 3.4 9.6 + - + -
800C ILE* 3.0 31.9 + - + +
805C LEU* 3.3 32.1 - - + -
815C LEU* 4.2 7.2 - - + -
819C ILE* 4.7 1.6 - - + -
838C PRO* 3.6 6.7 + - + +
841C ILE* 2.8 43.5 + - + +
843C ILE* 4.3 7.4 - - + -
914C ILE* 4.0 23.6 - - + -
918C MET* 3.9 23.1 - - + -
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Residues in contact with TYR 797 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795C THR* 2.5 21.2 + - - +
796C LEU* 1.3 74.4 - - - +
798C ASP* 1.3 65.7 + - - +
800C ILE* 3.7 2.9 + - + +
801C HIS* 3.1 60.7 + + + +
802C SER* 6.0 0.2 - - - -
838C PRO* 3.9 19.8 + - + -
839C MET* 3.8 42.2 - - + +
890C TYR* 5.7 2.0 - - - -
917C GLU* 5.7 2.7 - - - -
928C ARG* 5.9 3.9 + - - -
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Residues in contact with ASP 798 (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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793C ASN* 4.2 13.5 + - - +
794C ARG* 4.1 27.1 + - - +
795C THR* 3.7 23.0 + - - +
796C LEU 3.1 0.2 - - - -
797C TYR* 1.3 84.0 - - - +
799C LEU* 1.3 63.7 + - - +
800C ILE 2.8 2.2 + - - -
801C HIS 2.9 0.7 + - - -
802C SER* 2.5 52.0 + - - -
803C GLU* 5.3 0.7 - - - -
839C MET* 5.5 2.3 - - - +
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Residues in contact with LEU 799 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C ARG* 3.1 43.1 - - - +
795C THR 4.2 3.6 - - - +
796C LEU* 3.4 11.8 + - + +
798C ASP* 1.3 77.7 - - - +
800C ILE* 1.3 62.7 + - - +
803C GLU* 3.5 23.1 + - + +
805C LEU* 3.1 49.2 + - + +
808C GLN* 5.5 3.1 - - - +
811C GLU* 5.3 2.0 - - + +
815C LEU* 4.6 13.9 - - + -
843C ILE* 4.4 15.7 - - + -
847C ARG* 3.5 29.2 - - - +
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Residues in contact with ILE 800 (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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796C LEU* 3.0 42.2 - - + +
797C TYR* 3.9 2.9 - - - +
798C ASP 2.8 4.4 + - - -
799C LEU* 1.3 77.2 - - - +
801C HIS* 1.3 82.7 + - + +
802C SER 3.7 0.3 + - - -
804C ASN* 4.3 5.9 + - - -
805C LEU* 3.9 18.9 + - + -
806C ASN* 4.7 8.4 + - + +
838C PRO* 4.2 16.6 - - + -
914C ILE 4.7 0.7 - - - +
917C GLU* 2.9 42.4 - - + +
918C MET* 3.9 20.4 - - + +
922C PHE* 6.4 0.2 - - + -
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Residues in contact with HIS 801 (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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797C TYR* 3.1 56.2 + + + +
798C ASP 2.9 4.4 + - - -
800C ILE* 1.3 100.4 - - + +
802C SER* 1.3 66.6 + - - +
803C GLU 3.8 0.7 - - - -
804C ASN* 5.4 1.1 - - - -
917C GLU* 5.0 10.7 + - - +
922C PHE* 5.5 5.3 - + - -
928C ARG* 4.8 23.4 - - - -
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Residues in contact with SER 802 (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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797C TYR* 6.0 0.3 - - - -
798C ASP* 2.5 35.7 + - - +
801C HIS* 1.3 81.0 + - - +
803C GLU* 1.3 87.9 + - - +
804C ASN* 5.3 0.4 - - - -
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Residues in contact with GLU 803 (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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794C ARG* 3.0 40.7 + - - -
799C LEU* 3.5 22.7 + - + +
802C SER* 1.3 97.5 - - - +
804C ASN* 1.3 63.9 + - - +
805C LEU* 2.8 3.5 + - - -
808C GLN* 2.6 33.6 + - - +
847C ARG* 3.4 10.9 + - - +
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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