Contacts of the helix formed by residues 794 - 801 (chain A) in PDB entry 3ZFM
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 ALA 794 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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792A TRP 3.9 0.4 + - - -
793A THR* 1.3 78.9 - - - +
795A PRO* 1.4 74.7 - - + +
796A GLU* 3.4 28.0 - - - +
797A ALA* 3.3 4.6 + - + +
798A ILE* 3.3 15.8 + - - +
807A SER* 3.7 23.0 + - - -
810A TRP* 3.7 25.4 - - + +
870A ARG* 3.9 0.9 - - - +
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Residues in contact with PRO 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A THR 3.8 0.4 - - - -
794A ALA* 1.4 79.6 - - - +
796A GLU* 1.4 63.9 + - - +
798A ILE* 2.8 32.6 + - + +
799A GLN* 2.9 32.3 + - + +
810A TRP* 3.5 38.1 - - + -
839A ILE* 4.1 19.7 - - + +
840A GLU* 5.1 5.6 - - + +
844A ARG* 5.6 1.1 - - - +
865A LYS* 4.8 15.5 - - + +
870A ARG* 4.3 2.9 - - - +
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Residues in contact with GLU 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A ALA* 3.4 17.3 - - - +
795A PRO* 1.4 76.2 - - - +
797A ALA* 1.3 55.9 + - - +
799A GLN* 3.5 11.8 + - - +
800A TYR* 2.9 55.8 + - + +
802A LYS* 3.4 22.5 + - + +
804A THR* 4.9 0.2 + - - -
807A SER* 3.8 8.7 - - - -
865A LYS 4.6 2.7 - - - +
867A ARG* 3.6 26.6 - - - +
870A ARG* 2.8 45.6 + - - -
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Residues in contact with ALA 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A THR* 3.6 24.9 - - + -
794A ALA* 3.3 11.2 + - + +
795A PRO 3.2 0.8 - - - -
796A GLU* 1.3 77.6 - - - +
798A ILE* 1.3 61.3 + - - +
801A ARG* 3.1 21.7 + - - +
802A LYS 3.3 24.0 - - - +
803A PHE* 3.7 25.8 - - + -
807A SER* 4.5 2.5 - - - -
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Residues in contact with ILE 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A ILE* 3.7 34.1 - - + +
793A THR* 3.5 34.1 - - + +
794A ALA 3.3 9.3 + - - +
795A PRO* 2.8 11.4 + - + +
797A ALA* 1.3 78.6 - - - +
799A GLN* 1.4 63.6 + - + +
801A ARG 4.6 1.0 + - - -
835A VAL* 6.5 0.2 - - + -
836A ILE* 3.8 46.0 - - + -
839A ILE* 5.7 4.0 - - + -
840A GLU* 5.2 0.9 - - - +
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Residues in contact with GLN 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795A PRO* 2.9 21.4 + - - +
796A GLU* 3.5 19.8 + - - +
798A ILE* 1.4 78.7 - - + +
800A TYR* 1.4 75.9 + - + +
801A ARG 3.8 0.2 - - - -
840A GLU* 3.5 36.4 + - - +
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Residues in contact with TYR 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A GLU* 2.9 33.2 + - + +
799A GLN* 1.4 89.0 - - + +
801A ARG* 1.4 69.3 + - - +
802A LYS* 3.2 32.7 + - + +
867A ARG* 3.0 25.9 + - - -
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Residues in contact with ARG 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745A ARG* 5.1 1.8 + - - +
797A ALA 3.1 20.2 + - - +
798A ILE 4.6 1.0 + - - -
799A GLN 3.8 0.8 - - - -
800A TYR* 1.4 76.5 - - - +
802A LYS* 1.3 60.0 + - - +
803A PHE* 3.5 22.5 + - + -
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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