Contacts of the helix formed by residues 821 - 832 (chain A) in PDB entry 5ON2
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 821 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A ALA* 1.3 76.9 - - - +
822A GLU* 1.3 63.5 + - - +
823A GLU* 3.8 13.4 + - - +
824A GLN* 2.9 34.1 + - - +
825A VAL* 3.4 22.8 + - - +
849A TYR* 4.7 1.3 - - - -
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Residues in contact with GLU 822 (chain A).
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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821A THR* 1.3 74.9 - - - +
823A GLU* 1.3 70.2 + - - +
825A VAL* 3.4 2.3 + - - +
826A ARG* 3.0 40.4 + - + +
847A VAL* 3.7 26.3 - - - +
849A TYR* 3.7 50.9 - - + +
855A LEU* 4.9 0.7 - - + -
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Residues in contact with GLU 823 (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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821A THR* 3.2 12.1 - - - +
822A GLU* 1.3 93.4 + - - +
824A GLN* 1.3 59.2 + - + +
826A ARG* 3.6 10.2 + - - +
827A GLU* 3.1 28.6 + - - +
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Residues in contact with GLN 824 (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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816A VAL* 5.6 4.1 - - + +
819A ASP 4.5 2.2 + - - +
820A ALA* 3.4 15.8 - - + -
821A THR* 2.9 44.4 + - - +
822A GLU 3.4 0.6 - - - -
823A GLU* 1.3 77.2 - - + +
825A VAL* 1.3 57.9 + - - +
827A GLU* 3.6 7.0 + - - +
828A ARG* 3.1 27.5 + - - +
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Residues in contact with VAL 825 (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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802A VAL* 4.0 22.7 - - + -
804A VAL* 6.0 0.4 - - + -
814A ILE* 4.3 9.7 - - + +
816A VAL* 4.1 25.1 - - + -
820A ALA* 4.8 2.2 - - + -
821A THR 3.4 14.9 + - - +
822A GLU 3.8 7.0 - - - +
823A GLU 3.3 0.4 - - - -
824A GLN* 1.3 75.2 - - - +
826A ARG* 1.3 59.2 + - - +
828A ARG* 3.4 5.5 + - - +
829A ALA* 2.8 28.5 + - + +
849A TYR* 3.6 37.5 - - + +
855A LEU* 4.2 14.4 - - + -
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Residues in contact with ARG 826 (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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822A GLU* 3.0 28.1 + - + +
823A GLU* 3.8 10.1 - - - +
825A VAL* 1.3 76.9 - - - +
827A GLU* 1.3 57.4 + - - +
829A ALA* 3.4 1.8 + - - +
830A GLY* 3.0 25.1 + - - -
844A VAL* 3.7 31.1 - - - +
847A VAL* 3.7 32.7 - - - +
855A LEU* 4.1 26.7 - - + -
857A LEU* 4.3 9.5 - - + +
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Residues in contact with GLU 827 (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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823A GLU 3.1 19.0 + - - +
824A GLN* 3.8 8.5 - - - +
825A VAL 3.3 0.2 - - - -
826A ARG* 1.3 75.6 - - - +
828A ARG* 1.3 63.4 + - - +
830A GLY* 3.4 9.6 + - - -
831A GLN* 2.9 45.7 + - - +
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Residues in contact with ARG 828 (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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814A ILE* 3.6 34.9 - - + +
815A THR 4.8 8.1 + - - +
816A VAL* 4.8 9.2 - - + -
824A GLN 3.1 16.0 + - - +
825A VAL* 3.8 4.9 - - - +
827A GLU* 1.3 80.7 + - - +
829A ALA* 1.3 62.4 + - - +
831A GLN* 3.3 38.7 + - - +
832A GLU* 2.8 32.1 + - - +
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Residues in contact with ALA 829 (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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804A VAL* 3.9 29.8 - - + -
814A ILE* 4.2 6.7 - - + +
825A VAL 2.8 22.8 + - - +
826A ARG 3.7 4.7 - - - +
827A GLU 3.3 0.2 - - - -
828A ARG* 1.3 72.9 - - - +
830A GLY* 1.3 60.7 + - - +
832A GLU* 3.5 7.6 + - - +
835A VAL* 3.2 29.7 - - + +
855A LEU* 4.0 17.5 - - + -
857A LEU* 5.6 2.2 - - + -
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Residues in contact with GLY 830 (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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826A ARG 3.0 15.5 + - - -
827A GLU 3.4 3.3 + - - -
828A ARG 3.3 0.4 - - - -
829A ALA* 1.3 77.0 - - - +
831A GLN* 1.3 60.6 + - - +
832A GLU 3.3 9.0 + - - +
835A VAL* 4.6 6.7 - - - -
836A ALA* 3.8 14.1 - - - +
839A LEU* 5.2 7.9 - - - -
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Residues in contact with GLN 831 (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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827A GLU* 2.9 47.1 + - - +
828A ARG* 3.3 33.9 + - - +
830A GLY* 1.3 73.3 - - - +
832A GLU* 1.3 64.2 + - - +
833A HIS* 3.6 2.6 + - - +
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Residues in contact with GLU 832 (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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804A VAL* 5.6 0.4 - - + -
812A ALA* 3.8 24.7 - - + +
813A LYS 4.9 3.0 - - - +
814A ILE* 3.6 15.3 - - + +
828A ARG* 2.8 39.7 + - - +
829A ALA* 3.5 15.0 + - - +
830A GLY 3.2 7.7 - - - +
831A GLN* 1.3 76.2 - - - +
833A HIS* 1.3 64.9 + - - +
834A LEU 3.5 0.9 - - - +
835A VAL* 3.4 14.3 + - + +
836A ALA* 3.2 23.6 + - - +
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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