Contacts of the helix formed by residues 819 - 825 (chain A) in PDB entry 6A69
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 819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LYS* 6.4 1.3 - - - -
220A TYR* 4.7 7.6 - - + +
221A GLY* 3.5 25.8 - - - -
797A ASP* 3.3 22.2 + - - +
798A GLY* 3.8 13.6 + - - -
799A THR* 4.1 12.1 + - + -
818A GLY* 1.3 78.6 - - - +
820A ASP* 1.3 64.7 + - - +
821A VAL 4.5 0.3 + - - -
822A ALA* 3.3 19.6 + - - +
823A LYS* 3.4 7.3 + - - -
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Residues in contact with ASP 820 (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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192A GLN* 5.9 8.0 - - - +
193A LYS 4.7 10.2 + - - +
194A PHE* 5.2 3.1 - - - -
221A GLY 2.6 14.1 + - - +
222A ASP* 3.3 28.0 - - - +
223A LEU* 4.2 22.1 + - + +
818A GLY 3.9 7.1 - - - +
819A THR* 1.3 74.5 - - - +
821A VAL* 1.3 59.2 + - - +
822A ALA 3.2 0.7 - - - -
823A LYS* 3.2 18.3 + - + +
824A GLU* 3.0 32.4 + - + +
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Residues in contact with VAL 821 (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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221A GLY* 3.0 21.5 + - - +
265A HIS* 3.7 47.1 - - + +
266A VAL 4.1 10.1 - - - +
267A MET* 5.2 7.4 - - + -
799A THR* 4.0 24.9 - - - +
802A GLY* 5.7 7.2 - - - +
819A THR* 3.4 2.9 - - - +
820A ASP* 1.3 77.8 - - - +
822A ALA* 1.3 60.2 + - - +
824A GLU* 3.5 5.4 + - - +
825A ALA* 3.2 26.2 + - + +
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Residues in contact with ALA 822 (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 GLY 4.1 7.4 - - - +
797A ASP* 3.8 31.2 - - + -
798A GLY 4.1 8.1 + - - +
801A ASP* 5.3 4.3 - - + -
805A LEU* 3.9 14.3 - - + +
813A ALA* 4.0 6.7 - - + +
819A THR* 3.3 18.7 + - - +
820A ASP 3.2 0.8 - - - -
821A VAL* 1.3 79.6 - - - +
823A LYS* 1.3 60.8 + - + +
825A ALA* 3.6 1.2 + - - -
826A SER* 3.2 23.3 + - - -
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Residues in contact with LYS 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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191A GLU* 4.6 11.7 - - + +
192A GLN* 6.0 6.7 - - + +
458A ARG* 3.4 12.3 + - - +
813A ALA* 4.5 3.6 - - + -
814A MET 3.3 22.3 + - - +
815A GLY* 3.9 14.7 - - - -
818A GLY* 2.4 38.8 + - - +
819A THR 3.4 4.1 + - - +
820A ASP* 3.2 20.7 + - + +
822A ALA* 1.3 76.5 - - - +
824A GLU* 1.3 64.6 + - + +
826A SER* 2.5 26.4 + - - -
829A ILE* 3.8 34.1 - - + -
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Residues in contact with GLU 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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192A GLN* 5.3 9.3 + - - +
223A LEU* 3.3 44.6 - - + +
263A GLY* 5.2 4.3 - - - +
265A HIS* 4.0 14.2 + - - -
458A ARG* 3.3 32.2 + - - +
806A LYS* 5.5 1.7 + - - -
820A ASP 3.0 16.4 + - - +
821A VAL* 4.2 4.6 - - - +
822A ALA 3.4 0.2 - - - -
823A LYS* 1.3 77.9 - - + +
825A ALA* 1.3 58.7 + - - +
826A SER 3.3 0.2 - - - -
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Residues in contact with ALA 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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801A ASP 5.2 0.2 - - - +
802A GLY* 4.7 21.1 - - - +
805A LEU* 4.6 17.1 - - + +
806A LYS* 4.2 29.0 + - + +
821A VAL* 3.2 19.1 + - + +
822A ALA* 3.9 3.8 - - - +
824A GLU* 1.3 75.9 - - - +
826A SER* 1.3 66.4 + - - +
827A ASP* 5.2 0.9 - - - -
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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