Contacts of the helix formed by residues 797 - 804 (chain A) in PDB entry 7AUD
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 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686A PHE* 4.7 1.6 - - + -
794A ILE* 3.8 18.6 - - + +
795A ASP 3.5 0.4 - - - -
796A GLU* 1.3 70.4 - - - +
798A HIS* 1.3 64.6 + - - +
799A CYS 3.1 0.4 - - - -
800A VAL* 2.9 23.8 + - - +
828A ALA* 3.7 31.0 - - + -
829A LEU 2.8 18.6 + - - +
830A THR* 3.9 2.4 - - - -
841A ILE* 3.4 24.6 - - + +
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Residues in contact with HIS 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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796A GLU* 3.4 36.1 + - - +
797A ALA* 1.3 77.8 - - - +
799A CYS* 1.3 72.5 + - - +
801A SER* 2.9 6.9 + - - -
802A GLN* 2.7 50.8 + - + +
830A THR* 3.1 27.8 + - - +
831A ALA 5.0 1.3 - - - -
832A THR* 3.7 22.2 + - - +
837A VAL* 4.7 7.1 - - + +
841A ILE* 3.6 16.8 - - + +
951A MET* 4.1 5.8 - - + -
975A GLN* 3.7 25.5 + - - -
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Residues in contact with CYS 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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715A PRO* 4.1 8.3 - - - -
796A GLU* 3.0 24.6 + - - +
798A HIS* 1.3 87.4 - - - +
800A VAL* 1.3 63.5 + - - +
802A GLN* 3.8 9.6 - - - -
803A TRP* 2.9 39.2 + - + +
804A GLY 3.7 1.7 + - - -
811A TYR* 3.6 27.2 - - + -
951A MET* 3.6 31.0 - - - -
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Residues in contact with VAL 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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794A ILE* 3.8 20.9 - - + -
797A ALA* 2.9 17.2 + - - +
799A CYS* 1.3 76.5 - - - +
801A SER* 1.3 55.6 + - - +
804A GLY* 3.1 27.2 + - - -
805A HIS* 4.9 2.4 + - - -
811A TYR* 3.5 44.2 - - + +
812A LYS* 5.3 0.9 - - - +
814A MET* 3.9 5.6 - - + -
840A ASP* 5.1 0.2 - - - -
841A ILE* 4.7 6.7 - - + -
844A GLN* 3.6 33.0 - - + +
845A LEU* 4.2 14.1 - - + -
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Residues in contact with SER 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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797A ALA 3.9 0.6 + - - -
798A HIS 2.9 8.6 + - - -
800A VAL* 1.3 79.2 - - - +
802A GLN* 1.3 61.6 + - - +
804A GLY 4.4 0.7 - - - -
805A HIS* 3.7 16.7 + - - -
837A VAL* 3.7 32.7 - - - +
840A ASP* 2.7 34.7 + - - +
841A ILE* 4.0 11.4 - - - +
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Residues in contact with GLN 802 (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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798A HIS* 2.7 43.7 + - + +
799A CYS* 2.9 8.0 + - - +
801A SER* 1.3 76.2 - - - +
803A TRP* 1.3 102.9 + - + +
804A GLY 3.8 0.2 - - - -
805A HIS* 5.4 0.4 - - - -
806A ASP* 4.3 8.2 - - - +
947A ILE* 5.5 9.1 - - - +
951A MET* 4.7 2.5 - - - +
968A LYS* 6.0 1.6 - - - +
975A GLN* 5.4 1.7 - - - +
1019A HIS* 4.7 9.5 + - - -
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Residues in contact with TRP 803 (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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715A PRO* 3.9 15.5 - - + -
716A LEU* 5.5 5.6 - - + -
799A CYS* 2.9 17.1 + - + +
802A GLN* 1.3 119.6 - - + +
804A GLY* 1.3 62.4 + - - +
805A HIS 3.2 2.7 - - - -
806A ASP* 2.6 25.5 + - - +
807A PHE* 3.8 25.6 - + + -
808A ARG* 2.7 70.3 - - + +
811A TYR* 4.1 13.7 - + + -
947A ILE* 6.3 1.9 - - + +
951A MET* 3.7 24.7 - - + -
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Residues in contact with GLY 804 (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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799A CYS 3.7 1.2 + - - -
800A VAL 3.1 23.3 + - - -
801A SER 4.4 0.6 - - - -
802A GLN 3.8 0.8 - - - +
803A TRP* 1.3 78.1 - - - +
805A HIS* 1.3 60.7 + - - +
806A ASP 3.5 0.2 - - - -
808A ARG 3.6 8.5 - - - -
809A GLN* 3.5 18.0 - - - +
811A TYR* 3.9 10.1 - - - +
812A LYS* 3.5 27.9 - - - +
813A ARG* 5.4 0.2 + - - -
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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