Contacts of the strand formed by residues 819 - 822 (chain A) in PDB entry 1S0Q
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 MET 819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A THR* 3.5 25.1 - - - +
740A LEU 3.7 17.9 - - - +
741A ASN* 3.8 8.7 - - - +
742A ASN 6.1 0.2 - - - +
804A ASP* 4.2 7.8 - - - +
814A GLN 3.5 24.0 - - - +
815A ILE* 3.9 13.7 - - + +
816A THR* 3.1 38.4 + - + +
817A SER* 3.4 1.8 + - - -
818A ASN* 1.3 84.8 - - + +
820A PHE* 1.3 64.5 - - - +
851A SER* 5.9 0.9 - - - +
852A TRP* 3.6 22.2 - - + +
864A VAL* 3.8 15.3 - - + -
865A TYR 3.2 8.3 - - - +
866A THR* 5.4 0.7 - - - -
867A LYS* 4.4 7.7 + - - +
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Residues in contact with PHE 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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801A ILE* 4.0 39.5 - - + -
802A LEU 5.3 0.2 - - - +
804A ASP* 4.2 13.5 - - - +
807A CYS* 4.0 9.0 - - - -
819A MET* 1.3 75.1 - - - +
821A CYS* 1.3 72.9 + - - +
822A ALA* 4.2 11.2 - - + -
840A VAL* 4.3 11.0 - - + -
847A GLN* 3.3 26.5 - - + -
848A GLY* 3.7 17.3 - - - -
864A VAL* 3.5 2.3 - - - -
865A TYR* 2.8 51.0 + + + +
866A THR 3.7 11.0 - - - -
867A LYS* 3.9 23.1 - - + +
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Residues in contact with CYS 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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801A ILE* 3.8 1.2 - - - +
802A LEU* 2.8 33.8 + - + +
804A ASP* 5.2 0.2 + - - -
807A CYS* 2.0 58.7 - - + +
811A TYR* 4.2 3.6 - - - -
820A PHE* 1.3 83.1 - - - +
822A ALA* 1.3 63.2 + - - +
862A PRO* 3.9 24.7 - - + -
863A GLY 3.2 11.2 - - - +
864A VAL* 4.1 14.1 - - - -
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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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775A CYS* 6.1 0.9 - - + -
777A ILE* 4.5 12.5 - - + +
799A ALA* 4.7 2.5 - - + +
800A PRO 3.3 19.7 - - - +
801A ILE* 4.1 5.2 - - + -
802A LEU* 4.2 6.1 - - - +
820A PHE* 4.2 9.2 - - + -
821A CYS* 1.3 74.6 - - - +
823A GLY* 1.3 58.9 + - - +
830A ASP* 4.7 1.2 - - - +
840A VAL* 5.3 3.6 - - + -
862A PRO* 3.8 0.9 - - - +
863A GLY 3.1 28.1 + - - +
865A TYR* 3.7 24.7 + - + -
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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