Contacts of the strand formed by residues 843 - 851 (chain A) in PDB entry 6N8Q
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 VAL 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777A VAL* 3.6 24.1 - - + +
814A VAL* 4.0 7.6 - - + -
815A SER 3.5 21.5 - - - +
816A GLU* 2.8 34.8 + - - +
817A GLU 5.1 0.7 - - - +
819A PHE* 3.6 31.2 - - + -
835A LEU* 3.6 15.0 - - + -
842A ARG* 1.3 71.2 - - - +
844A ARG* 1.3 64.5 + - - +
845A ARG 4.0 8.3 - - - +
846A VAL* 4.1 9.0 - - + -
866A VAL* 4.1 15.3 - - + -
867A LEU 4.0 2.5 - - - -
868A THR* 4.6 0.9 - - - +
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Residues in contact with ARG 844 (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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714A ARG* 4.9 10.1 + - - +
777A VAL* 4.8 9.5 - - - +
816A GLU* 3.9 18.8 + - - -
842A ARG* 3.3 9.5 + - - +
843A VAL* 1.3 84.1 + - - +
845A ARG* 1.3 72.6 + - - +
867A LEU* 2.8 25.3 + - + +
868A THR 4.0 13.0 - - - +
869A ASN* 3.2 31.3 - - - +
898A ILE* 3.9 22.8 - - + +
899A ALA* 5.9 1.6 - - - +
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Residues in contact with ARG 845 (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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777A VAL* 5.4 3.1 - - - -
843A VAL* 3.7 5.1 - - - +
844A ARG* 1.3 90.1 + - - +
846A VAL* 1.3 65.9 + - - +
847A SER* 4.6 11.2 - - - +
865A ALA 3.9 0.3 - - - +
866A VAL* 3.5 2.1 - - - -
867A LEU* 2.7 48.6 + - + +
898A ILE 3.3 21.0 + - - -
899A ALA* 3.3 21.3 + - - +
901A CYS 2.8 29.8 + - - -
902A VAL* 4.8 9.4 - - - +
903A PHE* 4.2 7.7 - - + +
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Residues in contact with VAL 846 (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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777A VAL* 4.1 16.4 + - + +
778A GLY* 4.2 12.3 - - - -
814A VAL* 3.9 27.4 - - + -
819A PHE* 4.4 8.7 - - + -
843A VAL* 4.1 8.7 - - + -
845A ARG* 1.3 78.7 - - - +
847A SER* 1.3 69.3 + - - +
864A LEU* 4.1 25.1 - - + -
865A ALA 3.2 11.4 - - - +
866A VAL* 3.9 16.4 - - + -
903A PHE* 5.1 0.2 - - - -
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Residues in contact with SER 847 (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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845A ARG* 4.6 6.9 - - - +
846A VAL* 1.3 79.9 + - - +
848A VAL* 1.3 67.1 + - - +
849A ALA* 6.1 0.2 - - - -
864A LEU* 3.6 3.4 - - - -
865A ALA* 2.7 36.1 + - - +
903A PHE* 3.7 35.2 + - - +
904A THR 5.8 0.9 - - - -
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Residues in contact with VAL 848 (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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780A LEU* 3.5 31.9 - - + -
788A PRO* 3.7 30.7 - - + -
847A SER* 1.3 79.5 - - - +
849A ALA* 1.3 63.9 + - - +
862A HIS* 4.1 19.3 - - + -
863A HIS 3.7 8.7 - - - +
864A LEU* 4.4 4.9 - - + -
878A LEU* 4.5 4.3 - - + -
904A THR 4.5 0.5 - - - +
905A LYS* 4.0 16.2 - - - +
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Residues in contact with ALA 849 (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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847A SER* 3.7 0.4 + - - -
848A VAL* 1.3 77.0 - - - +
850A HIS* 1.3 59.5 + - - +
851A PHE* 3.4 31.1 - - + -
862A HIS* 3.5 4.2 - - - -
863A HIS 2.9 33.2 + - - +
865A ALA* 4.2 15.3 - - + -
903A PHE* 6.2 0.2 - - + -
904A THR 4.3 5.8 - - - +
905A LYS 3.4 7.4 - - - +
907A GLY* 4.2 14.1 - - - +
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Residues in contact with HIS 850 (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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849A ALA* 1.3 71.1 - - - +
851A PHE* 1.3 66.1 + - - +
852A GLY* 4.1 3.8 + - - -
859A TYR 4.0 6.6 + - - -
860A GLY* 3.3 38.9 - - - -
861A GLU 4.1 3.8 + - - -
862A HIS* 3.7 37.5 + + + +
905A LYS 2.8 15.4 + - - +
906A TYR* 3.4 48.9 - + + +
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Residues in contact with PHE 851 (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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20A LEU* 3.7 22.2 - - + +
21A PHE* 3.6 37.7 - + + -
849A ALA* 3.4 35.7 - - + -
850A HIS* 1.3 76.5 - - - +
852A GLY* 1.3 59.6 + - - +
860A GLY* 3.2 3.1 - - - -
861A GLU 3.1 31.2 + - - +
863A HIS* 3.8 28.7 - + + -
864A LEU 5.3 0.7 - - - -
865A ALA* 5.0 2.5 - - + -
875A VAL* 4.0 14.8 - - + -
907A GLY* 4.1 8.5 - - - -
923A LEU* 3.9 29.2 - - + -
924A SER* 4.1 18.2 - - - -
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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