Contacts of the strand formed by residues 862 - 868 (chain A) in PDB entry 6N8P
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 HIS 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786A SER 5.7 0.4 - - - +
787A VAL* 3.5 34.0 - - + +
788A PRO* 3.8 32.9 - - + +
848A VAL* 4.4 11.4 - - + -
849A ALA 3.6 6.1 - - - +
850A HIS* 3.6 34.2 - + + +
860A GLY 4.7 3.1 - - - -
861A GLU* 1.3 78.3 - - - +
863A HIS* 1.3 75.7 + - - +
878A LEU* 4.0 21.3 + - + +
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Residues in contact with HIS 863 (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* 4.9 6.6 - - + +
21A PHE* 4.3 8.0 - + - -
848A VAL* 3.7 10.2 - - - +
849A ALA* 2.9 30.3 + - - +
851A PHE* 4.0 18.4 - + + -
861A GLU* 3.1 43.9 + - - +
862A HIS* 1.3 87.3 - - - +
864A LEU* 1.3 63.0 + - - +
875A VAL* 3.7 18.2 - - + -
876A VAL 3.3 7.6 - - - +
877A SER* 3.3 25.3 + - - +
878A LEU* 4.0 10.0 - - - +
884A GLN* 3.7 29.9 - - + +
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Residues in contact with LEU 864 (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* 4.7 8.3 - - + -
812A LEU* 3.6 29.8 - - + -
814A VAL* 4.0 7.2 - - + -
819A PHE* 3.9 29.4 - - + -
846A VAL* 3.7 19.1 - - + -
847A SER 3.8 15.5 - - - +
848A VAL* 4.2 4.3 - - - +
849A ALA* 5.3 0.2 - - - -
863A HIS* 1.3 76.8 - - - +
865A ALA* 1.3 60.9 + - - +
866A VAL* 3.8 4.2 + - + +
874A GLN 3.5 0.9 - - - +
875A VAL* 3.2 7.7 - - - -
876A VAL* 2.5 48.8 + - + +
878A LEU* 3.6 17.0 - - + -
881A LEU* 4.5 4.9 - - + -
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Residues in contact with ALA 865 (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 4.1 0.2 - - - +
846A VAL* 3.4 5.5 - - - +
847A SER* 2.8 43.5 + - - +
849A ALA* 4.1 18.3 - - + +
851A PHE* 5.2 5.4 - - + -
863A HIS 4.2 0.8 - - - -
864A LEU* 1.3 70.8 - - - +
866A VAL* 1.3 59.9 + - - +
867A LEU 4.3 0.2 - - - -
873A ILE* 5.2 3.1 - - + -
874A GLN 3.7 4.5 - - - +
875A VAL* 4.7 4.7 - - + +
903A PHE* 4.3 29.8 - - + -
904A THR 6.1 0.2 - - - +
923A LEU* 5.7 2.7 - - + -
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Residues in contact with VAL 866 (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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819A PHE* 3.5 26.5 - - + -
835A LEU* 4.8 3.6 - - + -
843A VAL* 3.7 36.8 - - + -
845A ARG 3.7 2.7 - - - -
846A VAL* 3.8 11.9 - - + -
864A LEU* 4.1 11.2 - - + +
865A ALA* 1.3 77.7 - - - +
867A LEU* 1.3 67.0 + - - +
868A THR* 3.9 10.7 + - + +
873A ILE* 3.2 8.4 - - - +
874A GLN* 2.9 41.4 + - + +
876A VAL* 4.5 7.9 - - + -
903A PHE* 4.4 2.9 - - - -
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Residues in contact with LEU 867 (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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843A VAL* 3.8 0.5 - - - -
844A ARG* 2.7 44.7 + - + +
845A ARG* 2.9 20.0 + - + +
866A VAL* 1.3 72.5 - - - +
868A THR* 1.3 62.9 + - - +
871A GLY 4.4 5.8 - - - +
872A ASP 3.7 7.6 - - - +
873A ILE* 3.7 23.3 - - + -
890A ILE* 4.9 3.8 - - + -
898A ILE* 3.7 28.3 - - + +
901A CYS* 3.7 39.5 - - + +
903A PHE* 3.5 22.6 - - + -
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Residues in contact with THR 868 (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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835A LEU* 4.3 11.4 - - + -
841A SER* 3.9 24.1 - - - +
842A ARG 3.2 11.9 - - - +
843A VAL* 4.5 0.2 - - - +
844A ARG* 4.4 1.6 - - - -
866A VAL* 4.3 17.5 - - + +
867A LEU* 1.3 80.5 - - - +
869A ASN* 1.3 63.9 + - - +
870A LEU* 3.3 15.6 + - - +
871A GLY 3.3 3.3 + - - -
872A ASP* 3.1 27.5 + - - +
874A GLN* 4.3 17.0 - - - +
898A ILE* 3.2 17.0 - - - +
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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