Contacts of the strand formed by residues 857 - 862 (chain A) in PDB entry 2WAC
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 ASN 857 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813A GLU 4.3 4.6 + - - -
814A TYR* 3.4 20.5 - - + +
815A ALA 2.9 21.4 + - - -
848A VAL* 4.0 18.5 - - + +
850A LEU 3.4 8.5 - - - +
851A LYS* 3.4 25.5 - - - +
852A VAL* 2.8 30.5 + - - +
855A SER 3.8 1.5 - - - +
856A PRO* 1.3 71.4 - - - +
858A LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 858 (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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815A ALA* 3.5 19.1 - - + +
816A LEU 5.5 0.4 - - - +
817A ALA* 4.3 16.2 - - + -
818A LEU* 4.6 14.8 - - + +
848A VAL* 3.5 6.1 - - - +
849A GLU* 2.7 31.5 + - + -
850A LEU* 2.9 32.6 + - + +
852A VAL* 3.8 21.5 - - + -
856A PRO 4.5 1.3 - - - +
857A ASN* 1.3 72.4 - - - +
859A ALA* 1.3 53.6 + - - +
883A GLU* 5.1 0.7 - - - +
885A ARG* 3.7 35.9 - - - +
890A LEU* 4.3 12.8 - - + -
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Residues in contact with ALA 859 (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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716A PHE* 4.2 4.7 - - + -
814A TYR* 3.9 33.0 - - + -
815A ALA 2.9 9.8 + - - +
816A LEU* 3.7 8.1 - - - +
817A ALA* 2.9 25.9 + - - +
846A LEU* 4.1 17.5 - - + -
847A ASN 3.1 13.9 - - - +
848A VAL* 4.4 1.3 - - - -
849A GLU 4.2 0.4 - - - +
858A LEU* 1.3 74.9 - - - +
860A THR* 1.3 61.3 + - - +
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Residues in contact with THR 860 (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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702A TYR* 4.8 5.2 + - - -
816A LEU* 5.1 2.0 - - - -
817A ALA* 3.9 10.3 - - + +
845A GLN 3.8 0.6 - - - +
846A LEU* 3.4 6.1 - - - +
847A ASN* 2.9 36.9 + - - +
849A GLU* 2.8 36.3 + - + +
859A ALA* 1.3 74.6 - - - +
861A LEU* 1.3 66.5 + - - +
862A ARG* 5.8 0.7 - - - -
869A ASP* 3.9 14.4 - - - +
893A LEU* 4.0 9.4 - - + -
897A TYR* 3.8 22.4 - - - +
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Residues in contact with LEU 861 (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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705A VAL* 4.5 1.8 - - + -
707A VAL* 3.8 20.4 - - + -
716A PHE* 3.7 39.7 - - + -
816A LEU* 4.5 7.8 - - + +
835A PHE* 3.7 28.3 - - + -
839A VAL* 4.2 5.6 - - + -
844A VAL* 3.9 17.3 - - + -
845A GLN 3.4 1.3 - - - -
846A LEU* 3.8 20.6 - - + -
860A THR* 1.3 82.6 - - - +
862A ARG* 1.3 60.7 + - - +
869A ASP* 3.5 7.3 + - - +
870A PHE* 2.9 42.7 + - + -
871A GLY 5.5 0.4 - - - +
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Residues in contact with ARG 862 (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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702A TYR* 3.3 50.3 + - + -
844A VAL* 3.4 5.4 - - - +
845A GLN* 2.8 69.7 + - + +
860A THR* 6.1 0.7 - - - +
861A LEU* 1.3 76.1 - - - +
863A ASP* 1.3 65.6 + - - +
864A PRO 3.5 0.3 - - - -
867A LYS* 3.4 65.5 - - - +
868A VAL 3.4 5.2 - - - +
869A ASP* 4.6 3.1 - - - +
870A PHE* 3.7 5.6 - - - -
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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