Contacts of the strand formed by residues 843 - 850 (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 LYS 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A ASN* 6.4 1.3 - - + -
705A VAL 3.2 8.3 - - - +
706A ILE* 3.6 30.0 - - + +
721A VAL* 4.4 19.3 - - + +
841A ASN 4.2 2.0 + - - +
842A HIS* 1.3 73.1 - - - +
844A VAL* 1.3 64.6 + - - +
864A PRO* 3.5 20.6 - - + +
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Residues in contact with VAL 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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703A GLU 3.6 0.5 - - - +
704A ASN* 3.6 4.0 - - - +
705A VAL* 2.9 53.0 + - + +
707A VAL* 4.0 13.9 - - + -
839A VAL* 4.3 12.1 - - + -
842A HIS* 4.2 15.0 - - + +
843A LYS* 1.3 80.1 - - - +
845A GLN* 1.3 63.1 + - - +
861A LEU* 3.9 21.5 - - + -
862A ARG 3.4 11.9 - - - +
863A ASP* 5.9 0.2 - - - +
864A PRO* 4.2 6.1 - - + -
870A PHE* 3.8 26.7 - - + -
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Residues in contact with GLN 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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702A TYR* 3.7 29.1 - - + +
703A GLU 3.5 2.9 - - - -
704A ASN* 3.6 22.5 + - - +
844A VAL* 1.3 73.7 - - - +
846A LEU* 1.3 60.5 + - - +
860A THR 3.8 0.5 - - - +
861A LEU* 3.4 4.6 - - - -
862A ARG* 2.8 85.2 + - + +
863A ASP 4.3 0.3 - - - +
864A PRO* 3.9 31.5 + - + +
867A LYS* 4.0 3.6 - - - +
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Residues in contact with LEU 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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701A ASN 4.5 0.9 - - - +
702A TYR* 3.5 5.2 - - - -
703A GLU* 2.8 56.8 + - + +
705A VAL* 3.9 19.1 - - + -
716A PHE* 3.9 7.4 - - + -
718A ALA* 4.4 1.3 - - + -
814A TYR* 3.6 40.4 - - + +
844A VAL 3.9 0.2 + - - -
845A GLN* 1.3 73.7 - - - +
847A ASN* 1.3 65.2 + - - +
848A VAL* 3.9 27.1 - - + +
859A ALA* 4.1 7.2 - - + -
860A THR 3.4 5.2 - - - +
861A LEU* 3.8 19.5 - - + -
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Residues in contact with ASN 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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700A VAL* 3.4 27.5 - - - +
701A ASN 4.3 7.6 - - - +
702A TYR* 3.7 18.4 + - + -
846A LEU* 1.3 78.3 - - - +
848A VAL* 1.3 70.9 + - - +
849A GLU* 2.9 30.9 + - - +
859A ALA* 3.1 2.8 - - - -
860A THR* 2.9 43.4 + - - +
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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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814A TYR* 4.0 20.6 - - + +
846A LEU* 3.9 19.4 - - + +
847A ASN* 1.3 83.4 + - - +
849A GLU* 1.3 62.8 + - - +
850A LEU 4.1 11.0 - - - +
851A LYS* 4.5 11.9 - - + +
857A ASN* 4.0 24.7 - - + +
858A LEU 3.5 10.8 - - - +
859A ALA* 4.3 0.4 - - - +
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Residues in contact with GLU 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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817A ALA* 4.1 7.0 - - + -
847A ASN* 2.9 27.2 + - - +
848A VAL* 1.3 73.3 - - - +
850A LEU* 1.3 59.4 + - - +
858A LEU* 2.7 19.4 + - + +
860A THR* 2.8 47.4 + - + +
889A LYS* 3.4 25.7 + - - -
890A LEU* 3.7 23.6 - - + +
893A LEU* 3.9 18.8 - - + +
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Residues in contact with LEU 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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848A VAL* 3.7 3.8 - - - -
849A GLU* 1.3 79.9 - - - +
851A LYS* 1.3 76.7 + - - +
852A VAL* 3.7 8.3 + - + +
857A ASN* 3.4 3.6 - - - +
858A LEU* 2.9 41.3 + - + +
885A ARG* 3.7 16.8 - - - +
887A GLU* 3.4 42.0 - - + +
889A LYS* 4.1 26.7 - - + +
890A LEU* 4.1 14.6 - - + -
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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