Contacts of the strand formed by residues 906 - 913 (chain A) in PDB entry 2W18
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 TRP 906 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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859A SER* 2.9 29.2 + - - -
860A GLU 3.4 25.5 + - - +
861A LEU* 3.9 28.2 - - + +
885A PRO* 4.3 6.7 - - + -
887A ILE* 3.6 30.7 - - + +
898A TRP* 3.7 34.8 - - + -
899A LYS* 3.3 22.9 - - - +
900A ALA* 3.5 26.5 - - + -
901A LEU* 4.3 5.9 - - - +
904A TRP 3.9 2.2 - - - -
905A GLN* 1.3 80.9 - - - +
907A GLU* 1.3 59.6 + - - +
1182A VAL* 4.5 1.2 - - - +
2187A GOL 3.4 40.8 - - - -
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Residues in contact with GLU 907 (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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898A TRP* 3.3 5.5 - - - -
899A LYS* 2.9 41.0 + - - +
900A ALA 4.2 5.2 - - - +
901A LEU* 4.0 36.0 - - + +
906A TRP* 1.3 74.5 - - - +
908A LYS* 1.3 64.3 + - - +
909A LEU* 3.6 20.7 + - + +
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Residues in contact with LYS 908 (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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863A ASN* 4.1 11.7 + - - -
894A VAL* 5.9 1.2 - - - +
896A SER* 3.9 11.2 + - - +
897A LEU 3.7 6.1 - - - +
898A TRP* 3.3 37.3 - - + -
907A GLU* 1.3 76.4 - - - +
909A LEU* 1.3 67.8 + - - +
910A TYR* 3.9 11.9 - - - +
911A THR* 3.0 28.1 + - - +
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Residues in contact with LEU 909 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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877A TRP* 6.3 0.4 - - + -
886A CYS* 5.0 2.9 - - - -
897A LEU* 2.6 38.9 + - + -
899A LYS* 3.5 29.2 - - + -
907A GLU* 3.6 27.3 + - + +
908A LYS* 1.3 82.0 - - - +
910A TYR* 1.3 86.2 + - + +
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Residues in contact with TYR 910 (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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877A TRP* 4.1 15.2 + + - -
896A SER* 3.2 5.9 - - - -
897A LEU* 2.8 63.7 + - + +
908A LYS* 3.8 2.9 - - - +
909A LEU* 1.3 100.5 - - + +
911A THR* 1.3 63.9 + - - +
912A TRP* 4.0 20.0 - + + -
949A CYS* 3.9 42.9 - - + +
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Residues in contact with THR 911 (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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894A VAL* 3.0 35.2 - - + -
895A VAL 3.2 4.7 - - - -
896A SER* 2.8 14.9 + - - -
908A LYS* 3.0 24.1 + - - +
910A TYR* 1.3 70.3 - - - +
912A TRP* 1.3 67.5 + - - +
913A HIS* 3.4 30.5 + - + +
956A GLU 5.0 3.6 + - - -
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Residues in contact with TRP 912 (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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877A TRP* 4.4 7.6 - + - -
888A ILE* 5.4 0.2 - - + -
894A VAL* 3.5 5.4 - - - +
895A VAL* 2.7 53.4 + - + +
896A SER 4.3 2.0 - - - -
897A LEU* 4.0 30.7 - - + -
910A TYR* 4.0 18.6 - + + -
911A THR* 1.3 78.4 + - - +
913A HIS* 1.3 62.8 + - - +
914A PHE* 3.4 21.9 - - + -
932A VAL* 4.3 18.4 - - + -
947A LEU* 3.6 24.7 - - + -
948A PHE 2.8 43.3 + - - +
949A CYS* 3.8 12.1 + - - -
956A GLU 4.0 19.1 - - - +
957A LYS 3.8 13.9 - - - +
958A GLN* 4.3 4.0 - - + +
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Residues in contact with HIS 913 (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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893A ASP* 3.7 5.6 - - - +
894A VAL* 4.4 10.3 - - + +
911A THR* 3.4 36.5 + - + +
912A TRP* 1.3 73.7 - - - +
914A PHE* 1.3 64.9 + - - +
915A ALA 4.2 0.4 - - - -
956A GLU 5.1 4.4 + - - +
958A GLN* 2.9 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