Contacts of the helix formed by residues 900 - 907 (chain B) in PDB entry 5WRZ
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 MET 900 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820B ASN 5.3 0.4 - - - +
821B THR* 3.7 31.0 - - - +
822B HIS 4.5 0.7 - - - -
823B ALA* 3.9 29.2 - - + +
861B TRP* 3.7 3.6 - - - -
898B ALA* 3.4 5.6 - - + +
899B ASP* 1.3 91.9 - - - +
901B VAL* 1.3 67.5 + - - +
902B SER* 3.1 2.4 + - - +
903B LYS* 3.2 25.3 + - + +
904B SER 3.4 7.4 + - - -
954B THR* 5.1 3.1 - - + +
955B THR* 5.3 2.2 - - - -
956B PRO* 4.4 16.4 - - + -
973B THR 6.0 0.7 - - - -
974B GLY* 4.9 19.1 - - - +
986B TYR* 4.1 32.1 - - + -
987B ASN 6.1 0.2 - - - +
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Residues in contact with VAL 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818B VAL* 3.4 31.9 - - + +
821B THR* 3.0 32.0 + - - +
822B HIS* 4.1 3.8 - - + +
831B LEU* 4.1 24.9 - - + -
861B TRP* 3.5 42.2 - - + +
900B MET* 1.3 72.8 - - - +
902B SER* 1.3 59.4 + - - +
904B SER* 3.3 5.0 + - - -
905B ALA* 2.9 24.1 + - - +
919B ILE* 3.9 8.9 - - + +
1005B LEU* 4.7 5.8 - - + -
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Residues in contact with SER 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821B THR 3.8 1.8 + - - -
822B HIS* 3.8 29.6 - - - -
823B ALA* 3.0 22.6 + - - +
826B HIS* 2.7 27.3 + - - -
829B TYR* 3.1 28.3 + - - -
831B LEU* 4.8 0.9 - - - -
900B MET* 4.8 0.9 - - - +
901B VAL* 1.3 78.3 - - - +
903B LYS* 1.3 66.7 + - - +
905B ALA* 4.1 2.9 - - - -
906B ASN* 3.1 17.2 + - - -
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Residues in contact with LYS 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826B HIS* 3.6 16.9 + - + -
898B ALA* 3.9 4.9 - - + -
900B MET* 3.2 18.7 + - + +
902B SER* 1.3 82.5 + - - +
904B SER* 1.3 62.5 + - - +
906B ASN* 3.6 9.0 + - - +
907B TYR* 3.2 28.6 - - + -
984B LEU* 4.3 6.5 - - - +
986B TYR* 3.0 35.5 + - + +
987B ASN 2.9 28.2 + - - +
988B GLU* 2.9 29.2 + - - +
1101B 7U3 3.7 20.0 - - + -
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Residues in contact with SER 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861B TRP* 3.1 28.3 + - - +
863B GLY* 3.4 20.3 - - - -
898B ALA* 3.4 9.4 - - - +
900B MET 3.4 1.8 + - - -
901B VAL 3.3 3.6 + - - -
903B LYS* 1.3 79.7 - - - +
905B ALA* 1.3 59.4 + - - +
907B TYR* 2.9 19.1 + - - +
919B ILE* 3.4 24.7 - - - -
1101B 7U3 2.9 24.9 + - - -
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Residues in contact with ALA 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B TYR* 3.5 18.2 - - - +
831B LEU* 4.3 11.4 - - + -
901B VAL 2.9 15.5 + - - +
902B SER* 3.2 3.7 + - - -
904B SER* 1.3 78.1 - - - +
906B ASN* 1.3 56.7 + - - +
908B CYS* 3.0 34.6 + - - +
909B HIS 4.1 1.4 + - - -
910B THR* 5.0 0.7 + - - -
919B ILE* 4.3 6.7 - - + +
1005B LEU* 5.0 3.1 - - + -
1007B PHE* 3.7 27.8 - - + -
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Residues in contact with ASN 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826B HIS* 3.3 35.6 + - - +
829B TYR* 2.8 33.3 + - - -
902B SER 3.1 19.1 + - - +
903B LYS* 3.7 8.6 - - - +
905B ALA* 1.3 77.8 - - - +
907B TYR* 1.3 59.1 + - + +
909B HIS* 3.3 27.5 + - - -
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Residues in contact with TYR 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763B GLU* 4.1 14.4 - - - -
863B GLY 3.5 3.4 - - - +
864B SER* 3.4 16.0 - - - -
865B ARG* 3.6 2.8 + - - -
903B LYS* 3.2 36.6 - - + -
904B SER 2.9 10.4 + - - +
906B ASN* 1.3 76.6 - - + +
908B CYS* 1.3 59.7 + - - +
909B HIS* 3.2 21.3 - + - -
988B GLU* 5.0 2.1 + - - -
1101B 7U3 3.3 94.8 + + - +
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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