Contacts of the helix formed by residues 900 - 906 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A ASN 5.3 0.2 - - - +
821A THR* 3.5 33.7 - - - +
822A HIS 4.3 0.9 - - - +
823A ALA* 3.9 28.7 - - + +
861A TRP* 3.8 2.7 - - - -
898A ALA* 3.6 6.6 - - + +
899A ASP* 1.3 91.1 - - - +
901A VAL* 1.3 66.9 + - - +
902A SER* 3.3 2.2 - - - +
903A LYS* 3.1 26.4 + - + +
904A SER 3.5 6.2 + - - -
954A THR* 4.8 7.9 - - + +
956A PRO* 4.3 20.0 - - + -
974A GLY* 5.0 13.2 - - - +
986A TYR* 4.0 32.1 - - + -
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Residues in contact with VAL 901 (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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818A VAL* 3.7 26.9 - - + +
821A THR* 3.0 31.5 + - - +
822A HIS* 4.0 4.9 - - + +
831A LEU* 3.9 25.1 - - + -
861A TRP* 3.5 43.8 - - + +
900A MET* 1.3 70.1 - - - +
902A SER* 1.3 57.0 + - - +
904A SER* 3.2 3.8 + - - -
905A ALA* 2.8 31.4 + - - +
919A ILE* 4.1 9.6 - - + -
1005A LEU* 5.1 3.8 - - + -
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Residues in contact with SER 902 (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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821A THR 3.9 2.1 + - - -
822A HIS* 3.7 31.4 - - - -
823A ALA* 3.0 20.4 + - - +
826A HIS* 2.7 27.3 + - - -
829A TYR* 3.0 28.9 + - - -
831A LEU* 5.0 0.4 - - - -
900A MET* 4.6 1.4 - - - +
901A VAL* 1.3 79.1 - - - +
903A LYS* 1.3 67.1 + - - +
905A ALA* 4.0 2.2 - - - -
906A ASN* 3.1 15.8 + - - -
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Residues in contact with LYS 903 (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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826A HIS* 3.9 17.7 - - + -
898A ALA* 4.1 4.0 - - + -
900A MET* 3.1 17.9 + - + +
902A SER* 1.3 83.7 + - - +
904A SER* 1.3 60.8 + - - +
906A ASN* 3.6 9.9 + - - +
907A TYR* 3.3 24.0 - - + -
984A LEU* 4.1 6.6 - - - +
986A TYR* 3.0 44.9 + - + +
987A ASN 3.2 18.7 + - - +
988A GLU* 2.9 29.7 + - - +
1101A 7U3 3.5 22.7 - - + -
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Residues in contact with SER 904 (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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861A TRP* 3.1 39.5 + - - +
863A GLY* 3.4 13.8 - - - -
898A ALA* 3.5 9.9 - - - +
900A MET 3.5 1.8 + - - -
901A VAL 3.2 3.4 + - - -
903A LYS* 1.3 78.1 - - - +
905A ALA* 1.3 59.7 + - - +
907A TYR* 3.0 26.4 + - - +
908A CYS 4.0 0.2 + - - -
919A ILE* 3.5 11.9 - - - -
1101A 7U3 2.8 26.2 + - - -
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Residues in contact with ALA 905 (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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829A TYR* 3.5 17.5 - - - +
831A LEU* 4.1 13.2 - - + -
901A VAL* 2.8 17.3 + - + +
902A SER* 4.0 2.5 - - - -
903A LYS 3.3 0.4 - - - -
904A SER* 1.3 78.2 - - - +
906A ASN* 1.3 61.4 + - - +
908A CYS* 3.0 30.5 + - - +
909A HIS 4.3 0.9 + - - -
919A ILE* 4.0 7.8 - - + +
1005A LEU* 4.9 1.6 - - + -
1007A PHE* 3.6 26.3 - - + -
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Residues in contact with ASN 906 (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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826A HIS* 3.6 30.9 + - - -
829A TYR* 2.6 36.1 + - - -
902A SER 3.1 13.1 + - - -
903A LYS* 3.7 11.3 + - - +
904A SER 3.2 0.4 - - - -
905A ALA* 1.3 77.8 - - - +
907A TYR* 1.4 63.1 + - + +
908A CYS 3.2 0.7 - - - -
909A HIS* 3.5 24.3 + - - -
1007A PHE* 5.5 0.4 - - - -
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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