Contacts of the helix formed by residues 884 - 888 (chain A) in PDB entry 6WCW
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 CYS 884 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A MET* 3.7 25.5 - - + +
823A PHE* 4.2 10.5 - - - -
826A CYS* 3.3 15.9 - - - -
877A HIS* 3.2 11.0 - - - -
878A VAL* 3.9 12.1 - - + -
881A CYS 3.2 9.4 + - - +
883A LEU* 1.3 76.0 - - - +
885A GLN* 1.3 64.5 + - - +
886A ALA 3.1 1.3 - - - -
887A LYS* 3.1 16.6 + - - +
888A GLY 3.4 7.1 + - - -
902A PHE* 3.5 8.6 - - - -
1002A ZN 2.1 38.8 - - - -
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Residues in contact with GLN 885 (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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878A VAL 3.5 19.1 + - - +
879A GLU* 4.2 16.0 + - - -
881A CYS 3.3 4.4 + - - -
882A MET* 3.5 47.5 - - + +
883A LEU 3.5 0.2 - - - -
884A CYS* 1.3 79.0 - - - +
886A ALA* 1.3 60.9 + - - +
888A GLY* 3.1 13.3 + - - -
900A ILE* 3.8 25.2 + - - +
902A PHE* 3.7 27.3 - - + -
76B ALA* 4.1 3.6 - - - +
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Residues in contact with ALA 886 (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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882A MET 3.3 17.2 + - - +
883A LEU 3.7 8.7 - - - +
884A CYS 3.1 0.6 - - - -
885A GLN* 1.3 78.4 - - - +
887A LYS* 1.3 58.0 + - + +
888A GLY 3.2 0.2 - - - -
43B ALA* 5.6 1.3 - - + +
62B TRP* 3.8 21.5 - - + -
76B ALA* 3.4 7.2 + - - -
77B PHE* 3.2 55.4 + - + +
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Residues in contact with LYS 887 (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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822A MET* 4.9 12.1 + - + +
825A THR* 3.5 44.4 + - - +
826A CYS* 4.2 8.7 - - - +
883A LEU* 2.9 28.7 + - - +
884A CYS* 3.1 10.5 + - - +
886A ALA* 1.3 75.5 - - + +
888A GLY* 1.3 61.3 + - - +
889A PHE* 4.3 1.9 - - - -
902A PHE* 4.7 1.9 - - - -
903A PRO* 5.8 0.7 - - - +
42B GLY* 4.0 2.2 - - - -
43B ALA* 3.9 35.9 + - + +
73B LEU* 3.8 21.7 - - + +
74B GLY 2.6 41.3 + - - +
77B PHE* 5.2 1.3 - - + -
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Residues in contact with GLY 888 (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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884A CYS 3.4 3.0 + - - -
885A GLN 3.1 13.2 + - - -
886A ALA 3.2 0.4 - - - -
887A LYS* 1.3 77.0 - - - +
889A PHE* 1.3 62.6 + - - -
900A ILE* 3.7 3.6 - - - -
901A ILE 3.9 0.4 - - - -
902A PHE* 3.4 30.1 - - - -
75B VAL 2.8 25.1 + - - -
76B ALA* 2.9 10.8 + - - -
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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