Contacts of the helix formed by residues 881 - 890 (chain A) in PDB entry 6DBT
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 THR 881 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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863A MET* 4.6 5.0 - - - -
877A ARG 4.2 7.2 - - - +
878A ARG* 2.9 24.7 + - + +
879A LEU 3.3 2.5 + - - +
880A MET* 1.3 81.1 - - - +
882A ARG* 1.3 66.2 + - - +
883A GLU* 3.2 14.3 + - - +
884A ALA* 3.2 16.1 + - - +
885A VAL* 3.1 23.2 + - - +
905A MET* 3.6 6.2 - - - -
909A LEU* 4.3 6.5 - - + -
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Residues in contact with ARG 882 (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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881A THR* 1.3 70.8 - - - +
883A GLU* 1.3 69.0 + - + +
885A VAL* 3.2 7.6 + - - +
886A GLU* 2.9 50.2 + - - +
902A LEU* 3.9 24.9 - - + +
905A MET* 4.4 8.7 - - + +
906A ASP* 4.6 22.1 + - + +
909A LEU* 4.8 12.2 - - + +
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Residues in contact with GLU 883 (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 MET* 4.8 17.0 - - + -
881A THR* 3.1 10.1 - - - +
882A ARG* 1.3 88.5 + - + +
884A ALA* 1.3 59.7 + - - +
886A GLU* 3.3 10.5 + - - +
887A ALA* 2.9 27.8 + - - +
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Residues in contact with ALA 884 (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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830A PHE* 4.9 3.1 - - + -
859A LEU* 4.4 10.9 - - + +
863A MET* 4.0 22.7 - - + -
865A LEU* 6.0 0.4 - - + -
878A ARG 4.3 3.4 - - - +
879A LEU* 4.0 18.2 - - + +
881A THR* 3.2 22.6 + - - +
883A GLU* 1.3 78.4 - - - +
885A VAL* 1.3 57.9 + - - +
887A ALA* 3.2 8.6 + - - +
888A VAL* 3.0 28.4 + - - +
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Residues in contact with VAL 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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830A PHE* 3.5 20.9 - - + -
879A LEU 5.3 1.1 - - - +
881A THR 3.1 8.8 + - - +
882A ARG 3.5 7.4 - - - +
883A GLU 3.2 0.4 - - - -
884A ALA* 1.3 75.4 - - - +
886A GLU* 1.3 60.6 + - - +
888A VAL* 3.0 10.5 - - - +
889A CYS* 2.9 29.3 + - - -
901A LEU* 3.6 23.3 - - + +
902A LEU* 3.7 29.6 - - + -
905A MET* 3.5 44.6 - - + -
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Residues in contact with GLU 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 ARG* 2.9 50.7 + - - +
883A GLU* 3.9 8.4 - - - +
885A VAL* 1.3 75.9 - - - +
887A ALA* 1.3 61.0 + - - +
889A CYS* 3.3 22.2 + - + +
890A GLU* 3.4 7.8 + - - +
902A LEU* 4.0 23.7 - - + +
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Residues in contact with ALA 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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858A GLN* 2.8 25.7 + - - -
859A LEU* 4.6 8.1 - - + -
862A LYS* 3.4 38.0 - - + +
863A MET* 4.9 2.5 - - + -
883A GLU 2.9 14.8 + - - +
884A ALA* 3.3 14.6 - - - +
885A VAL 3.1 0.2 - - - -
886A GLU* 1.3 77.4 - - - +
888A VAL* 1.3 60.0 + - - +
890A GLU* 3.3 8.4 + - - +
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Residues in contact with VAL 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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830A PHE* 3.5 57.7 - - + +
833A GLU* 6.3 1.3 - - + -
834A ILE* 5.1 7.0 - - + -
855A LEU* 3.6 32.1 - - + -
858A GLN* 4.4 5.4 - - + +
859A LEU* 5.7 2.8 - - + +
884A ALA 3.0 11.5 + - - +
885A VAL 3.0 18.8 - - - +
887A ALA* 1.3 74.5 - - - +
889A CYS* 1.3 63.9 + - - +
890A GLU 3.1 0.9 - - - -
891A LEU* 3.3 13.0 + - + +
892A VAL* 3.5 11.9 + - + +
901A LEU* 4.7 4.7 - - + -
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Residues in contact with CYS 889 (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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885A VAL* 2.9 25.1 + - - -
886A GLU* 3.3 19.1 - - + +
887A ALA 3.2 0.2 - - - -
888A VAL* 1.3 76.3 - - - +
890A GLU* 1.3 58.3 + - - +
892A VAL* 3.1 16.2 + - - +
898A ARG* 2.4 66.4 + - + +
901A LEU* 3.6 23.1 - - - -
902A LEU* 4.6 8.3 - - - -
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Residues in contact with GLU 890 (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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858A GLN* 2.5 35.7 + - - +
861A LYS* 4.0 14.2 + - - -
862A LYS* 3.2 20.0 + - + +
886A GLU 3.4 6.3 + - - +
887A ALA* 3.3 10.4 + - - +
888A VAL 3.1 0.4 - - - -
889A CYS* 1.3 79.1 - - - +
891A LEU* 1.3 65.5 + - + +
892A VAL 4.3 1.6 - - - +
898A ARG* 3.3 17.1 + - - +
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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