Contacts of the helix formed by residues 855 - 866 (chain A) in PDB entry 4DTR
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 855 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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811A TYR* 3.9 22.1 + - + +
815A ILE* 4.2 14.4 - - + -
821A ALA* 4.6 1.5 - - + +
822A PRO* 3.9 24.5 - - + +
853A GLU 3.5 3.9 + - - -
854A ILE* 1.3 74.7 - - - +
856A ASP* 1.3 66.8 + - - +
857A LEU* 3.2 25.6 + - + +
858A ILE* 3.2 21.6 + - + +
859A LYS 3.1 14.9 + - - -
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Residues in contact with ASP 856 (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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854A ILE 3.5 1.4 + - - +
855A THR* 1.3 72.0 + - - +
857A LEU* 1.3 66.6 + - + +
858A ILE* 2.9 2.1 + - - -
859A LYS* 3.6 27.5 + - - +
860A ASP* 4.7 8.0 + - - +
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Residues in contact with LEU 857 (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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814A ALA 5.6 1.8 - - - +
815A ILE* 4.7 9.6 - - + -
818A ASN* 3.3 37.0 - - + +
820A ASP* 5.8 0.7 - - - +
821A ALA* 4.1 9.9 - - + -
855A THR* 3.1 21.5 - - + +
856A ASP* 1.3 77.8 - - + +
858A ILE* 1.3 69.1 + - + +
861A ASP* 4.7 5.0 - - - +
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Residues in contact with ILE 858 (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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811A TYR* 3.9 23.3 - - + -
814A ALA* 4.2 20.6 - - + +
815A ILE* 4.3 7.9 - - + -
841A PHE* 3.8 21.5 - - + -
846A ILE* 4.0 14.1 - - + -
854A ILE* 3.7 26.9 - - + -
855A THR* 3.7 14.6 - - + +
856A ASP 3.0 0.2 - - - -
857A LEU* 1.3 87.4 - - + +
859A LYS* 1.3 70.3 + - - +
860A ASP* 3.2 3.6 - - - -
861A ASP* 3.1 13.7 + - - +
862A VAL* 3.0 21.4 + - + +
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Residues in contact with LYS 859 (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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775A ASN* 5.8 1.0 - - - +
776A TYR* 3.8 15.9 - - + +
853A GLU* 2.8 33.2 + - + +
854A ILE* 3.7 26.7 - - + +
855A THR 3.1 14.9 + - - +
856A ASP* 3.6 22.9 + - - +
858A ILE* 1.3 76.8 - - - +
860A ASP* 1.3 63.0 + - - +
862A VAL* 3.2 4.1 + - - +
863A LEU* 2.9 53.5 + - + +
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Residues in contact with ASP 860 (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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856A ASP 4.7 7.1 + - - +
858A ILE 3.2 1.3 - - - -
859A LYS* 1.3 82.8 - - - +
861A ASP* 1.3 66.8 + - - +
863A LEU* 3.5 11.4 + - - +
864A HIS* 3.1 23.4 + - - +
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Residues in contact with ASP 861 (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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840A PRO* 4.4 15.6 - - + +
841A PHE* 3.6 25.2 - - + -
857A LEU 4.7 4.0 - - - +
858A ILE* 3.1 13.9 + - - +
860A ASP* 1.3 78.4 - - - +
862A VAL* 1.3 60.3 + - - +
864A HIS* 3.3 5.1 + - - +
865A TRP* 2.9 38.0 + - + +
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Residues in contact with VAL 862 (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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776A TYR* 4.9 8.7 - - + -
833A LEU* 3.9 27.1 - - + -
835A LEU* 4.7 5.7 - - + +
841A PHE* 3.7 22.2 - - + -
846A ILE* 4.2 21.8 - - + -
848A TRP* 5.1 0.7 - - + -
854A ILE* 4.0 27.8 - - + -
858A ILE* 3.0 18.7 + - + +
859A LYS* 3.5 8.3 - - - +
861A ASP* 1.3 75.9 - - - +
863A LEU* 1.3 59.8 + - - +
865A TRP 3.1 0.7 + - - -
866A MET* 2.8 35.9 + - + +
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Residues in contact with LEU 863 (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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776A TYR* 3.5 47.6 - - + -
859A LYS* 2.9 44.3 + - + +
860A ASP* 3.7 11.2 - - - +
862A VAL* 1.3 77.3 - - + +
864A HIS* 1.3 61.3 + - - +
865A TRP 3.6 0.2 + - - -
866A MET* 3.8 21.2 - - - +
868A TYR* 4.4 10.3 + - - +
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Residues in contact with HIS 864 (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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836A ARG* 3.0 31.2 + - - -
860A ASP 3.1 18.2 + - - +
861A ASP* 3.7 6.5 - - - +
862A VAL 3.1 0.2 - - - -
863A LEU* 1.3 77.0 - - - +
865A TRP* 1.3 93.3 + + + +
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Residues in contact with TRP 865 (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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835A LEU* 3.6 11.3 - - + -
836A ARG* 2.9 64.3 + - + +
837A GLU 3.5 20.9 - - - -
838A GLY* 3.4 20.0 - - - -
839A ASN* 3.6 26.9 - - + -
840A PRO* 3.3 27.9 - - + +
841A PHE* 5.3 2.0 - - + -
861A ASP* 2.9 28.7 + - + +
862A VAL 3.6 0.7 - - - +
864A HIS* 1.3 107.5 + + + +
866A MET* 1.3 68.0 + - - +
867A ASP 3.2 0.2 + - - -
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Residues in contact with MET 866 (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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776A TYR* 3.6 26.2 - - + -
779A ILE* 3.5 37.5 - - + -
833A LEU* 3.8 30.3 - - + -
834A PRO 3.7 7.2 - - - +
835A LEU* 4.4 2.2 - - - +
836A ARG* 3.0 17.7 + - - -
862A VAL* 2.8 24.4 + - + +
863A LEU* 3.8 19.7 - - - +
864A HIS 3.6 0.4 - - - -
865A TRP* 1.3 73.8 - - - +
867A ASP* 1.3 60.7 + - - +
868A TYR* 3.3 39.4 + - + +
871A LEU* 4.0 5.8 - - + -
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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