Contacts of the helix formed by residues 862 - 871 (chain A) in PDB entry 3DPK
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 ASN 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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860A LEU* 3.3 26.5 + - + +
861A VAL* 1.3 78.4 - - - +
863A SER* 1.3 57.3 + - - +
864A LYS* 2.8 28.1 + - - +
865A PHE* 2.7 34.4 + - - +
866A TYR* 3.2 17.7 + - - -
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Residues in contact with SER 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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862A ASN* 1.3 75.2 - - - +
864A LYS* 1.3 63.1 + - - +
866A TYR* 3.4 12.3 + - - +
867A LYS* 3.1 39.0 + - - +
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Residues in contact with LYS 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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859A ILE* 6.4 1.3 - - + -
862A ASN* 2.8 17.4 + - - +
863A SER* 1.3 79.3 - - - +
865A PHE* 1.3 63.7 + - - +
867A LYS* 3.3 12.6 + - + +
868A LEU* 3.0 33.2 + - + +
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Residues in contact with PHE 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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819A VAL* 3.7 28.3 - - + -
820A LYS* 4.2 17.5 - - + -
827A ILE* 4.9 3.6 - - + -
856A TYR* 3.8 40.2 - + + -
859A ILE* 4.1 19.4 - - + +
860A LEU 3.5 19.1 - - - +
861A VAL* 4.4 11.4 - - + -
862A ASN* 2.7 20.4 + - - +
864A LYS* 1.3 74.7 - - - +
866A TYR* 1.3 77.7 + + - +
868A LEU* 3.1 13.9 + - + +
869A VAL* 3.1 47.7 + - + +
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Residues in contact with TYR 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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810A ILE* 4.7 5.2 - - - +
819A VAL* 3.7 26.5 - - + +
827A ILE* 3.5 35.4 - - + -
828A PHE* 3.6 19.9 - + + -
861A VAL* 3.5 22.4 - - + +
862A ASN* 3.2 31.3 + - - -
863A SER* 3.8 9.2 - - - +
865A PHE* 1.3 85.9 - + - +
867A LYS* 1.3 62.9 + - + +
869A VAL* 3.4 5.1 - - - +
870A LYS* 3.0 26.2 + - - +
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Residues in contact with LYS 867 (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 SER* 3.1 30.6 + - - +
864A LYS* 3.8 9.6 - - + +
865A PHE 3.3 0.2 - - - -
866A TYR* 1.3 75.7 - - + +
868A LEU* 1.3 64.4 + - + +
870A LYS* 3.5 6.0 + - - -
871A ASP* 2.9 37.3 + - - +
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Residues in contact with LEU 868 (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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859A ILE* 4.7 24.5 - - + -
864A LYS* 3.0 26.6 + - + +
865A PHE* 3.1 15.0 + - + +
867A LYS* 1.3 77.5 - - + +
869A VAL* 1.3 64.8 + - + +
871A ASP* 3.0 15.9 + - + +
872A GLY 3.1 0.5 + - - -
873A TYR* 3.0 53.0 + - + +
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Residues in contact with VAL 869 (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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824A PRO* 4.6 10.4 - - + +
827A ILE* 4.7 10.8 - - + -
828A PHE* 4.0 19.1 - - + -
839A TRP* 5.0 14.8 - - + -
856A TYR* 4.4 16.6 - - + +
865A PHE* 3.1 43.7 + - + +
866A TYR* 3.4 13.0 - - - +
868A LEU* 1.3 77.5 - - + +
870A LYS* 1.3 66.8 + - - +
872A GLY* 3.2 10.0 + - - -
873A TYR* 4.4 10.6 - - + +
895A LEU* 3.4 16.1 - - - +
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Residues in contact with LYS 870 (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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824A PRO* 5.2 2.2 - - + -
828A PHE* 3.9 30.9 - - + +
866A TYR 3.0 15.1 + - - +
867A LYS* 3.7 7.0 - - - +
869A VAL* 1.3 83.7 - - - +
871A ASP* 1.3 66.8 + - - +
872A GLY 3.2 1.1 + - - -
895A LEU* 4.0 16.7 - - - +
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Residues in contact with ASP 871 (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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867A LYS* 2.9 31.0 + - - +
868A LEU* 3.0 7.4 + - + +
870A LYS* 1.3 85.3 - - - +
872A GLY* 1.3 59.2 + - - +
873A TYR 3.5 0.6 + - - -
895A LEU* 4.6 3.1 - - - +
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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