Contacts of the helix formed by residues 892 - 901 (chain B) in PDB entry 3HKV
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 PRO 892 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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890B THR* 3.6 13.7 - - - +
891B ALA* 1.3 96.2 - - + +
893B ALA* 1.3 60.4 + - - +
895B PRO* 3.3 13.9 - - + +
896B ASP* 3.7 12.3 - - - +
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Residues in contact with ALA 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B THR* 3.3 26.2 - - - +
890B THR* 3.1 12.9 + - - +
892B PRO* 1.3 78.3 - - - +
894B VAL* 1.3 66.6 + - - +
895B PRO 3.4 0.2 - - - -
896B ASP* 3.2 11.2 + - - +
897B ILE* 3.0 31.6 + - + +
906B PHE* 3.8 23.1 - - + +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820B LEU* 4.7 7.0 - - + -
889B THR* 4.0 6.1 - - + -
890B THR 3.7 10.1 - - - +
891B ALA* 3.2 9.6 + - - +
893B ALA* 1.3 77.5 - - - +
895B PRO* 1.3 72.8 - - + +
897B ILE* 3.3 2.3 + - - +
898B CYS* 3.1 32.3 + - - -
942B ALA* 3.5 32.3 - - + -
944B PHE* 4.2 11.7 - - + -
1001B LEU* 3.6 26.7 - - + -
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Residues in contact with PRO 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A LEU* 6.4 2.0 - - + -
819B ASN* 5.0 0.5 + - - -
820B LEU* 6.4 0.4 - - + -
891B ALA 3.5 7.2 - - - +
892B PRO* 3.3 16.4 - - + +
894B VAL* 1.3 98.3 - - + +
896B ASP* 1.3 58.9 + - - +
898B CYS* 3.4 7.8 + - + +
899B ALA* 2.9 30.2 + - - +
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Residues in contact with ASP 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A LEU* 4.9 12.6 - - - +
974A ARG* 5.1 8.1 + - - -
892B PRO 3.7 15.1 - - - +
893B ALA* 3.2 9.4 + - - +
895B PRO* 1.3 81.0 - - - +
897B ILE* 1.3 51.5 + - - +
899B ALA* 3.7 1.1 - - - +
900B HIS* 2.7 49.1 + - - +
906B PHE* 3.5 43.1 - - + +
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Residues in contact with ILE 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858B HIS* 5.2 0.5 - - - -
887B HIS* 4.5 0.4 - - + -
889B THR* 3.9 21.5 - - + +
893B ALA* 3.0 20.3 + - + +
894B VAL 3.8 3.1 - - - +
896B ASP* 1.3 75.8 - - - +
898B CYS* 1.3 59.5 + - - +
901B GLY* 2.7 44.8 + - - +
902B PHE* 3.7 27.4 - - + -
906B PHE* 4.5 7.0 - - + -
907B CYS* 4.0 25.1 - - - -
944B PHE* 3.6 38.1 - - + -
998B PRO* 4.1 9.4 - - + +
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Residues in contact with CYS 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819B ASN* 3.3 31.6 + - - +
820B LEU* 3.5 37.9 - - - -
856B VAL* 4.4 14.5 - - + +
857B SER 4.5 0.3 - - - +
858B HIS* 3.4 20.1 - - - +
894B VAL* 3.1 22.1 + - - +
895B PRO* 3.6 10.3 - - + +
897B ILE* 1.3 77.8 - - - +
899B ALA* 1.3 58.2 + - - +
944B PHE* 4.1 17.5 - - - -
998B PRO* 5.4 0.4 - - - +
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Residues in contact with ALA 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819B ASN* 3.8 12.1 - - - +
858B HIS* 2.5 28.2 + - - -
895B PRO 2.9 17.5 + - - +
896B ASP* 4.5 0.4 - - - -
898B CYS* 1.3 76.7 - - - +
900B HIS* 1.3 85.7 + - + +
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Residues in contact with HIS 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963A PRO* 6.3 1.7 - - + +
973A LEU* 6.3 1.4 - - - +
974A ARG* 5.4 16.8 - - + +
992A HIS* 3.6 40.8 + + + +
858B HIS* 4.3 3.4 - - - -
861B LEU* 4.6 6.1 - - - +
896B ASP* 2.7 25.6 + - - +
899B ALA* 1.3 96.9 + - + +
901B GLY* 1.3 62.0 + - - +
902B PHE 5.1 0.3 - - - -
903B ASN* 5.6 1.7 - - - +
906B PHE* 3.5 31.4 - + + -
993B ASP* 5.0 10.4 - - - +
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Residues in contact with GLY 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858B HIS* 4.7 0.4 - - - -
861B LEU* 3.6 25.7 - - - +
897B ILE* 2.7 40.3 + - - +
899B ALA 3.8 0.8 - - - -
900B HIS* 1.3 75.9 - - - +
902B PHE* 1.3 65.0 + - - -
903B ASN 3.6 2.4 + - - -
906B PHE* 3.9 9.2 - - - -
993B ASP 5.1 1.6 - - - -
998B PRO* 4.6 4.3 - - - -
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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