Contacts of the helix formed by residues 893 - 901 (chain A) 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 ALA 893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889A THR* 3.5 23.8 - - - +
890A THR* 3.2 11.2 + - - +
892A PRO* 1.3 78.9 - - - +
894A VAL* 1.3 65.5 + - - +
895A PRO 3.4 0.2 - - - -
896A ASP* 3.2 8.3 + - - +
897A ILE* 3.0 27.8 + - + +
906A PHE 4.1 10.3 - - - +
907A CYS 4.2 0.7 - - - -
908A GLY* 3.9 20.6 - - - +
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Residues in contact with VAL 894 (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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820A LEU* 4.9 6.1 - - + -
889A THR* 3.9 6.3 - - + -
890A THR 3.7 10.3 - - - +
891A ALA* 3.2 14.8 + - - +
893A ALA* 1.3 75.8 - - - +
895A PRO* 1.3 76.7 - - + +
897A ILE* 3.2 2.1 + - - +
898A CYS* 3.0 29.4 + - - -
942A ALA* 3.7 26.9 - - + -
944A PHE* 3.9 10.9 - - + -
1001A LEU* 3.5 27.8 - - + -
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Residues in contact with PRO 895 (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 ASN* 4.6 1.8 + - - +
891A ALA 3.7 6.1 - - - +
892A PRO* 3.5 15.0 - - + +
894A VAL* 1.3 101.0 - - + +
896A ASP* 1.3 57.2 + - - +
898A CYS* 4.0 5.8 - - + +
899A ALA* 3.1 29.6 + - - +
973B LEU* 4.5 20.4 - - + +
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Residues in contact with ASP 896 (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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892A PRO 4.6 7.4 + - - +
893A ALA* 3.2 8.0 + - - +
895A PRO* 1.3 77.7 - - - +
897A ILE* 1.3 56.5 + - - +
899A ALA 3.3 0.2 + - - -
900A HIS* 2.7 50.6 + - - +
906A PHE* 3.4 33.4 - - + +
962B ALA* 5.4 0.8 - - - +
973B LEU* 3.6 13.9 - - - +
974B ARG* 2.9 48.2 + - - -
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Residues in contact with ILE 897 (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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887A HIS* 4.4 4.7 - - + -
889A THR* 4.0 23.1 - - + +
893A ALA* 3.0 18.9 + - + +
894A VAL 3.2 0.2 + - - -
896A ASP* 1.3 76.2 - - - +
898A CYS* 1.3 58.8 + - - +
901A GLY* 2.7 41.8 + - - +
902A PHE* 3.9 21.3 - - + -
906A PHE 4.4 0.4 - - - +
907A CYS* 4.0 35.0 - - - -
944A PHE* 3.5 44.4 - - + -
998A PRO* 4.3 7.8 - - + +
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Residues in contact with CYS 898 (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 ASN* 3.6 30.6 + - + +
820A LEU* 3.8 32.5 - - + -
856A VAL* 4.3 16.4 - - + +
858A HIS* 3.5 20.3 - - - +
894A VAL* 3.0 28.5 + - - +
895A PRO* 4.0 5.4 - - + +
897A ILE* 1.3 76.1 - - - +
899A ALA* 1.3 60.4 + - - +
944A PHE* 3.9 19.3 - - - -
998A PRO* 5.4 0.6 - - - +
1001A LEU* 4.7 0.2 - - - -
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Residues in contact with ALA 899 (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 ASN* 3.5 16.8 - - - +
858A HIS* 2.8 20.5 + - - -
895A PRO 3.1 19.3 + - - +
896A ASP* 5.5 0.4 - - - +
898A CYS* 1.3 77.0 - - - +
900A HIS* 1.3 87.2 + - + +
972B LEU* 6.3 2.9 - - + -
973B LEU* 5.7 8.3 - - + -
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Residues in contact with HIS 900 (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 HIS* 4.2 7.4 + - - -
861A LEU* 4.7 3.7 - - - +
896A ASP* 2.7 28.4 + - - +
899A ALA* 1.3 97.0 + - + +
901A GLY* 1.3 61.8 + - - +
903A ASN* 4.6 4.3 + - - -
906A PHE* 3.2 45.3 - + + -
993A ASP* 5.4 2.9 - - - +
963B PRO* 6.2 0.2 - - + -
973B LEU* 5.7 1.8 - - - +
974B ARG* 4.4 22.6 + - + +
975B TYR 5.4 4.3 - - - -
976B ASP* 6.1 0.9 - - - -
992B HIS* 3.4 39.2 + + - +
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Residues in contact with GLY 901 (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 HIS* 4.5 1.6 - - - -
861A LEU* 3.7 24.2 - - - +
896A ASP 4.1 0.9 - - - +
897A ILE* 2.7 41.1 + - - +
899A ALA 3.9 0.4 - - - -
900A HIS* 1.3 77.4 - - - +
902A PHE* 1.3 63.3 + - - -
903A ASN 3.8 1.4 + - - -
906A PHE* 4.2 6.9 - - - +
993A ASP 5.3 0.9 - - - -
998A PRO* 4.5 7.9 - - - -
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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