Contacts of the helix formed by residues 923 - 928 (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 ARG 923 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A ASP 3.9 16.0 + - - -
840A THR* 3.6 22.7 - - + +
842A ASP* 2.8 40.8 + - - -
886A TYR* 3.9 3.4 - - - -
921A ALA* 3.5 15.6 - - - +
922A LYS* 1.3 89.6 - - + +
924A ALA* 1.3 64.7 + - - +
925A SER* 3.6 12.1 - - - +
926A LEU* 3.1 15.9 + - + +
927A SER 3.8 0.3 + - - -
986A SER* 4.7 8.0 + - - -
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Residues in contact with ALA 924 (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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837A PHE* 3.6 40.1 - - + +
840A THR* 2.9 18.4 + - - +
841A LEU* 3.7 10.8 - - + -
886A TYR* 3.6 22.6 - - + -
923A ARG* 1.3 71.7 - - - +
925A SER* 1.3 61.2 - - - +
926A LEU 3.1 0.2 - - - -
927A SER* 4.1 1.5 - - - +
928A VAL* 3.0 27.9 + - - +
943A VAL* 5.6 0.4 - - + -
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Residues in contact with SER 925 (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 THR 2.9 7.7 + - - -
841A LEU* 3.3 25.9 - - - +
842A ASP* 2.7 28.3 + - - -
844A ALA* 5.3 1.7 - - - +
923A ARG* 3.6 9.0 - - - +
924A ALA* 1.3 76.3 - - - +
926A LEU* 1.3 61.7 + - - +
928A VAL* 3.6 14.6 - - - +
929A GLN* 3.5 20.0 + - - +
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Residues in contact with LEU 926 (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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921A ALA* 3.8 8.5 - - + -
923A ARG* 3.1 12.6 + - + +
925A SER* 1.3 82.1 + - - +
927A SER* 1.3 64.1 + - - +
929A GLN* 3.1 36.3 + - - +
931A ARG* 4.1 8.3 - - - +
932A TYR* 3.3 33.0 - - + +
986A SER* 4.7 6.1 - - - +
987A ILE* 3.6 26.5 - - + -
1025A 3AB 3.5 31.4 - - + -
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Residues in contact with SER 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A TYR* 3.4 23.3 + - - +
888A GLY* 3.6 15.0 - - - -
921A ALA* 3.3 19.6 - - - +
923A ARG 3.8 0.8 + - - -
924A ALA 3.4 5.0 + - - -
926A LEU* 1.3 76.1 - - - +
928A VAL* 1.3 51.2 + - - +
929A GLN 3.2 4.1 + - - +
932A TYR* 3.8 4.2 - - - +
933A SER* 2.8 31.5 + - - -
943A VAL* 4.2 8.5 - - - +
1025A 3AB 2.9 25.9 + - - -
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Residues in contact with VAL 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A PHE* 4.2 5.6 - - + -
841A LEU* 4.0 18.8 - - + -
844A ALA* 4.3 14.6 - - + -
848A ILE* 4.0 23.2 - - + +
924A ALA 3.0 19.9 + - - +
925A SER* 3.6 13.5 - - - +
927A SER* 1.3 72.5 - - - +
929A GLN* 1.3 62.6 + - + +
930A ASP* 3.5 1.0 + - - +
933A SER* 3.4 4.7 - - - -
941A LYS* 2.7 31.3 + - - -
943A VAL* 4.5 5.5 - - + +
1004A CYS* 3.9 28.5 - - - -
1006A HIS* 5.6 3.3 - - + -
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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
------------------------------------------------------------
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