Contacts of the helix formed by residues 827 - 840 (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 THR 827 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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823A LEU* 4.5 4.3 - - + +
824A ALA* 2.6 41.6 + - + +
825A GLU 3.1 1.0 + - - -
826A ASN* 1.3 83.6 - - - +
828A GLY* 1.3 64.5 + - - +
829A GLU* 4.1 7.3 - - - +
830A PHE* 3.2 14.0 + - - +
831A GLN* 3.1 28.7 + - - +
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Residues in contact with GLY 828 (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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827A THR* 1.3 72.8 - - - +
829A GLU* 1.3 57.0 + - - +
831A GLN* 3.8 6.5 - - - +
832A GLU* 2.9 35.5 + - - +
835A ARG* 5.1 1.2 + - - -
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Residues in contact with GLU 829 (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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823A LEU* 3.8 14.7 - - + +
827A THR* 3.2 6.3 - - - +
828A GLY* 1.3 75.5 - - - +
830A PHE* 1.3 66.6 + - - +
832A GLU* 3.7 7.3 - - - +
833A VAL* 3.1 29.4 + - + +
855A ARG* 2.7 43.0 + - - +
1000A HIS* 2.7 32.7 + - + +
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Residues in contact with PHE 830 (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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823A LEU* 3.8 23.3 - - + +
824A ALA 3.2 22.9 - - - +
825A GLU* 3.4 51.8 - - + +
827A THR* 3.2 8.3 + - - +
829A GLU* 1.3 79.4 - - - +
831A GLN* 1.3 70.4 + - + +
833A VAL* 3.4 3.5 + - - +
834A VAL* 3.0 44.4 + - + +
850A VAL* 4.3 11.7 - - + -
851A VAL 6.0 0.4 - - - -
852A ARG* 4.8 2.2 - - - -
853A VAL* 3.6 38.1 - - + -
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Residues in contact with GLN 831 (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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825A GLU 3.6 16.8 + - - +
826A ASN* 5.2 8.1 + - - +
827A THR 3.1 21.6 + - - +
828A GLY* 4.0 5.3 - - - +
830A PHE* 1.3 87.0 - - + +
832A GLU* 1.3 57.1 + - - +
834A VAL* 3.4 3.2 + - - +
835A ARG* 3.0 53.1 + - + +
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Residues in contact with GLU 832 (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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828A GLY 2.9 19.4 + - - +
829A GLU* 3.7 7.7 - - + +
831A GLN* 1.3 75.2 - - - +
833A VAL* 1.4 66.1 + - + +
835A ARG* 3.4 25.9 + - - +
836A ALA* 3.2 22.8 + - + +
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Residues in contact with VAL 833 (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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829A GLU* 3.1 19.4 + - + +
830A PHE 3.9 3.6 - - - +
832A GLU* 1.4 75.0 - - + +
834A VAL* 1.3 63.3 + - - +
836A ALA* 3.4 6.7 + - - +
837A PHE* 3.1 19.8 + - - +
853A VAL* 4.1 20.9 - - + -
886A TYR* 4.9 0.7 + - - -
945A VAL* 4.3 14.4 - - + -
1000A HIS* 3.8 38.4 - - + +
1002A ILE* 3.9 25.0 - - + +
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Residues in contact with VAL 834 (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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830A PHE* 3.0 46.3 + - + +
831A GLN* 4.0 3.8 - - - +
833A VAL* 1.3 73.7 - - + +
835A ARG* 1.3 59.8 + - + +
837A PHE* 3.2 5.9 + - + +
838A TYR* 2.9 57.1 + - + -
850A VAL* 4.3 14.4 - - + -
853A VAL* 3.8 22.4 - - + -
1002A ILE* 5.8 1.1 - - + -
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Residues in contact with ARG 835 (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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828A GLY 5.1 0.8 + - - -
831A GLN* 3.0 47.0 + - + +
832A GLU* 3.7 31.6 - - - +
833A VAL 3.3 0.2 - - - -
834A VAL* 1.3 76.2 - - + +
836A ALA* 1.3 58.4 + - - +
838A TYR* 3.9 3.5 - - - -
839A ASP* 2.8 46.7 + - - +
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Residues in contact with ALA 836 (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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832A GLU* 3.2 14.3 + - + +
833A VAL* 3.9 5.6 - - - +
835A ARG* 1.3 78.3 - - - +
837A PHE* 1.3 64.9 + - - +
839A ASP* 3.5 9.8 + - - +
840A THR* 3.5 19.2 + - - +
884A VAL* 6.3 2.5 - - + -
886A TYR* 3.3 17.9 + - - +
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Residues in contact with PHE 837 (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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833A VAL 3.1 14.0 + - - +
834A VAL* 3.3 9.0 - - - +
836A ALA* 1.3 76.0 - - - +
838A TYR* 1.3 66.2 + + - +
840A THR 3.2 12.1 + - - -
841A LEU* 3.3 45.5 + - + +
848A ILE* 4.0 11.7 - - + -
850A VAL* 4.1 25.8 - - + -
886A TYR* 3.5 12.5 + + - +
924A ALA* 3.6 30.8 - - + +
928A VAL* 4.2 5.4 - - + -
943A VAL* 4.4 17.3 - - + -
1002A ILE* 3.6 36.3 - - + -
1004A CYS* 4.2 16.6 - - + -
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Residues in contact with TYR 838 (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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834A VAL* 2.9 48.7 + - + +
835A ARG* 4.1 4.3 - - - +
837A PHE* 1.3 79.6 - + - +
839A ASP* 1.3 65.7 + - - +
841A LEU* 3.1 30.1 + - + -
845A ARG* 3.3 49.4 - - + +
848A ILE 2.6 29.7 + - - -
849A ARG* 3.6 2.3 - - - +
850A VAL* 3.5 28.0 + - + +
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Residues in contact with ASP 839 (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 ARG* 2.8 37.0 + - - +
836A ALA* 3.7 9.6 - - - +
837A PHE 3.3 0.2 - - - -
838A TYR* 1.3 78.7 - - - +
840A THR* 1.3 65.5 + - + +
842A ASP* 4.6 2.6 + - - +
845A ARG* 5.3 3.1 - - - +
923A ARG* 3.9 9.0 + - - -
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Residues in contact with THR 840 (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 ALA 3.5 8.0 + - - +
837A PHE 3.2 3.6 + - - -
838A TYR 3.1 0.6 - - - -
839A ASP* 1.3 83.7 - - + +
841A LEU* 1.3 59.3 + - - +
842A ASP* 3.3 5.4 - - - +
886A TYR* 3.7 10.9 - - + -
922A LYS 4.5 4.9 - - - +
923A ARG* 3.6 38.3 - - + +
924A ALA* 2.9 29.1 + - - +
925A SER* 2.9 27.5 + - - -
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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