Contacts of the helix formed by residues 832 - 846 (chain E) in PDB entry 2BT4
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 832 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820E LEU* 3.4 18.2 - - - +
821E GLY* 4.9 4.3 - - - -
822E GLN* 6.3 1.1 - - + -
830E SER 4.5 5.4 - - - +
831E ASP* 1.3 77.4 - - - +
833E LEU* 1.3 66.8 + - - +
834E ALA* 3.4 11.0 + - - +
835E ASP* 2.9 31.6 + - - +
836E VAL* 3.0 21.1 + - - +
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Residues in contact with LEU 833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813E ASN* 3.9 20.6 - - + +
817E LEU* 3.6 33.7 - - + +
818E ASN* 4.1 11.5 + - - +
820E LEU* 4.0 21.4 + - + +
832E THR* 1.3 74.9 - - - +
834E ALA* 1.3 62.3 + - - +
836E VAL* 3.2 6.6 + - + +
837E GLU* 2.9 22.2 + - - +
853E PHE* 3.8 23.0 - - + -
855E GLN* 3.7 35.9 - - + -
938E TYR* 4.5 5.6 - - - +
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Residues in contact with ALA 834 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832E THR* 3.4 8.7 + - - +
833E LEU* 1.3 79.6 - - - +
835E ASP* 1.3 56.7 + - - +
837E GLU* 3.3 12.6 + - - +
838E ALA* 3.0 27.0 + - - +
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Residues in contact with ASP 835 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830E SER 4.6 1.0 - - - +
831E ASP* 3.6 25.4 - - + +
832E THR* 2.9 41.3 + - - +
834E ALA* 1.3 73.0 - - - +
836E VAL* 1.3 66.9 + - - +
838E ALA* 3.1 9.4 + - - +
839E LEU* 3.0 23.2 + - - +
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Residues in contact with VAL 836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820E LEU* 3.9 14.1 - - + -
831E ASP* 4.6 3.8 - - + -
832E THR 3.0 12.7 + - - +
833E LEU* 3.2 12.1 + - + +
835E ASP* 1.3 73.6 - - - +
837E GLU* 1.3 65.5 + - - +
839E LEU* 3.1 10.1 + - + +
840E CYS* 2.9 22.2 + - - -
853E PHE* 3.9 12.6 - - + -
935E VAL* 3.3 35.7 - - + +
938E TYR* 3.8 41.1 - - + -
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Residues in contact with GLU 837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833E LEU 2.9 13.1 + - - +
834E ALA* 3.4 15.6 - - - +
835E ASP 3.2 0.2 - - - -
836E VAL* 1.3 74.2 - - - +
838E ALA* 1.3 59.3 + - - +
840E CYS* 3.0 3.5 + - - +
841E VAL* 2.9 39.4 + - + +
851E VAL* 5.5 1.0 - - - +
853E PHE* 3.7 54.0 + - + +
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Residues in contact with ALA 838 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834E ALA 3.0 12.2 + - - +
835E ASP* 3.3 12.6 - - - +
836E VAL 3.1 0.2 - - - -
837E GLU* 1.3 77.7 - - - +
839E LEU* 1.3 61.7 + - - +
841E VAL* 3.4 7.6 + - - +
842E LYS* 3.1 23.6 + - - +
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Residues in contact with LEU 839 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831E ASP* 5.6 1.8 - - - +
835E ASP 3.0 12.1 + - - +
836E VAL* 3.1 13.7 + - + +
838E ALA* 1.3 74.0 - - - +
840E CYS* 1.3 62.2 + - - +
842E LYS* 3.5 26.1 + - + +
843E ALA* 2.9 28.3 + - - +
935E VAL* 4.1 35.2 - - + +
936E GLN* 4.9 1.3 - - - +
938E TYR* 5.9 0.7 - - + -
939E VAL* 3.9 27.8 - - + +
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Residues in contact with CYS 840 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811E ILE* 3.6 32.1 - - + -
836E VAL* 2.9 17.5 + - - +
837E GLU* 3.0 8.5 + - - +
839E LEU* 1.3 75.6 - - - +
841E VAL* 1.3 61.7 + - - +
843E ALA* 3.7 6.0 - - - +
844E ALA* 2.8 32.7 + - - +
851E VAL* 3.6 5.0 - - + +
853E PHE* 4.0 15.7 - - + -
938E TYR* 3.8 32.5 - - - -
939E VAL* 5.6 0.9 - - - -
942E VAL* 4.5 6.1 - - + +
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Residues in contact with VAL 841 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837E GLU* 2.9 30.6 + - + +
838E ALA* 3.7 8.1 - - - +
840E CYS* 1.3 78.3 - - - +
842E LYS* 1.3 64.0 + - - +
844E ALA* 3.6 1.6 + - - +
845E ALA* 3.1 25.1 + - + +
849E GLY 4.9 0.7 - - - +
850E THR* 5.8 1.1 - - - +
851E VAL* 3.7 26.5 - - + +
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Residues in contact with LYS 842 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838E ALA 3.1 15.4 + - - +
839E LEU* 3.7 24.2 - - + +
841E VAL* 1.3 79.7 - - - +
843E ALA* 1.3 67.0 + - - +
845E ALA* 3.3 6.8 + - - +
846E ALA* 3.0 30.1 + - + +
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Residues in contact with ALA 843 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839E LEU 2.9 17.6 + - - +
840E CYS* 3.2 5.4 + - - +
842E LYS* 1.3 79.0 - - - +
844E ALA* 1.3 62.4 + - - +
846E ALA* 3.2 9.0 + - - +
847E HIS* 3.1 28.4 - - + -
939E VAL* 4.0 31.0 - - + +
942E VAL* 3.8 18.4 - - + -
943E GLU* 5.6 1.1 - - + -
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Residues in contact with ALA 844 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804E LEU* 4.5 0.8 - - - +
809E ILE* 4.6 4.5 - - + -
840E CYS 2.8 16.3 + - - +
841E VAL 3.9 2.9 - - - +
843E ALA* 1.3 77.1 - - - +
845E ALA* 1.3 57.6 + - - +
847E HIS* 2.9 20.2 + - - +
848E GLY 3.1 0.3 + - - -
849E GLY* 2.9 34.8 + - - +
850E THR* 4.0 2.0 - - - +
851E VAL* 3.5 22.9 - - + -
942E VAL* 3.6 16.7 - - + +
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Residues in contact with ALA 845 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841E VAL* 3.1 18.7 + - + +
842E LYS* 3.5 7.6 - - - +
844E ALA* 1.3 79.4 - - - +
846E ALA* 1.3 57.9 + - - +
847E HIS 3.0 4.9 + - - -
848E GLY* 3.0 12.7 + - - +
849E GLY 3.3 11.6 + - - +
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Residues in contact with ALA 846 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842E LYS* 3.0 20.9 + - + +
843E ALA* 3.5 12.8 - - - +
844E ALA 3.1 0.4 - - - -
845E ALA* 1.3 75.3 - - - +
847E HIS* 1.3 74.7 + - + +
848E GLY 3.7 0.2 - - - -
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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