Contacts of the helix formed by residues 824 - 835 (chain B) in PDB entry 2BKU
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 GLN 824 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780B PHE* 5.5 0.2 - - - +
820B GLN 4.0 10.8 - - - +
821B PHE* 3.5 42.1 + - - +
822B TYR 3.4 1.4 - - - -
823B GLY* 1.3 78.5 - - - +
825B ASP* 1.3 65.3 + - - +
826B TRP* 3.4 43.1 + - + +
827B VAL* 3.4 5.9 + - + +
828B ILE* 3.3 24.5 + - - +
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Residues in contact with ASP 825 (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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823B GLY 3.9 3.8 + - - +
824B GLN* 1.3 71.3 - - - +
826B TRP* 1.3 57.3 + - - +
828B ILE* 3.1 11.6 + - - +
829B ASP* 2.7 50.2 + - - +
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Residues in contact with TRP 826 (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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780B PHE* 3.3 39.5 - + - -
783B ILE* 3.9 17.5 - - + -
784B ALA* 3.5 29.6 - - + -
787B ALA* 4.1 17.6 - - + +
788B GLU* 5.6 5.4 - - - +
806B ILE* 5.6 0.4 - - + -
824B GLN* 3.4 42.2 + - + +
825B ASP* 1.3 79.8 - - - +
827B VAL* 1.3 76.4 + - + +
829B ASP* 3.6 6.8 - - - +
830B TYR* 2.6 40.3 + + + +
833B ARG* 5.2 1.2 + - - -
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Residues in contact with VAL 827 (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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780B PHE* 4.1 17.5 - - + -
806B ILE* 4.4 15.7 - - + -
821B PHE 3.6 23.8 - - - +
822B TYR* 4.8 10.8 - - + +
824B GLN* 3.4 12.5 + - + +
825B ASP 3.1 0.8 - - - -
826B TRP* 1.3 112.7 - - + +
828B ILE* 1.3 64.4 + - - +
830B TYR* 3.9 2.5 - - - +
831B ILE* 3.1 38.2 + - + +
855B GLN* 4.9 2.2 - - + +
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Residues in contact with ILE 828 (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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822B TYR 4.3 9.9 - - - +
823B GLY 4.8 6.7 - - - +
824B GLN 3.3 15.7 - - - +
825B ASP* 3.1 11.3 + - - +
827B VAL* 1.3 76.3 - - - +
829B ASP* 1.3 65.2 + - - +
831B ILE* 3.6 3.7 + - - +
832B LYS* 3.2 36.8 + - + +
852B ARG* 3.5 27.7 + - - +
855B GLN* 3.3 21.3 - - - +
856B LYS* 5.7 1.8 - - - +
859B LEU* 4.7 11.4 - - + -
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Residues in contact with ASP 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B ASP* 2.7 38.8 + - - +
826B TRP* 3.8 5.9 - - - +
828B ILE* 1.3 77.1 - - - +
830B TYR* 1.3 55.8 + - - +
832B LYS* 3.4 15.4 + - - +
833B ARG* 3.0 39.6 + - + +
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Residues in contact with TYR 830 (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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783B ILE* 4.4 9.6 - - + -
786B VAL* 3.5 16.8 - - + +
787B ALA* 3.5 35.2 - - + -
793B TYR* 3.9 9.2 - + + -
799B SER* 3.1 33.9 + - - -
802B ALA* 3.5 15.2 - - + +
803B VAL* 4.3 13.2 - - + -
806B ILE* 4.0 21.3 - - + -
826B TRP* 2.6 24.0 + + + +
827B VAL* 3.4 5.1 + - - +
828B ILE 3.3 0.2 - - - -
829B ASP* 1.3 72.2 - - - +
831B ILE* 1.3 63.6 + - - +
833B ARG* 3.5 24.9 + - + +
834B THR* 2.8 42.1 + - - -
840B PHE* 6.2 0.9 - + - -
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Residues in contact with ILE 831 (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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803B VAL* 4.3 19.1 - - + -
806B ILE* 4.4 11.7 - - + -
827B VAL* 3.1 29.6 + - + +
828B ILE* 3.8 4.0 - - - +
829B ASP 3.4 0.2 - - - -
830B TYR* 1.3 75.8 - - - +
832B LYS* 1.3 64.0 + - + +
834B THR* 3.3 14.7 + - - -
835B ARG* 3.5 16.4 + - - +
848B ALA* 3.5 26.4 - - + +
851B ALA* 4.1 19.1 - - + +
852B ARG* 3.7 21.8 - - + -
855B GLN* 3.8 25.4 - - + +
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Residues in contact with LYS 832 (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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828B ILE* 3.2 33.1 + - + +
829B ASP* 3.6 14.8 - - - +
830B TYR 3.2 0.2 - - - -
831B ILE* 1.3 79.5 - - + +
833B ARG* 1.3 66.6 + - - +
835B ARG* 3.1 16.5 + - - +
836B SER* 3.0 17.4 + - - -
852B ARG* 5.3 12.3 - - - +
627D ALA 4.5 7.6 + - - +
628D SER* 3.1 28.9 + - - +
629D LEU 5.0 0.4 - - - -
630D GLY* 4.7 8.3 - - - +
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Residues in contact with ARG 833 (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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787B ALA* 2.9 30.4 + - - +
793B TYR* 3.6 33.2 - - - -
826B TRP 5.2 0.8 + - - -
829B ASP* 3.0 27.8 + - + +
830B TYR* 3.6 40.1 - - + +
831B ILE 3.4 0.6 - - - -
832B LYS* 1.3 74.2 - - - +
834B THR* 1.3 60.5 + - - +
836B SER* 3.4 19.7 + - - +
840B PHE* 3.5 18.1 - - + -
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Residues in contact with THR 834 (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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799B SER* 4.6 8.4 + - - -
803B VAL* 4.4 11.3 - - + +
830B TYR* 2.8 33.3 + - - -
831B ILE* 3.3 11.1 + - - -
832B LYS 3.1 1.0 - - - -
833B ARG* 1.3 78.0 - - - +
835B ARG* 1.3 58.1 + - - +
836B SER 3.3 1.8 + - - -
840B PHE* 3.6 23.1 - - + +
844B THR* 3.3 28.7 - - + +
845B LYS* 3.7 14.7 - - - +
848B ALA* 3.8 15.7 - - + -
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Residues in contact with ARG 835 (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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831B ILE* 3.5 13.0 + - - +
832B LYS* 3.1 10.8 + - - +
834B THR* 1.3 75.1 - - - +
836B SER* 1.3 59.8 + - - +
845B LYS* 2.9 47.0 + - - +
846B ASP* 4.9 1.8 + - - +
848B ALA* 3.4 34.5 - - + -
849B ARG* 3.5 38.8 - - - +
852B ARG* 4.8 5.6 - - - -
665D ASP* 4.3 2.6 - - - +
668D ASN* 3.2 73.7 + - + +
669D SER* 6.1 0.2 - - - +
712D ASN* 4.1 6.1 - - - +
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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