Contacts of the helix formed by residues 922 - 933 (chain A) in PDB entry 1B0P
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 LYS 922 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913A TRP* 4.8 0.9 - - - -
916A GLY* 3.8 20.4 - - - +
919A ASP* 3.1 28.7 + - - +
921A ILE* 1.3 84.8 - - + +
923A SER* 1.3 64.8 + - - +
925A GLU* 2.8 38.1 + - - +
926A TYR* 3.1 52.7 + - + +
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Residues in contact with SER 923 (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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913A TRP* 3.3 16.1 + - - -
916A GLY 3.2 14.4 + - - -
917A LYS* 3.4 17.9 - - - -
919A ASP 2.5 29.4 + - - -
920A PRO* 3.5 4.9 + - - +
922A LYS* 1.3 72.5 - - - +
924A LYS* 1.3 58.9 + - - +
927A GLY* 2.9 24.6 + - - -
952A TYR 3.6 17.4 - - - +
953A THR* 3.6 0.8 - - - -
954A LYS 3.0 18.6 + - - -
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Residues in contact with LYS 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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831A ARG* 6.6 0.2 - - - -
858A LEU* 6.4 0.2 - - - +
860A GLN* 5.3 7.3 + - - +
920A PRO 3.3 18.6 - - - +
921A ILE* 3.2 4.4 + - - +
922A LYS 3.1 0.2 - - - -
923A SER* 1.3 79.2 + - - +
925A GLU* 1.3 60.0 + - - +
926A TYR 3.1 1.8 - - - -
927A GLY* 4.1 0.4 - - - +
928A ASP* 2.8 61.3 + - - +
953A THR* 3.9 28.5 - - + +
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Residues in contact with GLU 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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921A ILE* 2.7 30.0 + - + +
922A LYS* 2.8 43.1 + - - +
924A LYS* 1.3 75.8 - - - +
926A TYR* 1.3 73.8 + - + +
928A ASP* 4.4 3.8 - - - +
929A LYS* 3.4 34.2 + - - +
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Residues in contact with TYR 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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908A GLU* 4.5 8.3 - - + -
909A ALA* 3.6 15.0 - - - +
912A GLY* 3.4 34.3 - - - -
913A TRP* 3.5 19.5 - - - +
915A ALA* 6.2 0.9 - - + -
922A LYS* 3.1 48.8 + - + +
925A GLU* 1.3 90.8 + - - +
927A GLY* 1.3 59.4 + - - +
928A ASP 3.2 2.0 - - - -
929A LYS* 3.1 36.8 + - + +
930A LEU* 2.9 31.0 + - - +
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Residues in contact with GLY 927 (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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913A TRP* 4.1 5.3 - - - -
923A SER 2.9 23.9 + - - -
924A LYS* 3.3 1.7 + - - -
926A TYR* 1.3 78.2 - - - +
928A ASP* 1.3 59.7 + - - +
930A LEU* 3.4 1.7 + - - -
931A LYS* 3.0 23.4 + - - +
952A TYR* 3.0 37.0 - - - -
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Residues in contact with ASP 928 (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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924A LYS* 2.8 60.7 + - - +
925A GLU* 4.4 4.0 - - - +
927A GLY* 1.3 74.8 - - - +
929A LYS* 1.3 69.1 + - - +
931A LYS* 3.2 34.8 + - + +
932A LYS* 3.3 20.0 + - + +
953A THR* 4.8 2.6 - - - +
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Residues in contact with LYS 929 (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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908A GLU* 6.4 0.4 - - - -
909A ALA* 4.0 13.9 - - + -
925A GLU* 3.4 30.1 + - - +
926A TYR* 3.1 41.9 + - + +
928A ASP* 1.3 75.5 - - - +
930A LEU* 1.3 57.8 + - - +
932A LYS* 2.9 26.8 + - + +
933A LEU* 3.0 24.5 + - + +
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Residues in contact with LEU 930 (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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890A LEU* 6.3 0.2 - - + -
906A VAL* 4.0 8.1 - - + +
909A ALA* 4.0 21.1 - - + +
910A LEU* 3.5 30.5 - - + -
913A TRP* 4.3 22.2 - - + -
926A TYR 2.9 15.8 + - - +
927A GLY* 3.5 7.2 - - - +
929A LYS* 1.3 75.7 - - - +
931A LYS* 1.3 64.8 + - - +
933A LEU* 4.4 7.0 - - + +
934A LEU* 3.1 56.0 + - + +
945A ILE* 4.8 2.0 - - + -
952A TYR* 3.7 26.5 + - + +
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Residues in contact with LYS 931 (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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860A GLN* 5.5 2.8 + - - -
927A GLY 3.0 19.9 + - - +
928A ASP* 3.5 29.7 + - - +
929A LYS 3.1 0.6 - - - -
930A LEU* 1.3 79.7 - - - +
932A LYS* 1.3 60.6 + - + +
934A LEU* 4.1 1.3 - - - -
935A ALA* 3.4 19.4 + - - +
949A SER* 3.8 33.2 + - - -
952A TYR* 3.6 18.8 - - + -
953A THR* 5.1 1.7 - - - +
211B GLU* 3.5 26.7 + - - +
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Residues in contact with LYS 932 (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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928A ASP* 3.3 14.1 + - + +
929A LYS* 2.9 11.7 + - + +
931A LYS* 1.3 78.0 - - + +
933A LEU* 1.3 66.1 + - + +
934A LEU 3.1 2.1 + - - -
935A ALA* 3.3 18.1 + - - +
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Residues in contact with LEU 933 (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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903A SER* 5.3 0.2 - - - +
905A ASP* 3.5 57.2 - - + +
906A VAL* 3.5 23.0 - - + +
909A ALA* 3.9 17.0 - - + -
929A LYS* 3.0 24.6 + - + +
930A LEU* 4.4 2.5 - - + +
932A LYS* 1.3 75.7 - - + +
934A LEU* 1.3 68.8 + - + +
935A ALA 3.5 1.8 - - - +
937A GLN* 5.6 1.0 - - - +
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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