Contacts of the helix formed by residues 904 - 915 (chain B) 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 GLY 904 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902B ALA 3.6 1.0 + - - -
903B SER* 1.3 73.7 - - - +
905B ASP* 1.3 59.5 + - - +
907B LYS* 3.9 8.0 - - - +
908B GLU* 3.0 29.2 + - - +
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Residues in contact with ASP 905 (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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903B SER* 3.1 9.0 + - - +
904B GLY* 1.3 78.3 - - - +
906B VAL* 1.3 64.8 + - - +
908B GLU* 3.8 17.1 - - - +
909B ALA* 3.1 19.4 + - - +
933B LEU* 3.2 32.1 - - + +
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Residues in contact with VAL 906 (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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902B ALA* 4.0 19.1 - - + -
903B SER* 3.0 31.8 + - - +
905B ASP* 1.3 80.5 - - - +
907B LYS* 1.3 59.2 + - - +
909B ALA* 3.3 2.3 + - - +
910B LEU* 2.9 43.7 + - + +
930B LEU* 4.2 5.9 - - + +
933B LEU* 3.5 31.9 - - + +
934B LEU* 4.0 24.9 - - + -
942B LEU* 4.4 6.1 - - + -
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Residues in contact with LYS 907 (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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897B ALA 3.7 15.3 - - - +
898B LEU* 3.4 39.1 + - + +
900B SER 2.8 28.8 + - - -
901B ASP* 4.4 3.4 - - - +
902B ALA* 3.3 25.8 + - + +
903B SER 2.9 16.7 + - - +
904B GLY* 4.0 7.2 - - - +
906B VAL* 1.3 77.7 - - - +
908B GLU* 1.3 56.5 + - - +
910B LEU* 3.9 3.8 - - + -
911B GLN* 2.9 42.2 + - - +
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Residues in contact with GLU 908 (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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904B GLY 3.0 17.0 + - - +
905B ASP* 3.8 20.2 - - - +
906B VAL 3.3 0.2 - - - -
907B LYS* 1.3 75.8 - - - +
909B ALA* 1.3 57.5 + - - +
911B GLN* 3.4 15.8 + - - +
912B GLY* 3.1 22.2 + - - -
926B TYR* 4.7 5.0 - - + -
929B LYS* 6.3 1.6 - - - -
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Residues in contact with ALA 909 (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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905B ASP 3.1 17.5 + - - +
906B VAL 3.7 3.8 - - - +
908B GLU* 1.3 74.3 - - - +
910B LEU* 1.3 60.2 + - - +
912B GLY* 3.3 1.2 + - - -
913B TRP* 2.8 28.9 + - - +
926B TYR* 3.7 20.2 - - + +
929B LYS* 4.1 21.5 - - + -
930B LEU* 4.0 18.5 - - + +
933B LEU* 4.0 9.2 - - + -
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Residues in contact with LEU 910 (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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890B LEU* 6.3 0.2 - - + -
894B ALA* 3.9 30.2 - - + +
897B ALA* 3.7 30.1 - - + -
898B LEU* 3.9 12.1 - - + -
906B VAL* 2.9 32.6 + - + +
907B LYS* 3.4 8.5 - - + +
909B ALA* 1.3 76.8 - - - +
911B GLN* 1.3 59.1 + - - +
913B TRP* 3.3 4.0 + - + +
914B LEU* 2.9 36.5 + - - +
930B LEU* 3.6 30.7 - - + -
934B LEU* 5.4 0.9 - - + -
942B LEU* 4.9 0.2 - - + -
945B ILE* 4.3 16.2 - - + -
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Residues in contact with GLN 911 (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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898B LEU* 3.6 23.1 - - + +
907B LYS* 2.9 39.3 + - - +
908B GLU* 3.6 14.6 - - - +
910B LEU* 1.3 76.4 - - - +
912B GLY* 1.3 60.3 + - - +
914B LEU* 3.6 10.7 + - - +
915B ALA* 3.1 23.4 + - - +
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Residues in contact with GLY 912 (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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908B GLU 3.1 13.8 + - - -
909B ALA 3.3 4.0 + - - -
910B LEU 3.1 0.2 - - - -
911B GLN* 1.3 75.5 - - - +
913B TRP* 1.3 64.0 + - - +
915B ALA* 3.0 14.6 + - - +
916B GLY 3.1 11.3 + - - -
926B TYR* 3.5 35.3 - - - -
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Residues in contact with TRP 913 (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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887B ARG* 3.2 42.0 - - + +
890B LEU* 3.5 36.6 - - + -
891B ALA* 3.8 28.9 - - + -
894B ALA* 4.6 8.1 - - + -
909B ALA 2.8 16.4 + - - +
910B LEU* 3.3 4.7 + - + +
912B GLY* 1.3 74.6 - - - +
914B LEU* 1.3 70.8 + - + +
917B LYS* 2.8 51.2 + - + +
922B LYS 4.9 2.2 - - - -
923B SER* 3.4 24.9 - - - -
926B TYR* 3.6 9.9 - - + +
927B GLY* 4.2 11.0 - - - -
930B LEU* 4.4 15.3 - - + -
952B TYR* 2.6 27.3 + + + +
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Residues in contact with LEU 914 (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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891B ALA* 3.8 35.9 - - + +
894B ALA* 3.5 30.1 - - + -
895B ALA* 4.0 6.1 - - + +
898B LEU* 4.1 15.5 - - + -
910B LEU 2.9 27.8 + - - +
911B GLN* 3.7 7.6 - - - +
913B TRP* 1.3 89.7 - - + +
915B ALA* 1.3 59.2 + - - +
917B LYS* 3.4 32.5 + - - +
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Residues in contact with ALA 915 (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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911B GLN 3.1 15.3 + - - +
912B GLY* 3.0 6.5 + - - +
914B LEU* 1.3 78.5 - - - +
916B GLY* 1.3 59.3 + - - +
917B LYS* 3.5 1.3 + - - -
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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
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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