Contacts of the helix formed by residues 916 - 928 (chain B) in PDB entry 1PKG
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 916 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849B GLU* 5.5 8.3 - - + +
852B VAL* 4.2 2.5 - - - -
914B ARG 5.5 0.7 - - - +
915B PRO* 1.3 75.3 - - - +
917B PHE* 1.3 62.2 + - - +
918B LYS* 4.0 9.2 - - - +
919B GLN* 3.1 36.8 + - - +
920B ILE* 2.9 31.0 + - - +
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Residues in contact with PHE 917 (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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777B ALA* 3.7 11.9 - - - +
780B MET* 3.3 58.8 - - + -
781B ALA* 3.5 23.1 - - + +
784B ALA* 4.7 11.4 - - + -
848B PHE* 3.9 6.5 - - + -
851B ASP* 3.4 29.6 - - + -
852B VAL* 3.5 24.0 - - + -
855B TYR* 3.4 30.1 - + + -
916B THR* 1.3 71.3 - - - +
918B LYS* 1.3 68.3 + - - +
920B ILE* 2.9 10.8 + - + +
921B VAL* 2.9 26.9 + - - +
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Residues in contact with LYS 918 (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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778B LYS* 4.3 23.2 + - - +
781B ALA* 3.9 27.7 - - + +
916B THR* 3.2 7.0 - - - +
917B PHE* 1.3 78.8 - - - +
919B GLN* 1.3 61.2 + - - +
921B VAL* 3.3 20.3 + - - +
922B GLN* 3.5 12.0 + - - +
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Residues in contact with GLN 919 (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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914B ARG 4.9 0.3 - - - +
915B PRO* 3.5 25.3 - - + +
916B THR* 3.1 30.9 + - - +
918B LYS* 1.3 78.0 - - - +
920B ILE* 1.3 61.2 + - - +
922B GLN* 3.7 7.4 + - - +
923B LEU* 3.4 25.8 + - + +
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Residues in contact with ILE 920 (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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777B ALA* 3.7 15.9 - - + -
852B VAL* 4.2 13.0 - - + -
855B TYR* 3.7 42.8 - - + +
902B ILE* 4.1 11.2 - - + +
906B CYS* 3.8 21.3 - - - -
915B PRO* 3.8 17.9 - - + -
916B THR 2.9 24.0 + - - +
917B PHE* 2.9 13.5 + - + +
919B GLN* 1.3 73.8 - - - +
921B VAL* 1.3 65.3 + - - +
923B LEU* 3.2 17.5 + - + +
924B ILE* 3.2 18.1 + - + +
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Residues in contact with VAL 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B TYR* 4.0 24.1 - - + +
777B ALA* 3.8 8.7 - - + +
778B LYS* 3.7 48.5 - - + +
781B ALA* 4.7 2.9 - - + -
917B PHE 2.9 18.1 + - - +
918B LYS* 3.5 18.4 - - - +
920B ILE* 1.3 75.4 - - - +
922B GLN* 1.3 60.5 + - + +
924B ILE* 3.0 8.9 + - - +
925B GLU* 2.9 31.3 + - + +
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Residues in contact with GLN 922 (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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918B LYS 3.5 8.6 + - - +
919B GLN* 4.1 9.2 - - - +
920B ILE 3.4 0.6 - - - -
921B VAL* 1.3 81.4 - - + +
923B LEU* 1.3 60.5 + - + +
925B GLU* 3.9 15.5 - - + +
926B LYS* 3.3 56.8 + - - +
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Residues in contact with LEU 923 (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 ILE* 3.8 33.1 - - + +
905B THR* 6.0 0.9 - - - +
915B PRO* 5.6 9.0 - - + -
919B GLN* 3.4 14.5 + - + +
920B ILE* 3.2 13.2 + - - +
921B VAL 3.1 1.0 - - - -
922B GLN* 1.3 80.2 - - - +
924B ILE* 1.3 60.2 - - - +
926B LYS* 3.9 14.4 - - + +
927B GLN* 3.3 25.0 + - - +
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Residues in contact with ILE 924 (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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770B LEU* 4.2 5.2 - - + +
773B SER* 3.4 20.6 - - - +
774B TYR* 3.7 17.0 - - + +
777B ALA* 4.2 2.5 - - + -
855B TYR* 3.3 27.1 - - + +
899B MET* 3.9 25.4 - - + -
902B ILE* 4.3 9.4 - - + -
920B ILE* 3.4 19.5 - - + +
921B VAL* 3.0 6.8 + - - +
923B LEU* 1.3 77.0 - - - +
925B GLU* 1.3 53.1 + - - +
926B LYS 3.3 0.2 - - - -
927B GLN* 2.9 11.3 + - + +
928B ILE* 2.7 54.1 + - + +
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Residues in contact with GLU 925 (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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774B TYR* 2.9 44.4 + - + +
921B VAL* 2.9 20.2 + - + +
922B GLN* 4.2 17.5 - - + +
923B LEU 3.6 0.2 - - - -
924B ILE* 1.3 72.7 - - - +
926B LYS* 1.3 66.6 + - - +
928B ILE* 3.1 27.9 + - - +
929B SER* 3.9 8.1 + - - -
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Residues in contact with LYS 926 (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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922B GLN* 3.3 45.4 + - - +
923B LEU* 3.9 17.5 - - + +
925B GLU* 1.3 79.3 - - - +
927B GLN* 1.3 62.2 + - + +
929B SER* 3.4 20.4 + - - +
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Residues in contact with GLN 927 (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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770B LEU* 4.3 21.5 - - + +
896B PRO* 4.2 11.3 - - - +
898B GLU* 3.4 39.7 - - + +
899B MET* 2.9 44.5 + - - +
902B ILE* 4.2 3.5 - - + +
923B LEU 3.3 15.0 - - - +
924B ILE* 2.9 16.1 + - + +
926B LYS* 1.3 75.5 - - + +
928B ILE* 1.3 50.6 + - - +
929B SER 2.7 23.7 + - - +
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Residues in contact with ILE 928 (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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767B GLU* 6.0 6.3 - - + +
770B LEU* 3.9 28.0 - - + +
771B SER* 5.1 2.9 - - - +
774B TYR* 3.7 38.4 - - + -
924B ILE* 2.7 28.2 + - + +
925B GLU* 3.1 13.9 + - + +
927B GLN* 1.3 69.4 - - - +
929B SER* 1.3 65.9 + - - +
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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