Contacts of the helix formed by residues 916 - 925 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A GLU* 6.2 4.5 - - + -
852A VAL* 4.6 4.0 - - - -
914A ARG 4.9 3.6 - - - +
915A PRO* 1.3 76.7 - - + +
917A PHE* 1.3 60.3 + - - +
918A LYS* 3.8 11.0 - - - +
919A GLN* 2.7 49.1 + - - +
920A ILE* 2.8 11.2 + - - +
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Residues in contact with PHE 917 (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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777A ALA* 3.7 7.2 - - - +
780A MET* 3.6 44.0 - - + -
781A ALA* 3.6 21.3 - - + +
784A ALA* 5.0 6.7 - - + -
793A LEU* 4.3 0.2 - - + -
848A PHE 4.3 4.5 - - - -
851A ASP* 3.5 26.0 - - + -
852A VAL* 3.5 35.4 - - + +
855A TYR* 3.4 34.3 - + + -
915A PRO 4.1 0.8 + - - -
916A THR* 1.3 72.7 - - - +
918A LYS* 1.3 54.1 + - - +
920A ILE* 3.5 15.9 - - + +
921A VAL* 2.6 41.0 + - - +
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Residues in contact with LYS 918 (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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781A ALA* 3.9 14.0 - - + +
916A THR* 3.0 11.8 - - - +
917A PHE* 1.3 80.4 - - - +
919A GLN* 1.3 59.6 + - + +
921A VAL* 3.4 7.2 - - + +
922A GLN* 3.2 32.4 + - - +
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Residues in contact with GLN 919 (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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914A ARG 4.7 0.3 - - - +
915A PRO* 3.3 17.9 - - + +
916A THR* 2.7 44.0 + - - +
918A LYS* 1.3 72.5 - - + +
920A ILE* 1.3 59.0 + - - +
922A GLN* 3.5 6.8 + - - +
923A LEU* 2.8 35.8 + - + +
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Residues in contact with ILE 920 (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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777A ALA* 3.8 3.4 - - + -
852A VAL* 4.0 12.3 - - + -
855A TYR* 3.5 35.9 - - + +
902A ILE* 4.1 13.2 - - + -
906A CYS* 3.8 26.5 - - - -
915A PRO* 3.8 15.5 - - + -
916A THR 2.8 9.1 + - - +
917A PHE* 3.5 30.5 - - + +
919A GLN* 1.3 72.8 - - - +
921A VAL* 1.3 67.4 + - - +
923A LEU* 2.9 7.1 + - - +
924A ILE* 2.8 32.6 + - + +
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Residues in contact with VAL 921 (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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774A TYR* 3.7 31.3 - - + +
777A ALA* 3.5 34.5 - - + +
778A LYS* 3.6 13.9 - - + +
781A ALA* 4.0 7.2 - - + -
917A PHE 2.6 29.9 + - - +
918A LYS* 3.4 8.3 - - - +
920A ILE* 1.3 73.6 - - - +
922A GLN* 1.3 61.5 + - + +
924A ILE* 3.3 4.5 + - - +
925A GLU* 3.1 22.2 + - + +
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Residues in contact with GLN 922 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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918A LYS* 3.2 20.5 + - - +
919A GLN* 4.1 6.4 - - - +
920A ILE 3.2 0.8 - - - -
921A VAL* 1.3 81.4 - - + +
923A LEU* 1.3 64.3 + - - +
925A GLU* 3.5 16.0 + - + +
926A LYS* 3.6 17.7 + - - +
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Residues in contact with LEU 923 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898A GLU* 6.5 1.3 - - + -
902A ILE* 3.8 33.9 - - + -
905A THR* 5.5 2.5 - - - +
915A PRO* 5.2 11.7 - - + -
919A GLN* 2.8 23.2 + - + +
920A ILE* 2.9 7.4 + - - +
922A GLN* 1.3 79.3 - - - +
924A ILE* 1.3 60.9 + - - +
926A LYS* 3.6 18.4 + - + +
927A GLN* 3.5 15.3 + - - +
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Residues in contact with ILE 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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770A LEU* 4.3 15.9 - - + +
773A SER* 3.4 22.2 - - - +
774A TYR* 3.7 28.9 - - + +
777A ALA* 3.9 3.8 - - + -
855A TYR* 3.2 26.7 - - - +
859A LEU* 6.2 0.2 - - + -
899A MET* 4.1 21.1 - - + -
902A ILE* 4.4 2.2 - - + -
920A ILE* 2.8 34.5 + - + +
921A VAL* 3.9 4.5 - - - +
923A LEU* 1.3 69.2 - - - +
925A GLU* 1.3 56.6 + - - +
926A LYS 2.9 11.4 + - - -
927A GLN* 3.0 27.9 + - + +
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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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774A TYR* 3.6 31.5 + - + +
921A VAL* 3.1 16.1 + - + +
922A GLN* 3.5 10.8 + - + +
924A ILE* 1.3 73.0 - - - +
926A LYS* 1.3 60.7 + - - +
927A GLN 3.4 5.1 + - - +
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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