Contacts of the helix formed by residues 899 - 910 (chain A) in PDB entry 5J68
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 PRO 899 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806A TRP* 4.2 23.6 - - + -
882A TYR* 3.6 2.0 - - - +
897A SER 4.2 4.7 - - - +
898A MET* 1.3 89.0 - - + +
900A PHE* 1.3 65.7 + - - +
901A ILE* 4.3 8.7 - - + +
902A THR* 2.9 34.1 + - + +
903A TYR* 3.2 11.8 + - - +
938A LEU* 3.6 28.9 - - + +
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Residues in contact with PHE 900 (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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778A LEU* 3.8 26.5 - - + -
804A GLN* 3.4 21.8 - - - -
806A TRP* 5.6 3.7 - - + -
867A ILE* 4.3 8.1 - - + -
869A PHE* 3.9 12.3 - + - -
875A GLN* 4.7 2.5 - - - -
878A LEU* 4.0 9.2 - - + -
879A TRP* 3.7 33.9 - + + -
882A TYR* 3.4 52.6 + + + +
899A PRO* 1.3 73.5 - - - +
901A ILE* 1.3 59.9 + - - +
903A TYR* 3.4 2.0 + + - +
904A LEU* 3.1 57.3 + - + +
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Residues in contact with ILE 901 (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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778A LEU* 6.1 1.1 - - + +
806A TRP* 3.6 47.5 - - + +
865A CYS* 3.6 33.4 - - + -
867A ILE* 4.0 22.2 - - + -
899A PRO* 4.5 4.7 - - + -
900A PHE* 1.3 79.5 - - - +
902A THR* 1.3 70.9 + - + +
904A LEU* 3.3 3.3 + - - +
905A SER* 2.8 28.1 + - - -
924A ILE* 3.9 28.7 - - + +
926A CYS* 4.9 0.2 - - - -
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Residues in contact with THR 902 (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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898A MET* 3.4 22.1 - - - +
899A PRO* 2.9 40.4 + - + +
901A ILE* 1.3 83.1 - - + +
903A TYR* 1.3 59.8 + - - +
905A SER* 2.9 11.1 + - - +
906A GLY* 2.8 23.6 + - - -
938A LEU 5.7 4.7 - - - +
940A ARG 6.2 0.2 - - - +
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Residues in contact with TYR 903 (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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878A LEU* 4.3 6.7 - - + -
881A GLN* 3.0 36.7 + - - +
882A TYR* 3.5 55.4 - + + -
885A GLU* 3.6 25.9 + - + -
898A MET* 3.7 23.3 - - - +
899A PRO 3.2 10.2 + - - +
900A PHE* 3.7 5.8 - + - +
902A THR* 1.3 78.1 + - - +
904A LEU* 1.3 76.8 + - + +
906A GLY* 3.4 1.0 + - - -
907A LEU* 3.2 45.1 + - + +
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Residues in contact with LEU 904 (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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867A ILE* 3.7 34.3 - - + -
869A PHE* 3.9 6.5 - - + -
878A LEU* 3.8 31.2 - - + -
900A PHE* 3.1 51.0 + - + +
901A ILE 3.6 6.5 - - - +
903A TYR* 1.3 84.1 - - + +
905A SER* 1.3 60.2 + - - +
907A LEU* 3.1 4.5 + - - +
908A LEU* 2.8 39.2 + - + +
919A ILE* 4.7 7.0 - - + -
922A VAL* 4.7 4.7 - - + -
924A ILE* 4.4 7.6 - - + -
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Residues in contact with SER 905 (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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901A ILE* 2.8 17.8 + - - -
902A THR* 2.9 26.2 + - - +
904A LEU* 1.3 72.6 - - - +
906A GLY* 1.3 56.5 + - - +
908A LEU* 4.1 7.6 - - - -
909A THR* 2.9 41.6 + - - +
924A ILE* 4.1 15.1 - - - +
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Residues in contact with GLY 906 (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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898A MET* 5.3 4.5 - - - -
902A THR 2.8 21.6 + - - -
903A TYR* 3.4 3.6 + - - -
904A LEU 3.2 0.2 - - - -
905A SER* 1.3 74.6 + - - +
907A LEU* 1.3 58.7 + - - +
909A THR* 3.2 7.2 + - - -
910A ALA* 3.2 28.4 + - - +
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Residues in contact with LEU 907 (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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881A GLN* 4.1 7.2 - - - +
885A GLU* 5.7 0.4 - - - +
903A TYR* 3.2 53.4 + - + +
904A LEU* 3.1 3.0 + - - +
906A GLY* 1.3 76.1 - - - +
908A LEU* 1.3 64.5 + - - +
910A ALA* 4.1 7.5 - - + +
911A GLN* 3.4 22.5 + - - +
917A GLN* 6.0 3.8 - - - +
919A ILE* 3.5 35.3 - - + +
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Residues in contact with LEU 908 (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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904A LEU* 2.8 30.5 + - + +
905A SER* 3.3 7.1 + - - +
907A LEU* 1.3 76.5 - - - +
909A THR* 1.3 67.1 + - + +
911A GLN* 3.4 22.8 + - - +
912A MET* 4.6 2.3 + - - +
919A ILE* 3.4 27.4 - - + +
922A VAL* 3.7 38.1 - - + +
923A GLU* 4.5 3.8 - - - -
924A ILE* 4.4 22.2 - - + +
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Residues in contact with THR 909 (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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905A SER* 2.9 22.0 + - - +
906A GLY* 3.2 9.5 + - - -
908A LEU* 1.3 79.2 - - + +
910A ALA* 1.3 64.7 + - - +
911A GLN 3.3 0.9 + - - -
912A MET* 3.5 33.2 + - - +
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Residues in contact with ALA 910 (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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906A GLY 3.2 16.2 + - - +
907A LEU* 4.2 9.2 - - + +
908A LEU 3.4 0.2 - - - -
909A THR* 1.3 76.8 + - - +
911A GLN* 1.3 57.1 + - - +
912A MET* 3.1 6.3 - - - -
913A LEU* 2.9 43.0 + - + +
914A SER* 4.1 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