Contacts of the helix formed by residues 899 - 911 (chain B) in PDB entry 5J67
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806B TRP* 4.2 22.7 - - + -
882B TYR* 3.6 2.0 - - - +
897B SER 4.1 5.8 - - - +
898B MET* 1.3 87.7 - - + +
900B PHE* 1.3 65.2 + - - +
901B ILE* 4.4 7.9 - - + +
902B THR* 2.9 33.0 + - + +
903B TYR* 3.1 10.0 + - - +
938B LEU* 3.5 31.6 - - + +
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Residues in contact with PHE 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU* 3.8 22.4 - - + -
804B GLN* 3.4 21.3 - - - -
806B TRP* 5.7 3.3 - - + -
867B ILE* 4.3 10.8 - - + -
869B PHE* 3.8 17.9 - + - -
875B GLN* 4.6 2.2 - - - -
878B LEU* 3.9 21.1 - - + -
879B TRP* 3.7 37.5 - + + -
882B TYR* 3.3 41.4 + + + -
899B PRO* 1.3 73.0 - - - +
901B ILE* 1.3 63.0 + - - +
903B TYR* 3.4 2.2 + + - +
904B LEU* 3.1 49.7 + - + +
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Residues in contact with ILE 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU* 5.9 0.6 - - + +
806B TRP* 3.6 46.5 - - + +
865B CYS* 3.6 33.4 - - + -
867B ILE* 4.0 22.2 - - + +
899B PRO* 4.5 4.5 - - + -
900B PHE* 1.3 79.5 - - - +
902B THR* 1.3 71.7 + - + +
904B LEU* 3.3 4.3 + - - +
905B SER* 2.8 28.6 + - - -
924B ILE* 3.8 29.0 - - + +
926B CYS* 4.8 0.2 - - - -
938B LEU 6.0 0.4 - - - +
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Residues in contact with THR 902 (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 MET* 3.3 28.9 - - - +
899B PRO* 2.9 32.4 + - + +
901B ILE* 1.3 87.5 - - + +
903B TYR* 1.3 58.9 + - - +
905B SER* 2.9 12.5 + - - +
906B GLY* 2.8 22.7 + - - -
938B LEU 5.6 5.8 - - - +
940B ARG 5.9 2.7 - - - +
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Residues in contact with TYR 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B LEU* 4.1 7.4 - - + -
881B GLN* 2.9 36.5 + - - +
882B TYR* 3.6 52.9 - + + -
885B GLU* 3.5 27.1 + - + -
898B MET* 3.7 24.1 - - - +
899B PRO 3.1 9.8 + - - +
900B PHE* 3.6 9.6 - + - +
902B THR* 1.3 77.0 + - - +
904B LEU* 1.3 68.6 + - + +
906B GLY* 3.5 2.1 + - - -
907B LEU* 3.1 48.9 + - + +
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Residues in contact with LEU 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B ILE* 3.7 35.9 - - + -
869B PHE* 3.9 4.9 - - + -
878B LEU* 3.8 32.5 - - + -
900B PHE* 3.1 51.3 + - + +
901B ILE 3.6 6.1 - - - +
903B TYR* 1.3 85.0 - - + +
905B SER* 1.3 55.0 + - - +
907B LEU* 3.2 5.1 + - - +
908B LEU* 2.8 45.3 + - + +
919B ILE* 4.7 6.1 - - + -
922B VAL* 4.7 5.2 - - + -
924B ILE* 4.4 7.4 - - + -
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Residues in contact with SER 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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901B ILE* 2.8 19.1 + - - -
902B THR* 2.9 21.8 + - - +
904B LEU* 1.3 72.2 - - - +
906B GLY* 1.3 59.1 + - - +
908B LEU* 3.7 7.5 - - - +
909B THR* 3.0 40.3 + - - +
924B ILE* 4.1 14.3 - - - +
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Residues in contact with GLY 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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898B MET* 5.3 4.9 - - - -
902B THR 2.8 17.8 + - - -
903B TYR* 3.7 3.4 - - - -
904B LEU 3.2 0.2 - - - -
905B SER* 1.3 77.1 + - - +
907B LEU* 1.3 56.8 + - - +
909B THR* 3.3 6.9 + - - -
910B ALA* 3.2 29.3 + - - +
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Residues in contact with LEU 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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881B GLN* 4.0 7.4 - - - +
885B GLU* 6.1 0.4 - - - +
903B TYR* 3.1 52.5 + - + +
904B LEU 3.2 4.2 + - - +
906B GLY* 1.3 74.9 - - - +
908B LEU* 1.3 64.0 + - - +
910B ALA* 4.1 7.6 - - + +
911B GLN* 3.3 22.2 + - - +
917B GLN* 6.0 4.0 - - - +
919B ILE* 3.3 39.2 - - + +
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Residues in contact with LEU 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 LEU* 2.8 35.3 + - + +
905B SER* 3.7 7.2 - - - +
907B LEU* 1.3 73.2 - - - +
909B THR* 1.3 63.6 + - + +
911B GLN* 3.5 22.2 - - - +
912B MET* 4.6 1.9 + - - +
919B ILE* 3.3 29.2 - - + +
922B VAL* 3.6 38.1 - - + +
923B GLU* 4.4 3.8 - - - -
924B ILE* 4.4 23.3 - - + +
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Residues in contact with THR 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 SER* 3.0 23.3 + - - +
906B GLY* 3.3 9.0 + - - -
908B LEU* 1.3 75.7 - - + +
910B ALA* 1.3 66.1 + - - +
911B GLN 3.2 1.0 + - - -
912B MET* 3.5 34.3 + - - +
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Residues in contact with ALA 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B GLY 3.2 15.9 + - - +
907B LEU* 4.3 10.1 - - + +
909B THR* 1.3 76.1 + - - +
911B GLN* 1.3 55.1 + - - +
912B MET 3.1 5.8 - - - -
913B LEU* 2.9 46.2 + - + +
914B SER* 4.0 0.9 + - - -
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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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907B LEU 3.3 13.3 + - - +
908B LEU* 3.5 18.5 - - - +
909B THR 3.2 1.4 - - - -
910B ALA* 1.3 71.8 - - - +
912B MET* 1.3 55.8 + - - +
913B LEU 3.1 1.6 - - - -
914B SER* 2.8 41.1 - - - +
915B ASP* 2.7 31.4 + - - +
916B ASP* 4.5 0.2 - - - +
917B GLN* 4.3 9.5 - - + +
919B ILE* 4.3 12.6 - - - +
920B SER* 4.0 33.8 - - - +
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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