Contacts of the helix formed by residues 897 - 911 (chain B) in PDB entry 1DJL
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 ALA 897 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892B LEU* 3.0 21.5 + - + +
895B ALA* 3.2 1.1 - - + -
896B LYS* 1.3 74.6 - - - +
898B GLN* 1.3 65.8 + - - +
899B TYR 3.2 2.9 - - - -
900B PRO* 3.2 10.8 - - + +
901B ILE* 3.2 23.4 + - - +
963B ILE* 5.2 0.4 - - + -
1026B ALA* 3.8 16.2 - - + +
1027B LYS* 3.8 29.2 - - - +
1030B CYS* 4.3 8.5 - - - -
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Residues in contact with GLN 898 (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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892B LEU* 3.6 22.4 - - + +
893B CYS* 4.9 0.8 + - - -
896B LYS* 2.8 34.6 - - - +
897B ALA* 1.3 72.3 + - - +
899B TYR* 1.3 80.3 + - + +
901B ILE* 2.9 27.0 - - - +
902B ALA* 2.9 15.9 + - - +
933B LEU* 3.5 53.4 + - + +
934B LEU* 4.5 4.8 - - + +
936B GLU* 5.2 0.4 + - - -
937B ALA* 3.6 19.5 - - + +
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Residues in contact with TYR 899 (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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896B LYS* 3.9 20.2 - - + -
897B ALA 3.2 0.4 - - - -
898B GLN* 1.3 95.1 + - - +
900B PRO* 1.3 74.5 - - + +
902B ALA* 3.1 12.4 + - - +
903B ASP* 3.2 18.9 + - - +
933B LEU 5.4 0.4 + - - -
936B GLU* 3.5 33.2 + - + +
937B ALA* 3.9 29.8 - - + -
1027B LYS* 6.2 2.0 - - - -
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Residues in contact with PRO 900 (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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896B LYS 4.2 3.4 - - - +
897B ALA* 3.2 25.4 - - + +
899B TYR* 1.3 94.3 - - + +
901B ILE* 1.3 61.6 + - - +
903B ASP* 3.3 3.1 + - - +
904B LEU* 3.0 23.3 + - - +
1027B LYS* 4.5 8.3 - - + -
1030B CYS* 3.7 29.6 - - + +
1031B ASP* 3.2 31.0 - - - +
1034B GLN* 4.0 19.9 - - + +
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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
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886B ILE* 4.1 24.7 - - + -
892B LEU* 4.3 8.5 - - + -
897B ALA 3.2 14.9 + - - +
898B GLN* 2.9 26.5 - - - +
900B PRO* 1.3 77.7 - - - +
902B ALA* 1.3 63.6 + - - +
904B LEU* 3.3 25.4 + - + +
905B VAL* 2.9 24.0 + - - +
917B PHE* 4.3 8.3 - - + -
934B LEU* 4.3 16.8 - - + -
961B LEU* 5.1 3.1 - - + -
963B ILE* 3.5 30.7 - - + -
1030B CYS* 4.4 12.5 - - - +
1033B LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 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 GLN 2.9 18.8 + - - +
899B TYR 3.1 4.9 + - - +
901B ILE* 1.3 77.4 - - - +
903B ASP* 1.3 65.0 + - - +
905B VAL* 3.3 5.9 + - - +
906B LYS* 3.1 20.4 + - - +
937B ALA* 3.3 27.6 - - + +
938B GLY 4.9 1.3 - - - +
939B VAL* 3.7 27.6 - - + +
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Residues in contact with ASP 903 (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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899B TYR 3.2 13.2 + - - +
900B PRO* 3.7 6.7 - - - +
902B ALA* 1.3 78.2 - - - +
904B LEU* 1.3 64.9 + - - +
906B LYS* 3.1 18.7 + - - +
907B MET* 3.1 22.2 + - + +
937B ALA 5.3 1.9 - - - +
1034B GLN* 3.3 27.5 + - + +
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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
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878B ILE* 5.1 6.5 - - + -
900B PRO 3.0 14.5 + - - +
901B ILE* 3.4 29.2 - - + +
903B ASP* 1.3 78.1 - - - +
905B VAL* 1.3 62.3 + - + +
907B MET* 3.4 7.4 + - - +
908B LEU* 3.1 45.1 + - + +
961B LEU* 5.3 4.9 - - + -
1030B CYS* 5.0 3.8 - - - +
1033B LEU* 4.0 29.6 - - + -
1034B GLN* 4.2 12.8 - - + +
1037B VAL* 3.4 40.2 - - + -
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Residues in contact with VAL 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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886B ILE* 3.4 33.4 - - + -
901B ILE* 2.9 21.1 + - + +
902B ALA* 3.8 6.1 - - - +
903B ASP 3.3 0.2 - - - -
904B LEU* 1.3 76.0 - - + +
906B LYS* 1.3 56.7 + - - +
908B LEU* 3.8 7.2 - - + +
909B THR* 2.6 46.2 + - - +
915B VAL* 3.8 15.0 - - + -
917B PHE* 3.6 15.0 - - + -
939B VAL* 5.6 1.1 - - + -
940B PRO* 6.0 0.9 - - + -
943B ILE* 3.6 31.4 - - + -
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Residues in contact with LYS 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 3.1 12.2 + - - +
903B ASP* 3.1 14.1 + - - +
905B VAL* 1.3 77.2 - - - +
907B MET* 1.3 58.7 + - + +
909B THR* 3.4 5.3 + - - -
910B GLU* 2.9 54.6 + - + +
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Residues in contact with MET 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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903B ASP* 3.1 19.1 + - + +
904B LEU* 3.9 8.3 - - - +
906B LYS* 1.3 77.6 - - + +
908B LEU* 1.3 64.8 + - - +
910B GLU* 3.0 16.7 + - - +
911B GLN* 3.0 30.0 + - + +
1034B GLN* 3.5 43.3 - - + +
1037B VAL* 3.8 20.6 - - + +
1038B ARG* 3.7 40.6 - - + +
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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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878B ILE* 3.8 33.7 - - + -
884B ILE* 4.4 11.9 - - + -
886B ILE* 6.2 0.9 - - + -
904B LEU* 3.1 40.3 + - + +
905B VAL* 3.9 7.2 - - + +
907B MET* 1.3 71.4 - - - +
909B THR* 1.3 66.2 + - - +
911B GLN* 3.0 32.6 + - - +
913B LYS* 3.2 29.7 + - + +
915B VAL* 3.9 17.9 - - + -
961B LEU* 5.7 4.7 - - + -
1037B VAL* 4.3 16.2 - - + -
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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 VAL* 2.6 34.6 + - - +
906B LYS* 3.6 6.7 - - - -
908B LEU* 1.3 76.5 - - - +
910B GLU* 1.3 57.8 + - + +
912B GLY* 3.0 21.1 + - - -
913B LYS 3.5 14.7 + - - +
915B VAL* 4.1 11.5 + - - +
943B ILE* 5.1 6.1 - - + +
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Residues in contact with GLU 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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906B LYS* 2.9 48.1 + - + +
907B MET* 3.0 18.1 + - - +
909B THR* 1.3 79.3 - - - +
911B GLN* 1.3 56.1 + - + +
912B GLY 3.1 3.1 + - - -
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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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879B ARG* 5.9 0.7 - - - -
907B MET* 3.0 21.5 + - + +
908B LEU* 3.0 29.0 + - - +
910B GLU* 1.3 77.5 - - + +
912B GLY* 1.3 59.3 + - - +
913B LYS* 3.4 20.1 + - + +
1037B VAL* 4.8 13.3 + - - +
1040B SER* 4.0 20.0 + - - -
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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