Contacts of the helix formed by residues 870 - 881 (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 ASN 870 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869B ILE* 1.3 76.9 - - - +
871B LEU* 1.3 64.9 + - - +
872B ASP* 4.0 16.4 + - - +
873B ASN* 2.9 30.6 + - - +
874B ALA* 3.1 11.4 + - - +
1022B LEU* 4.2 5.2 - - - -
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Residues in contact with LEU 871 (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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870B ASN* 1.3 73.4 - - - +
872B ASP* 1.3 58.5 + - - +
874B ALA* 3.1 7.6 + - - +
875B ILE* 2.9 33.3 + - - +
1022B LEU* 4.3 17.1 - - + +
1029B THR* 4.2 11.0 - - + +
1032B ALA* 3.6 33.4 - - + -
1033B LEU* 4.0 24.3 - - + +
1036B LYS* 4.6 25.4 - - + +
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Residues in contact with ASP 872 (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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870B ASN* 3.3 15.8 + - - +
871B LEU* 1.3 76.2 - - - +
873B ASN* 1.3 62.8 + - - +
875B ILE* 3.3 10.6 + - - +
876B ASP* 3.0 28.0 + - - +
1036B LYS* 2.6 37.0 + - - +
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Residues in contact with ASN 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B ILE* 3.7 31.1 - - + +
870B ASN* 2.9 24.2 + - - +
872B ASP* 1.3 77.6 - - - +
874B ALA* 1.3 61.7 + - - +
876B ASP* 3.2 11.7 + - - +
877B MET* 3.1 39.3 + - - +
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Residues in contact with ALA 874 (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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869B ILE* 4.0 6.8 - - + +
870B ASN 3.1 7.5 + - - +
871B LEU 3.1 8.6 + - - +
873B ASN* 1.3 76.8 - - - +
875B ILE* 1.3 62.6 + - - +
877B MET* 3.2 2.8 + - - +
878B ILE* 2.9 30.8 + - + +
996B ILE* 4.0 21.9 - - + +
998B MET* 6.2 0.2 - - + -
1022B LEU* 3.8 29.2 - - + -
1033B LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 875 (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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871B LEU 2.9 20.0 + - - +
872B ASP* 3.5 14.6 - - - +
873B ASN 3.2 0.2 - - - -
874B ALA* 1.3 78.0 - - - +
876B ASP* 1.3 61.8 + - - +
878B ILE* 3.1 8.6 + - + +
879B ARG* 2.8 38.5 + - + +
1033B LEU* 4.0 17.0 - - + +
1036B LYS* 3.2 50.3 - - + -
1037B VAL* 5.4 13.0 - - + +
1040B SER* 6.1 0.7 - - - +
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Residues in contact with ASP 876 (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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872B ASP* 3.0 18.6 + - - +
873B ASN* 3.2 13.2 + - - +
875B ILE* 1.3 79.1 - - - +
877B MET* 1.3 58.5 + - + +
879B ARG* 3.8 15.6 - - - +
880B GLU* 3.0 35.0 + - - +
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Residues in contact with MET 877 (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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869B ILE* 4.1 16.4 - - + -
873B ASN* 3.1 36.9 + - - +
874B ALA 3.6 7.4 - - - +
875B ILE 3.2 0.2 - - - -
876B ASP* 1.3 76.8 - - + +
878B ILE* 1.3 62.5 + - - +
880B GLU* 3.5 5.8 + - - +
881B ALA* 3.2 23.4 + - - +
959B LEU* 3.7 10.2 - - + +
994B GLN* 3.9 31.9 - - + +
996B ILE* 3.7 33.4 - - + -
1020B ALA* 4.4 5.8 - - + -
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Residues in contact with ILE 878 (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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874B ALA* 2.9 22.8 + - + +
875B ILE* 3.1 8.5 + - - +
877B MET* 1.3 74.3 - - - +
879B ARG* 1.3 69.4 + - - +
881B ALA* 2.9 14.9 + - - +
884B ILE* 4.0 13.0 - - + +
904B LEU* 5.1 9.0 - - + -
908B LEU* 3.8 32.1 - - + -
913B LYS* 3.1 12.3 + - - +
959B LEU* 3.7 21.3 - - + -
961B LEU* 4.5 23.1 - - + -
996B ILE* 5.0 0.7 - - + -
1033B LEU* 4.5 23.6 - - + -
1037B VAL* 5.3 9.2 - - + -
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Residues in contact with ARG 879 (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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875B ILE* 2.8 28.0 + - + +
876B ASP* 3.8 15.8 + - - +
878B ILE* 1.3 72.5 - - - +
880B GLU* 1.3 60.0 + - + +
911B GLN* 5.9 0.9 - - - -
913B LYS* 2.7 27.5 + - - +
1040B SER* 4.8 18.4 + - - -
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Residues in contact with GLU 880 (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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876B ASP* 3.0 22.4 + - - +
877B MET* 3.9 5.8 - - - +
878B ILE 3.1 0.2 - - - -
879B ARG* 1.3 79.7 - - + +
881B ALA* 1.3 59.8 + - - +
882B ASN* 3.8 7.6 + - - +
958B ASP* 4.6 1.7 - - - +
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Residues in contact with ALA 881 (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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877B MET 3.2 15.6 + - - +
878B ILE 2.9 7.5 + - - +
880B GLU* 1.3 77.5 - - - +
882B ASN* 1.3 60.7 + - - +
884B ILE* 3.9 11.0 - - + -
913B LYS* 2.5 35.5 + - - +
958B ASP* 3.8 14.4 - - + -
959B LEU* 3.7 26.9 - - + -
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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