Contacts of the helix formed by residues 870 - 881 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869A ILE* 1.3 77.3 - - - +
871A LEU* 1.3 64.7 + - - +
872A ASP* 3.8 11.3 - - - +
873A ASN* 2.7 39.7 + - - +
874A ALA* 3.0 18.5 + - - +
1022A LEU* 4.1 4.9 - - - -
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Residues in contact with LEU 871 (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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870A ASN* 1.3 74.8 - - - +
872A ASP* 1.3 63.4 + - - +
874A ALA* 3.3 4.3 + - - +
875A ILE* 3.0 30.5 + - - +
1022A LEU* 4.1 17.9 - - + +
1029A THR* 4.3 7.4 - - + +
1032A ALA* 3.3 32.1 - - + -
1033A LEU* 3.5 32.1 - - + -
1036A LYS* 4.1 31.0 - - + +
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Residues in contact with ASP 872 (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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870A ASN* 3.2 13.5 + - - +
871A LEU* 1.3 76.6 - - - +
873A ASN* 1.3 62.1 + - - +
875A ILE* 3.3 8.4 + - - +
876A ASP* 3.0 27.5 + - - +
1036A LYS* 2.5 36.8 + - - +
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Residues in contact with ASN 873 (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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869A ILE* 3.6 31.5 - - + +
870A ASN* 2.7 27.3 + - - +
872A ASP* 1.3 74.6 - - - +
874A ALA* 1.3 56.7 + - - +
876A ASP* 3.1 13.4 + - - +
877A MET* 3.0 43.6 + - - +
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Residues in contact with ALA 874 (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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869A ILE* 3.9 19.6 - - + +
870A ASN 3.0 11.9 + - - +
871A LEU 3.5 8.5 - - - +
872A ASP 3.3 0.2 - - - -
873A ASN* 1.3 74.5 - - - +
875A ILE* 1.3 61.3 + - - +
877A MET* 3.2 3.0 + - - +
878A ILE* 2.9 37.8 + - + +
996A ILE* 4.2 11.4 - - + +
1022A LEU* 3.9 22.2 - - + -
1033A LEU* 4.1 10.5 - - + -
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Residues in contact with ILE 875 (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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871A LEU* 3.0 27.5 + - + +
872A ASP* 3.6 10.1 - - - +
873A ASN 3.3 0.2 - - - -
874A ALA* 1.3 76.5 - - - +
876A ASP* 1.3 64.3 + - - +
878A ILE* 3.3 6.5 + - + +
879A ARG* 2.9 42.7 + - + +
1033A LEU* 3.4 25.8 - - + -
1036A LYS* 3.7 39.5 - - + +
1037A VAL* 4.4 16.2 - - + -
1040A SER* 5.5 7.2 - - - +
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Residues in contact with ASP 876 (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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872A ASP 3.0 16.8 + - - +
873A ASN* 3.3 17.8 - - - +
875A ILE* 1.3 83.2 - - - +
877A MET* 1.3 58.1 + - + +
879A ARG* 3.8 4.3 - - - +
880A GLU* 2.9 32.9 + - - +
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Residues in contact with MET 877 (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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869A ILE* 3.9 26.2 - - + -
873A ASN* 3.0 26.1 + - - +
874A ALA 3.6 5.4 - - - +
876A ASP* 1.3 76.7 - - + +
878A ILE* 1.3 62.6 + - - +
880A GLU* 3.5 17.9 + - - +
881A ALA* 3.0 25.3 + - - +
959A LEU* 3.8 9.6 - - + +
994A GLN* 3.4 40.8 - - + +
996A ILE* 3.7 27.6 - - + -
1020A ALA* 4.7 1.3 - - + -
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Residues in contact with ILE 878 (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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874A ALA* 2.9 25.1 + - + +
875A ILE* 3.6 6.1 - - - +
877A MET* 1.3 76.8 - - - +
879A ARG* 1.3 68.0 + - + +
881A ALA* 3.2 13.7 + - - +
884A ILE* 4.2 4.3 - - + +
904A LEU* 4.7 8.5 - - + -
908A LEU* 3.7 38.1 - - + -
913A LYS* 3.2 13.3 + - - +
959A LEU* 3.8 20.9 - - + -
961A LEU* 4.6 20.0 - - + -
996A ILE* 5.1 1.1 - - + -
1033A LEU* 4.2 29.8 - - + -
1037A VAL* 4.9 9.9 - - + -
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Residues in contact with ARG 879 (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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875A ILE* 2.9 30.0 + - + +
876A ASP* 3.9 4.5 - - - +
878A ILE* 1.3 82.9 - - + +
880A GLU* 1.3 58.8 + - - +
882A ASN* 5.4 0.3 - - - +
908A LEU* 3.9 11.5 - - - +
911A GLN* 3.4 46.0 - - - +
913A LYS* 2.8 34.3 + - - +
1037A VAL* 3.8 31.0 + - + +
1040A SER* 4.1 24.1 + - - +
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Residues in contact with GLU 880 (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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876A ASP 2.9 15.0 + - - +
877A MET* 3.8 21.2 - - - +
879A ARG* 1.3 76.5 - - - +
881A ALA* 1.3 66.0 + - + +
882A ASN* 3.7 12.5 + - - +
958A ASP* 4.7 1.2 - - - +
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Residues in contact with ALA 881 (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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877A MET 3.0 18.7 + - - +
878A ILE 3.2 7.0 + - - +
880A GLU* 1.3 79.8 - - + +
882A ASN* 1.3 59.1 + - - +
884A ILE* 4.0 11.4 - - + -
913A LYS* 2.7 34.5 + - - +
958A ASP* 3.9 14.4 - - + -
959A LEU* 3.8 26.7 - - + -
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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