Contacts of the helix formed by residues 889 - 896 (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 GLY 889 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888A PRO* 1.3 75.1 - - - +
890A TYR* 1.3 66.8 + - - -
892A LEU* 3.0 14.6 + - - +
893A CYS* 3.5 9.9 + - - -
923A ALA* 4.5 1.6 - - - -
924A GLY 4.2 7.9 - - - -
930A LEU* 4.0 4.7 - - - +
963A ILE 3.0 10.7 + - - -
964A GLY 3.1 10.7 + - - -
965A ALA* 3.7 5.7 - - - +
968A THR* 5.1 0.2 - - - -
1136A NAP 3.2 12.6 - - - -
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Residues in contact with TYR 890 (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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889A GLY* 1.3 70.3 - - - -
891A GLY* 1.3 59.5 + - - +
893A CYS* 3.0 12.2 + - + +
894A ALA* 2.9 44.4 + - + +
924A GLY* 3.7 13.9 - - - +
925A ARG* 3.5 66.0 - - + +
929A GLN* 5.5 1.1 - - - -
964A GLY 3.2 0.8 + - - -
1136A NAP 2.7 50.6 + + - +
1138A SO4 5.9 2.9 - - - -
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Residues in contact with GLY 891 (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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890A TYR* 1.3 73.8 - - - +
892A LEU* 1.3 61.8 + - - +
894A ALA* 3.4 1.2 + - - +
895A ALA* 3.1 25.8 + - - +
964A GLY* 2.7 24.2 + - - -
1026A ALA* 4.0 2.6 - - - +
1136A NAP 3.4 41.4 + - - -
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Residues in contact with LEU 892 (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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888A PRO* 3.7 22.4 - - + -
889A GLY 3.0 11.3 + - - +
891A GLY* 1.3 75.9 - - - +
893A CYS* 1.3 66.8 + - - +
895A ALA 3.4 0.3 + - - -
896A LYS* 2.9 18.7 + - - -
897A ALA* 3.1 22.6 + - + -
898A GLN* 3.8 29.6 - - + +
901A ILE* 4.2 25.4 - - + -
917A PHE* 5.5 0.9 - - + -
930A LEU* 4.1 15.0 - - + -
933A LEU* 4.7 1.8 - - + -
934A LEU* 4.9 6.7 - - + -
963A ILE* 4.0 31.5 + - + +
964A GLY* 4.0 0.4 - - - -
1026A ALA* 4.4 10.1 - - - -
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Residues in contact with CYS 893 (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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889A GLY 3.8 7.6 - - - -
890A TYR* 3.0 16.2 + - + +
892A LEU* 1.3 77.1 - - - +
894A ALA* 1.3 63.6 + - - +
896A LYS* 3.1 23.6 + - - +
929A GLN* 3.8 25.6 - - - +
930A LEU* 3.7 33.0 - - - -
933A LEU* 3.7 33.3 - - + +
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Residues in contact with ALA 894 (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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890A TYR* 2.9 38.5 + - + +
891A GLY 3.9 3.8 - - - +
892A LEU 3.3 0.2 - - - -
893A CYS* 1.3 78.3 - - - +
895A ALA* 1.3 60.4 + - - +
896A LYS* 3.3 10.4 + - - +
1136A NAP 4.1 18.6 - - - +
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Residues in contact with ALA 895 (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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891A GLY 3.1 16.8 + - - +
892A LEU 4.1 1.1 - - - +
894A ALA* 1.3 75.6 - - - +
896A LYS* 1.3 73.8 + - - +
897A ALA 4.4 0.4 - - - +
1025A ASP* 3.7 9.4 - - - +
1026A ALA* 3.7 6.5 - - + -
1027A LYS* 3.3 41.8 - - - +
1136A NAP 3.6 18.8 - - - +
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Residues in contact with LYS 896 (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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892A LEU 2.9 5.5 + - - -
893A CYS 3.1 17.9 + - - +
894A ALA 3.8 8.5 - - - +
895A ALA* 1.3 83.1 - - - +
897A ALA* 1.3 58.3 + - - +
898A GLN* 2.8 27.6 + - - +
899A TYR* 3.9 17.7 - - + -
900A PRO* 4.5 1.2 - - - +
933A LEU* 6.3 0.7 - - + -
1027A LYS* 3.9 13.6 - - + +
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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