Contacts of the helix formed by residues 928 - 937 (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 928 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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919A ILE* 6.1 1.1 - - - -
921A PRO 4.5 6.1 + - - -
923A ALA 5.4 0.8 + - - -
926A MET 3.2 1.0 + - - -
927A PRO* 1.3 71.6 - - - +
929A GLN* 1.3 64.7 + - - +
930A LEU 3.3 2.7 - - - -
931A ASN* 3.3 22.0 + - - +
932A VAL* 3.2 28.0 + - - +
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Residues in contact with GLN 929 (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* 5.5 1.0 - - - -
893A CYS* 3.8 29.9 - - - +
923A ALA 4.8 1.0 + - - +
924A GLY* 3.5 4.9 - - - -
925A ARG* 2.6 36.6 + - - +
926A MET* 3.0 54.0 + - + +
927A PRO 3.1 1.6 + - - -
928A GLY* 1.3 77.6 - - - +
930A LEU* 1.3 65.5 + - + +
932A VAL* 3.4 7.3 + - - +
933A LEU* 3.1 31.6 + - + +
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Residues in contact with LEU 930 (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* 3.8 39.0 - - + +
889A GLY 4.0 7.4 - - - +
892A LEU* 4.1 13.5 - - + -
893A CYS* 3.7 31.9 - - - -
919A ILE* 4.1 25.1 - - + +
923A ALA* 3.7 35.8 + - + +
924A GLY* 3.7 4.0 - - - +
928A GLY 3.3 0.6 - - - -
929A GLN* 1.3 75.0 - - + +
931A ASN* 1.3 66.0 - - - +
933A LEU* 3.2 3.4 + - + +
934A LEU* 2.9 32.5 + - + +
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Residues in contact with ASN 931 (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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919A ILE* 3.8 17.0 - - - +
928A GLY* 3.3 23.5 + - - +
930A LEU* 1.3 75.5 - - - +
932A VAL* 1.3 59.7 + - + +
934A LEU* 3.9 5.3 - - - +
935A ALA* 2.9 30.8 + - - +
941A TYR* 5.5 1.9 - - + -
944A VAL* 3.7 24.5 + - + +
946A GLU* 2.9 27.5 + - - +
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Residues in contact with VAL 932 (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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928A GLY 3.2 14.9 + - - +
929A GLN* 3.6 9.9 - - - +
930A LEU 3.1 0.6 - - - -
931A ASN* 1.3 77.8 - - + +
933A LEU* 1.3 68.4 + - + +
935A ALA* 3.2 6.9 + - - +
936A GLU* 2.9 29.5 + - + +
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Residues in contact with LEU 933 (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* 4.7 3.8 - - + -
893A CYS* 3.7 46.4 - - + +
896A LYS* 6.3 0.9 - - + -
898A GLN* 3.3 36.6 - - + +
929A GLN* 3.1 23.1 + - + +
930A LEU* 3.2 4.2 + - - +
932A VAL* 1.3 86.1 - - + +
934A LEU* 1.3 63.6 + - + +
936A GLU* 3.2 23.9 + - - +
937A ALA 3.1 16.5 + - - -
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Residues in contact with LEU 934 (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* 4.5 4.5 - - + -
892A LEU* 4.9 9.2 - - + -
898A GLN* 4.7 9.0 - - + -
901A ILE* 4.6 11.9 - - + -
917A PHE* 3.8 50.5 - - + -
919A ILE* 4.0 20.6 - - + -
930A LEU* 2.9 23.0 + - + +
931A ASN 4.0 3.1 - - - +
933A LEU* 1.3 74.8 - - + +
935A ALA* 1.3 66.5 + - - +
937A ALA* 3.1 8.3 + - - -
938A GLY 3.2 0.2 + - - -
939A VAL* 3.0 41.0 + - + +
944A VAL* 4.2 16.6 - - + -
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Residues in contact with ALA 935 (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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931A ASN 2.9 20.1 + - - +
932A VAL* 3.5 6.7 - - - +
934A LEU* 1.3 77.1 - - - +
936A GLU* 1.3 58.1 + - - +
938A GLY* 2.9 20.0 + - - +
939A VAL 4.5 9.2 - - - -
941A TYR* 3.2 39.0 + - + +
944A VAL* 6.1 0.2 - - - +
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Residues in contact with GLU 936 (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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898A GLN* 3.5 14.2 + - - -
899A TYR* 3.1 32.4 + - + +
932A VAL* 2.9 16.5 + - + +
933A LEU* 3.2 21.5 + - - +
935A ALA* 1.3 77.4 - - - +
937A ALA* 1.3 57.5 + - - +
938A GLY 3.2 1.0 + - - -
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Residues in contact with ALA 937 (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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898A GLN* 3.5 44.9 - - + +
899A TYR* 3.9 17.6 - - + +
902A ALA* 3.5 18.8 - - + +
903A ASP* 5.4 1.0 - - - +
933A LEU 3.1 3.0 + - - -
934A LEU* 3.1 10.4 + - - +
935A ALA 3.1 1.0 - - - -
936A GLU* 1.3 76.4 - - - +
938A GLY* 1.3 61.6 + - - +
939A VAL* 3.4 0.7 - - + -
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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