Contacts of the helix formed by residues 952 - 957 (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 HIS 952 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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948A ASP 4.2 9.2 - - - -
949A GLU* 2.7 35.4 + - - +
951A ASN* 1.3 78.2 - - - +
953A ASP* 1.3 90.8 + - - +
954A PHE 3.4 0.4 - - - -
955A PRO* 3.5 13.0 - - - +
956A ASP* 3.6 8.7 - - - +
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Residues in contact with ASP 953 (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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885A ILE* 4.2 5.8 - - + -
914A LYS* 6.2 0.7 - - - -
916A ARG* 2.7 44.4 + - - +
949A GLU 4.5 0.5 - - - +
950A ILE* 2.8 16.5 + - - +
952A HIS* 1.3 103.0 + - - +
954A PHE* 1.3 60.7 + - - +
955A PRO* 3.3 1.3 - - - -
956A ASP* 3.0 20.2 + - + +
957A THR* 2.7 22.2 + - - +
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Residues in contact with PHE 954 (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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885A ILE* 3.7 28.3 - - + -
887A THR* 3.8 21.8 - - + -
950A ILE* 4.0 4.7 + - + -
951A ASN* 3.3 46.0 - - - +
953A ASP* 1.3 77.7 - - - +
955A PRO* 1.3 71.1 - - + +
957A THR* 3.0 13.5 + - - -
960A VAL* 3.7 33.2 - - + -
987A LEU* 4.0 13.5 - - + -
988A GLU* 3.3 31.9 - - + +
989A VAL* 3.9 14.8 - - + -
991A LYS* 4.2 3.4 - - + -
992A SER* 3.2 21.8 - - - +
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Residues in contact with PRO 955 (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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951A ASN 4.2 2.7 - - - +
952A HIS* 3.5 18.2 - - - +
953A ASP 3.5 0.4 - - - -
954A PHE* 1.3 94.6 - - + +
956A ASP* 1.3 65.1 + - - +
957A THR 3.3 3.0 + - - +
991A LYS* 3.6 40.4 - - + +
992A SER* 4.8 1.0 - - - -
993A LYS* 5.3 4.9 + - - +
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Residues in contact with ASP 956 (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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883A SER* 3.8 9.0 + - - -
952A HIS 3.6 19.2 - - - +
953A ASP* 3.0 12.6 + - + +
955A PRO* 1.3 83.6 - - - +
957A THR* 1.3 59.7 + - - +
958A ASP* 4.9 2.5 - - - +
993A LYS* 6.2 0.9 - - - -
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Residues in contact with THR 957 (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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883A SER* 3.5 15.9 + - - +
885A ILE* 3.3 32.6 - - + +
916A ARG* 5.0 1.6 + - - -
953A ASP* 2.7 21.0 + - - +
954A PHE* 3.0 12.5 + - - -
955A PRO 3.3 1.1 - - - +
956A ASP* 1.3 80.3 - - - +
958A ASP* 1.3 64.2 + - - +
959A LEU 3.4 27.8 - - - +
960A VAL* 4.4 4.5 - - + -
992A SER* 3.4 5.1 - - - -
993A LYS* 3.0 29.7 + - - +
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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