Contacts of the strand formed by residues 883 - 888 (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 SER 883 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B ASN* 1.3 81.8 - - - +
884B ILE* 1.3 64.1 + - - +
885B ILE* 6.3 0.2 - - - -
914B LYS* 3.5 19.7 - - - -
956B ASP 3.8 6.5 + - - -
957B THR* 3.5 14.6 - - - +
958B ASP* 2.9 34.1 + - - +
959B LEU 3.0 22.9 + - - -
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Residues in contact with ILE 884 (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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878B ILE* 4.0 27.8 - - + -
881B ALA* 3.9 15.5 - - + +
882B ASN 5.2 0.2 - - - -
883B SER* 1.3 80.8 - - - +
885B ILE* 1.3 78.1 + - - +
886B ILE* 4.3 3.4 - - + -
908B LEU* 4.4 11.4 - - + -
913B LYS* 4.2 19.5 - - + -
914B LYS 2.9 13.7 + - - +
915B VAL* 4.2 18.2 - - + -
916B ARG* 3.0 23.7 + - - +
959B LEU* 3.1 19.5 - - + +
961B LEU* 4.2 20.9 - - + -
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Residues in contact with ILE 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B SER* 6.3 0.2 - - - -
884B ILE* 1.3 81.6 - - - +
886B ILE* 1.3 72.1 + - - +
887B THR* 4.1 2.9 - - + -
916B ARG* 3.2 21.5 - - - +
918B GLY* 4.1 5.2 - - - +
950B ILE* 3.7 36.3 - - + -
953B ASP* 4.7 4.3 - - + -
954B PHE* 3.6 38.6 - - + -
957B THR* 3.3 31.2 - - + +
959B LEU 2.9 6.4 + - - +
960B VAL* 3.1 6.8 - - + +
961B LEU 2.9 23.7 + - - -
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Residues in contact with ILE 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B ILE* 4.3 5.2 - - + -
885B ILE* 1.3 77.0 - - - +
887B THR* 1.3 59.8 + - - +
888B PRO* 3.4 11.5 - - + +
892B LEU* 5.9 0.2 - - + -
901B ILE* 4.1 13.5 - - + -
905B VAL* 3.4 33.4 - - + -
908B LEU* 6.2 1.1 - - + -
915B VAL* 4.0 9.6 - - + -
916B ARG 2.7 12.2 + - - +
917B PHE* 3.2 32.5 - - + -
918B GLY 2.8 27.7 + - - -
961B LEU* 3.4 28.7 - - + +
963B ILE* 4.0 21.5 - - + -
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Residues in contact with THR 887 (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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885B ILE* 4.2 4.0 - - + -
886B ILE* 1.3 76.8 - - - +
888B PRO* 1.4 65.3 - - - +
918B GLY* 3.5 6.3 - - - +
954B PHE* 4.0 14.4 - - + -
960B VAL* 4.0 5.0 - - + +
961B LEU 3.0 6.1 + - - -
962B VAL* 3.4 27.2 - - - +
963B ILE 3.0 17.8 + - - -
965B ALA* 3.7 6.7 - - - +
969B VAL* 3.9 8.8 - - - +
987B LEU* 3.6 30.1 - - + -
989B VAL* 3.7 19.0 - - + +
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Residues in contact with PRO 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886B ILE* 3.4 17.5 - - + +
887B THR* 1.4 87.4 - - - +
889B GLY* 1.3 58.2 + - - +
892B LEU* 3.6 28.9 - - + -
917B PHE* 4.2 11.4 - - + -
918B GLY 3.7 11.0 - - - +
919B ILE* 3.6 23.6 - - + +
920B HIS 5.4 0.7 + - - -
923B ALA* 3.8 16.3 - - - +
930B LEU* 3.7 15.5 - - + -
934B LEU* 4.3 3.1 - - + -
963B ILE* 3.3 9.0 - - + +
965B ALA* 4.0 4.6 - - - +
968B THR* 4.9 1.2 + - - -
987B LEU* 5.9 1.2 - - - +
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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