Contacts of the strand formed by residues 914 - 919 (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 LYS 914 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882B ASN 3.1 14.7 + - - +
883B SER* 3.5 12.6 - - - -
884B ILE 2.9 27.9 + - - +
912B GLY 3.8 2.0 + - - -
913B LYS* 1.3 69.2 - - - +
915B VAL* 1.3 58.5 + - - +
916B ARG* 3.9 45.8 + - + +
953B ASP* 5.1 2.4 + - - -
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Residues in contact with VAL 915 (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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884B ILE* 3.3 24.2 - - + -
886B ILE* 4.0 14.4 - - + -
905B VAL* 3.8 36.1 - - + +
908B LEU* 3.9 28.3 - - + -
909B THR* 4.1 9.7 + - - +
913B LYS* 3.3 20.5 + - + +
914B LYS* 1.3 77.2 - - - +
916B ARG* 1.3 69.5 + - - +
943B ILE* 3.8 21.5 - - - +
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Residues in contact with ARG 916 (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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884B ILE 3.0 9.5 + - - +
885B ILE* 3.2 15.4 - - + +
886B ILE* 2.7 35.0 + - - +
914B LYS* 3.9 39.4 - - + +
915B VAL* 1.3 82.4 - - - +
917B PHE* 1.3 60.5 + - - +
942B ASP 5.7 0.9 - - - -
943B ILE* 3.4 20.6 - - + +
945B LEU* 3.6 31.4 - - + +
949B GLU 5.5 0.2 + - - -
950B ILE* 4.0 22.7 - - + +
953B ASP* 3.0 39.0 + - - +
957B THR* 4.9 2.0 + - - -
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Residues in contact with PHE 917 (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* 4.6 0.2 - - - -
886B ILE* 3.2 36.8 - - + +
888B PRO* 4.2 8.7 - - + -
901B ILE* 4.3 12.6 - - + -
905B VAL* 3.6 33.2 - - + -
916B ARG* 1.3 77.8 - - - +
918B GLY* 1.3 59.9 + - - +
919B ILE* 4.0 13.5 - - + -
934B LEU* 3.6 28.3 - - + -
939B VAL* 3.6 39.0 - - + -
943B ILE* 2.7 27.2 + - + +
944B VAL* 4.1 8.3 - - + -
945B LEU* 2.9 29.7 + - - +
950B ILE* 3.9 5.1 - - - +
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Residues in contact with GLY 918 (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* 4.1 6.5 - - - +
886B ILE 2.8 12.2 + - - -
887B THR* 3.5 21.3 - - - -
888B PRO* 3.7 4.7 - - - +
917B PHE* 1.3 73.0 - - - +
919B ILE* 1.3 60.8 + - - -
920B HIS 4.0 0.2 + - - -
945B LEU 3.4 4.5 - - - -
950B ILE* 4.1 22.0 - - - -
987B LEU* 3.6 16.9 - - - +
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Residues in contact with ILE 919 (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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888B PRO* 3.6 33.4 - - + -
917B PHE* 4.1 6.3 - - + -
918B GLY* 1.3 77.7 - - - +
920B HIS* 1.3 76.0 + - - +
921B PRO* 3.7 0.9 - - - +
923B ALA* 4.6 4.3 - - + -
930B LEU* 4.2 15.7 - - + -
931B ASN* 3.6 25.8 - - - +
934B LEU* 4.1 16.2 - - + -
944B VAL* 3.6 25.8 - - + -
945B LEU 2.8 15.3 + - - +
946B GLU* 3.5 5.6 - - - +
947B MET 2.9 25.4 + - - +
987B LEU* 4.5 1.1 - - - -
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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