Contacts of the strand formed by residues 959 - 963 (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 LEU 959 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B MET* 3.7 9.6 - - + +
878B ILE* 3.7 42.8 - - + +
881B ALA* 3.7 15.9 - - + -
883B SER 3.0 3.5 + - - +
884B ILE* 3.1 16.9 - - + -
885B ILE 2.9 23.9 + - - +
957B THR* 3.4 3.7 - - - +
958B ASP* 1.3 80.7 - - - +
960B VAL* 1.3 68.0 + - - +
961B LEU* 4.0 11.4 - - + -
994B GLN* 3.2 30.3 - - + +
996B ILE* 3.7 30.5 - - + -
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Residues in contact with VAL 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B ILE 3.1 10.8 - - - +
887B THR* 4.0 16.2 - - + +
954B PHE* 3.9 17.7 - - + -
957B THR* 4.5 2.7 - - + -
959B LEU* 1.3 78.7 - - - +
961B LEU* 1.3 66.6 + - - +
962B VAL* 4.0 5.4 - - + -
989B VAL* 3.6 35.0 - - + +
992B SER* 3.5 32.3 - - - +
994B GLN 2.9 9.1 + - - +
995B VAL* 3.5 5.0 - - + +
996B ILE 2.9 27.0 + - - +
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Residues in contact with LEU 961 (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* 4.5 19.5 - - + -
884B ILE* 4.2 18.4 - - + -
885B ILE 2.9 9.1 + - - -
886B ILE* 3.4 28.4 - - + +
887B THR 3.0 23.5 + - - -
901B ILE* 5.1 4.9 - - + -
904B LEU* 5.3 6.1 - - + -
908B LEU* 5.7 3.8 - - + -
959B LEU* 4.0 16.8 - - + -
960B VAL* 1.3 78.6 - - - +
962B VAL* 1.3 62.1 + - - +
963B ILE* 3.4 8.5 + - + -
996B ILE* 3.6 22.9 - - + -
998B MET* 3.9 29.6 - - + -
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Residues in contact with VAL 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B THR* 3.4 15.5 - - - +
960B VAL* 4.0 7.6 - - + -
961B LEU* 1.3 71.4 - - - +
963B ILE* 1.3 57.4 + - - +
965B ALA* 3.4 38.1 - - + +
969B VAL* 3.9 12.6 - - + -
989B VAL* 4.1 13.7 - - + -
995B VAL* 3.8 25.8 - - + -
996B ILE 2.9 11.1 + - - +
997B VAL* 4.0 17.9 - - + -
998B MET* 2.7 34.5 + - - +
1013B ILE* 4.8 0.2 - - + -
1014B PHE* 6.4 0.2 - - + -
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Residues in contact with ILE 963 (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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886B ILE* 4.0 14.1 - - + -
887B THR 3.0 10.1 + - - -
888B PRO* 3.3 8.5 - - + +
889B GLY 2.9 23.6 + - - -
892B LEU* 3.7 24.3 - - + +
901B ILE* 3.5 33.9 - - + -
961B LEU* 4.0 10.8 - - + +
962B VAL* 1.3 75.6 - - - +
964B GLY* 1.3 62.2 + - - +
965B ALA 3.2 0.4 - - - -
998B MET* 3.9 28.5 - - + -
1026B ALA* 4.3 13.7 - - + -
1030B CYS* 4.0 23.6 - - - -
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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