Contacts of the strand formed by residues 959 - 963 (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 LEU 959 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A MET* 3.8 11.2 - - + +
878A ILE* 3.8 35.2 - - + +
881A ALA* 3.8 15.7 - - + -
883A SER 3.2 2.4 + - - -
884A ILE* 3.2 15.9 - - + +
885A ILE 2.9 23.0 + - - -
957A THR* 3.4 2.9 - - - +
958A ASP* 1.3 82.0 - - - +
960A VAL* 1.3 65.8 + - - +
961A LEU* 3.8 21.1 - - + -
994A GLN* 3.3 38.6 - - + +
996A ILE* 3.7 20.4 - - + -
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Residues in contact with VAL 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ILE 3.1 11.4 - - - +
887A THR* 4.1 9.2 - - + +
954A PHE* 3.7 22.7 - - + -
957A THR* 4.4 4.3 - - + -
959A LEU* 1.3 78.0 - - - +
961A LEU* 1.3 67.2 + - - +
962A VAL* 3.7 13.1 + - + -
989A VAL* 3.8 26.7 - - + +
992A SER* 3.2 30.3 - - - +
994A GLN 2.9 7.9 + - - -
995A VAL* 3.5 9.0 - - + +
996A ILE* 2.9 26.9 + - - +
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Residues in contact with LEU 961 (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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878A ILE* 4.6 19.7 - - + -
884A ILE* 4.1 18.8 - - + -
885A ILE 2.8 8.1 + - - -
886A ILE* 3.3 29.4 - - + +
887A THR 3.0 21.7 + - - -
901A ILE* 4.9 4.0 - - + -
904A LEU* 4.8 13.2 - - + -
908A LEU* 5.7 2.2 - - + -
959A LEU* 3.8 27.1 - - + -
960A VAL* 1.3 74.4 - - - +
962A VAL* 1.3 62.3 + - - +
963A ILE* 3.5 13.2 + - + -
996A ILE* 3.7 26.5 - - + -
998A MET* 5.1 9.2 - - - -
1033A LEU* 5.5 2.9 - - + -
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Residues in contact with VAL 962 (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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887A THR* 3.6 15.9 - - - +
960A VAL* 4.0 8.3 - - + -
961A LEU* 1.3 71.2 - - - +
963A ILE* 1.3 58.1 + - - +
965A ALA* 3.4 38.6 - - + +
969A VAL* 4.0 11.2 - - + -
989A VAL* 4.3 13.9 - - + -
995A VAL* 3.8 25.6 - - + -
996A ILE 2.9 12.6 + - - +
997A VAL* 4.1 16.8 - - + -
998A MET* 2.7 34.7 + - - +
1013A ILE* 4.9 0.4 - - + -
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Residues in contact with ILE 963 (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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886A ILE* 3.8 15.7 - - + -
887A THR 3.2 9.3 + - - -
888A PRO* 3.4 8.3 - - + +
889A GLY 3.0 18.5 + - - -
892A LEU* 4.0 21.4 - - + +
897A ALA* 5.2 0.2 - - + -
901A ILE* 3.7 33.2 - - + -
961A LEU* 3.9 13.5 - - + +
962A VAL* 1.3 77.0 - - - +
964A GLY* 1.3 65.9 + - - +
965A ALA 3.1 0.4 - - - -
998A MET* 3.8 26.7 - - + +
1026A ALA* 4.1 23.1 - - + -
1030A CYS* 4.0 14.1 - - - -
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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
------------------------------------------------------------
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