Contacts of the strand formed by residues 776 - 783 (chain A) in PDB entry 1JZ3
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 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765A LEU* 4.0 24.7 - - + +
766A SER 3.9 13.0 - - - +
767A GLN* 2.8 55.9 + - - +
768A MET* 4.3 8.3 - - + +
774A LYS* 4.7 2.3 - - - +
775A GLN* 1.3 89.3 - - + +
777A LEU* 1.3 65.5 + - - +
778A THR 3.7 14.8 - - - +
779A PRO* 4.5 1.1 - - + -
780A LEU* 4.5 4.3 - - + +
886A CYS* 4.2 10.8 - - - -
887A GLN 3.7 3.8 - - - +
888A LEU* 4.0 20.4 - - + -
889A ALA* 4.4 1.5 - - - +
1020A TRP* 4.1 15.3 - - + -
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Residues in contact with LEU 777 (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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776A LEU* 1.3 75.2 - - - +
778A THR* 1.3 64.3 + - - +
779A PRO* 4.9 0.3 - - - +
887A GLN* 2.8 26.8 + - - +
888A LEU 3.9 2.7 - - - +
889A ALA* 3.8 23.3 - - + +
980A GLU* 3.0 66.9 - - + +
981A GLY* 3.9 7.9 - - - +
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Residues in contact with THR 778 (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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766A SER 5.0 1.1 - - - -
776A LEU* 3.7 15.8 - - - +
777A LEU* 1.3 81.5 - - - +
779A PRO* 1.3 78.9 + - - +
781A ARG* 6.1 0.9 - - - -
886A CYS* 3.7 4.7 - - - +
887A GLN* 2.9 52.1 + - + +
983A TRP* 3.8 17.0 - - + -
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Residues in contact with PRO 779 (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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762A SER* 5.8 2.5 - - - +
764A PHE* 4.2 9.2 - - + -
765A LEU 3.3 16.8 - - - +
766A SER* 3.9 22.8 - - - +
776A LEU* 4.5 1.3 - - + -
777A LEU 4.9 0.4 - - - +
778A THR* 1.3 97.1 + - - +
780A LEU* 1.3 64.9 + - - +
781A ARG* 3.4 32.1 + - + +
885A ASN* 3.5 8.0 - - - +
886A CYS* 3.8 0.8 - - - +
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Residues in contact with LEU 780 (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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764A PHE* 3.3 23.6 - - - +
765A LEU* 3.0 33.2 + - + +
776A LEU* 4.5 3.6 - - + +
779A PRO* 1.3 73.7 - - - +
781A ARG* 1.3 59.5 + - - +
856A TYR* 4.5 14.6 + - + +
866A ILE* 4.2 18.4 - - + -
884A LEU* 3.9 39.4 - - + +
885A ASN* 3.4 16.4 - - - +
886A CYS* 3.8 20.6 - - + +
984A LEU* 6.2 1.1 - - + -
1020A TRP* 4.3 19.7 - - + -
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Residues in contact with ARG 781 (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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762A SER* 4.8 4.9 - - - -
764A PHE* 2.8 56.5 - - + -
778A THR* 6.1 1.1 - - - -
779A PRO* 3.7 29.3 - - + +
780A LEU* 1.3 80.2 - - - +
782A ASP* 1.3 67.6 + - - +
820A ALA* 4.5 15.8 - - - +
842A TRP* 5.5 3.6 - - + +
884A LEU* 3.3 7.0 - - - -
885A ASN* 2.8 39.0 + - - +
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Residues in contact with ASP 782 (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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764A PHE* 3.5 6.3 - - - -
781A ARG* 1.3 82.8 - - - +
783A GLN* 1.3 60.6 + - - +
784A PHE* 3.7 17.1 - - + -
842A TRP* 3.2 39.4 + - + -
852A SER* 2.7 23.1 + - - -
854A LYS* 2.6 33.5 + - - -
868A VAL* 4.4 4.7 - - - +
870A VAL* 4.8 1.4 - - - +
883A GLY 3.2 10.7 - - - +
884A LEU* 3.9 6.8 - - - +
885A ASN* 4.9 1.0 - - - +
1016A TYR* 4.7 0.5 + - - -
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Residues in contact with GLN 783 (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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782A ASP* 1.3 77.8 - - - +
784A PHE* 1.3 65.6 + - - +
785A THR* 3.5 26.6 + - - +
881A ARG* 3.5 30.2 - - - +
883A GLY 2.8 36.3 + - - +
884A LEU 4.9 0.8 + - - -
885A ASN* 3.7 25.8 + - + +
964A GLN* 3.3 23.6 - - - +
985A ASN* 2.7 29.2 + - - +
987A ASP* 4.9 0.2 + - - -
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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