Contacts of the strand formed by residues 914 - 921 (chain C) 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 CYS 914 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697C THR* 4.8 9.6 - - + +
699C ARG* 6.2 1.6 - - - +
717C TRP* 3.5 33.7 - - - -
719C GLN* 3.4 27.8 - - - +
900C LEU* 3.9 2.7 - - - -
901C GLY 2.9 28.7 + - - +
912C ALA 3.7 1.3 + - - -
913C ALA* 1.3 81.3 - - - +
915C PHE* 1.3 59.7 + - - +
916C ASP* 5.2 1.3 - - + +
918C TRP* 3.1 28.6 + - + -
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Residues in contact with PHE 915 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C ASP* 4.9 11.2 - - - -
660C GLY 5.1 1.3 - - - -
695C TRP* 3.1 62.4 - + + +
719C GLN* 2.8 30.6 + - - +
721C ARG* 6.0 0.4 - - - -
898C LEU* 3.6 36.8 - - + -
899C GLY* 3.4 24.0 - - - -
900C LEU* 3.7 13.2 - - + +
914C CYS* 1.3 68.0 - - - +
916C ASP* 1.3 69.2 + - - +
940C GLY 3.5 20.4 - - - -
942C ARG* 3.9 18.6 - - + -
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Residues in contact with ASP 916 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655C MET* 5.5 5.7 - - - +
657C ALA* 5.2 8.5 - - - +
660C GLY* 3.8 21.0 - - - +
697C THR* 4.8 8.1 + - - -
699C ARG* 5.1 8.1 + - - -
719C GLN* 5.0 0.5 + - - -
898C LEU* 3.5 10.0 - - - -
899C GLY 3.1 29.9 + - - +
914C CYS* 3.4 2.3 + - + +
915C PHE* 1.3 84.1 - - - +
917C ARG* 1.3 77.4 + - - +
918C TRP* 3.4 33.7 - - + -
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Residues in contact with ARG 917 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C ASP* 4.5 6.3 + - - +
660C GLY* 4.3 12.5 - - - +
661C LYS* 6.2 1.6 - - - +
896C ASN* 2.9 39.6 + - - +
897C TRP 3.4 6.3 - - - -
898C LEU* 3.9 36.8 - - + +
916C ASP* 1.3 88.2 + - - +
918C TRP* 1.3 68.9 + - - +
919C ASP* 6.0 0.4 - - + -
943C GLU* 2.7 40.4 + - - -
945C ASN* 3.4 3.4 - - - +
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Residues in contact with TRP 918 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699C ARG* 5.6 7.4 - - - -
896C ASN* 3.2 7.9 + - - -
897C TRP* 2.7 78.0 + + + -
899C GLY 3.2 11.9 + - - -
901C GLY* 3.4 25.3 - - - +
902C PRO* 3.9 30.7 - - + -
914C CYS* 3.1 34.1 + - + -
916C ASP* 3.4 40.8 + - + +
917C ARG* 1.3 80.9 - - - +
919C ASP* 1.3 61.7 + - - +
920C LEU* 5.3 1.8 - - + -
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Residues in contact with ASP 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C ARG* 2.7 56.2 + - - +
895C VAL 3.2 7.6 - - - -
896C ASN* 3.0 27.5 + - - +
917C ARG* 6.0 0.4 - - + -
918C TRP* 1.3 76.9 - - - +
920C LEU* 1.3 71.8 + - - +
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Residues in contact with LEU 920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C ARG* 3.4 8.2 - - - +
895C VAL* 2.9 28.5 + - - +
897C TRP* 3.8 10.8 - - + -
902C PRO* 3.8 36.6 - - + +
918C TRP* 5.4 1.3 - - + -
919C ASP* 1.3 88.8 + - - +
921C PRO* 1.3 82.1 - - + +
924C ASP* 3.8 20.0 - - + +
925C MET* 3.7 25.4 - - - -
938C ARG* 3.8 6.5 - - - +
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Residues in contact with PRO 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893C GLU 3.5 11.2 - - - +
894C ARG* 3.5 24.0 - - - +
920C LEU* 1.3 92.6 - - + +
922C LEU* 1.3 66.6 + - - +
923C SER* 4.2 11.4 - - - +
924C ASP* 2.9 38.8 + - - +
925C MET* 3.9 2.1 + - - +
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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