Contacts of the strand formed by residues 881 - 888 (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 ARG 881 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783C GLN* 3.7 33.2 - - - +
784C PHE* 3.1 24.6 + - - +
785C THR 2.9 40.1 + - - +
786C ARG* 3.3 19.0 - - - +
879C PRO* 3.1 3.6 - - - +
880C ALA* 1.3 85.0 - - + +
882C ILE* 1.3 71.9 + - - +
934C GLU* 2.9 20.0 + - - -
937C LEU* 4.4 1.4 - - - +
958C ASN* 3.7 10.9 - - - +
964C GLN* 3.3 15.2 + - - -
985C ASN* 3.9 9.2 - - - +
987C ASP* 2.9 36.0 + - - +
989C PHE 3.6 11.2 - - - +
990C HIS* 3.4 18.9 - - + +
1009C LEU* 3.7 4.9 - - - -
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Residues in contact with ILE 882 (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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783C GLN 3.9 1.6 - - - -
784C PHE* 4.1 14.1 - - + -
870C VAL* 4.0 28.9 - - + -
872C VAL* 4.1 16.4 - - + -
879C PRO* 4.2 7.4 - - + -
881C ARG* 1.3 79.0 - - - +
883C GLY* 1.3 57.4 + - - +
987C ASP* 3.7 1.7 - - - -
988C GLY* 2.9 22.3 + - - -
989C PHE* 2.8 28.3 + - + +
1009C LEU* 4.0 13.2 - - + -
1014C TYR* 3.4 42.2 - - + -
1016C TYR* 4.0 13.3 - - + +
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Residues in contact with GLY 883 (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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782C ASP* 3.3 7.4 - - - +
783C GLN* 2.8 35.7 + - - -
784C PHE* 4.9 1.4 - - - -
882C ILE* 1.3 78.4 - - - +
884C LEU* 1.3 59.6 + - - +
986C ILE 3.3 12.3 - - - -
987C ASP* 3.7 10.4 + - - -
1016C TYR* 3.3 20.6 + - - -
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Residues in contact with LEU 884 (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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780C LEU* 3.9 33.4 - - + -
781C ARG 3.2 6.5 - - - +
782C ASP* 3.9 13.9 - - - +
783C GLN* 4.2 3.6 + - - +
854C LYS* 3.8 27.1 - - + -
856C TYR* 5.7 0.4 - - - +
866C ILE* 4.5 16.6 - - + -
868C VAL* 4.7 0.9 - - + -
883C GLY* 1.3 78.0 - - - +
885C ASN* 1.3 66.7 + - - +
985C ASN* 3.7 1.0 - - - +
986C ILE* 2.8 36.8 + - + +
987C ASP* 4.9 0.9 - - - +
1016C TYR* 3.4 21.8 - - + +
1018C LEU* 3.7 27.8 - - + -
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Residues in contact with ASN 885 (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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779C PRO 3.5 2.3 - - - +
780C LEU* 3.4 4.3 - - - -
781C ARG* 2.6 46.0 + - - +
782C ASP 4.7 0.7 - - - +
783C GLN* 3.6 25.7 + - - +
884C LEU* 1.3 78.8 - - - +
886C CYS* 1.3 65.3 - - - +
964C GLN* 5.3 2.8 - - - +
983C TRP* 3.7 25.0 - - - -
984C LEU 3.2 7.2 - - - +
985C ASN* 3.1 29.7 + - - +
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Residues in contact with CYS 886 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776C LEU* 4.2 9.2 - - + -
778C THR* 3.7 19.7 - - - +
779C PRO 3.8 4.5 - - - +
780C LEU* 3.9 22.4 - - + +
885C ASN* 1.3 82.6 - - - +
887C GLN* 1.3 60.6 + - - +
888C LEU* 3.7 29.4 - - - -
983C TRP* 3.6 7.7 - - - -
984C LEU* 2.8 42.0 + - - +
1020C TRP* 4.2 6.7 - - - -
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Residues in contact with GLN 887 (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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776C LEU* 3.7 3.1 - - - +
777C LEU* 2.8 43.6 + - + +
778C THR* 2.9 40.2 + - + +
886C CYS* 1.3 74.6 - - - +
888C LEU* 1.3 62.5 + - - +
979C GLU* 3.9 4.9 + - - +
980C GLU* 2.5 41.0 + - - +
982C THR 3.4 5.6 - - - +
983C TRP* 3.4 42.4 - - + +
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Residues in contact with LEU 888 (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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775C GLN 3.5 6.1 - - - +
776C LEU* 3.9 14.1 - - + -
777C LEU* 3.9 2.7 - - - +
886C CYS* 3.7 24.7 - - - -
887C GLN* 1.3 74.3 - - - +
889C ALA* 1.3 62.5 + - - +
890C GLN* 4.1 13.2 - - + +
946C TYR* 4.0 22.9 - - + -
949C HIS* 4.4 11.2 - - + +
951C TRP* 3.9 24.7 - - + -
959C ILE* 5.1 1.1 - - + -
981C GLY* 3.2 4.7 - - - -
982C THR* 2.6 44.4 + - + +
984C LEU* 4.4 10.8 - - + -
1020C TRP* 4.0 17.9 - - + -
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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