Contacts of the strand formed by residues 982 - 990 (chain B) 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 THR 982 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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887B GLN* 4.3 1.3 - - - +
888B LEU* 2.7 45.9 + - + +
890B GLN 2.7 24.1 + - - -
891B VAL* 3.5 4.7 - - - +
922B LEU* 4.5 4.5 - - + -
946B TYR* 2.7 30.4 + - + +
959B ILE* 3.4 33.7 - - + -
960B SER 3.7 13.7 - - - +
961B ARG* 4.6 1.4 - - - +
980B GLU 3.8 0.6 + - - -
981B GLY* 1.3 75.4 + - - -
983B TRP* 1.3 63.0 + - - +
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Residues in contact with TRP 983 (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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778B THR* 3.8 16.2 - - + -
885B ASN* 4.0 26.2 - - - -
886B CYS* 3.6 19.7 - - - -
887B GLN* 3.3 51.5 - - + +
958B ASN* 4.0 1.0 - - - +
959B ILE* 3.3 5.9 - - - +
960B SER* 2.7 36.1 + - - +
961B ARG* 4.2 7.9 - - - -
962B TYR 3.7 12.8 - - - +
963B SER* 3.4 39.7 - - - -
964B GLN 5.6 0.4 - - - -
979B GLU* 2.8 29.3 + - + -
980B GLU 5.2 0.7 - - - -
981B GLY 5.6 0.2 - - - -
982B THR* 1.3 71.7 - - - +
984B LEU* 1.3 60.3 + - - +
985B ASN* 4.1 10.4 + - - +
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Residues in contact with LEU 984 (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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780B LEU* 6.1 1.6 - - + -
885B ASN* 3.2 6.4 + - - +
886B CYS* 2.9 48.3 + - - +
888B LEU* 4.4 13.0 - - + -
944B LEU* 3.8 25.4 - - + -
951B TRP* 3.5 42.6 - - + +
957B PHE* 4.7 1.8 - - + -
958B ASN 3.7 10.5 - - - +
959B ILE* 4.2 15.0 - - + -
982B THR 3.6 0.6 + - - -
983B TRP* 1.3 74.7 - - - +
985B ASN* 1.3 73.5 + - - +
986B ILE* 4.6 13.9 - - + +
1020B TRP* 5.7 0.2 - - + -
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Residues in contact with ASN 985 (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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783B GLN* 2.6 30.1 + - - +
881B ARG* 3.9 20.6 - - - +
884B LEU 3.6 4.0 - - - +
885B ASN* 3.1 18.2 + - - +
957B PHE* 3.2 6.1 - - - +
958B ASN* 2.8 57.0 + - - +
962B TYR 5.6 1.8 + - - -
964B GLN* 3.7 21.0 - - - +
983B TRP* 4.7 11.1 + - - +
984B LEU* 1.3 75.4 - - - +
986B ILE* 1.3 61.5 + - - +
987B ASP* 4.0 1.6 + - - +
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Residues in contact with ILE 986 (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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780B LEU* 5.6 3.8 - - + -
883B GLY* 3.2 1.0 - - - -
884B LEU* 2.8 55.3 + - + +
885B ASN* 5.6 0.2 - - - -
944B LEU* 4.6 9.0 - - + -
951B TRP* 4.0 32.3 - - + -
955B PHE* 3.5 44.9 - - + -
956B GLN 3.5 1.8 - - - -
957B PHE* 4.4 1.6 - - + -
984B LEU* 4.1 13.9 - - + -
985B ASN* 1.3 72.3 - - - +
987B ASP* 1.3 62.3 + - - +
988B GLY 4.0 0.3 + - - -
1016B TYR* 4.8 2.9 - - - -
1018B LEU* 3.9 28.7 - - + -
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Residues in contact with ASP 987 (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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881B ARG* 2.8 42.8 + - - -
882B ILE 3.8 2.2 - - - +
883B GLY* 3.6 10.6 - - - -
884B LEU 4.6 0.9 + - - +
937B LEU* 3.7 9.0 - - - +
955B PHE* 3.3 6.8 - - - +
956B GLN* 2.7 50.6 + - + +
985B ASN* 4.8 1.9 - - - +
986B ILE* 1.3 80.6 + - - +
988B GLY* 1.4 62.7 + - - +
989B PHE 3.6 13.7 - - - +
990B HIS* 2.8 27.0 + - - -
1016B TYR* 4.9 0.7 - - - -
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Residues in contact with GLY 988 (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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882B ILE 2.8 10.7 + - - -
883B GLY* 4.0 0.4 - - - -
954B ASP 4.6 3.8 - - - +
955B PHE* 4.8 4.3 - - - -
956B GLN* 3.0 18.5 + - - -
986B ILE 4.0 0.8 + - - -
987B ASP* 1.4 72.9 - - - +
989B PHE* 1.3 74.3 + - - +
1016B TYR* 3.5 42.1 - - - +
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Residues in contact with PHE 989 (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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881B ARG* 3.4 3.8 - - - +
882B ILE* 3.0 37.6 + - + +
956B GLN* 4.5 4.5 - - - +
987B ASP* 3.2 5.3 - - - +
988B GLY* 1.3 88.3 - - - +
990B HIS* 1.3 61.2 + - - +
1009B LEU* 4.0 24.0 - - + -
1014B TYR* 3.5 47.6 - + + -
1015B HIS 3.2 32.5 - - - -
1016B TYR* 4.0 8.5 - + + -
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Residues in contact with HIS 990 (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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786B ARG* 3.0 28.9 + - - -
880B ALA 3.8 3.1 + - - -
881B ARG* 3.4 36.4 - - + +
906B TYR* 3.8 19.5 - + - -
907B PRO* 3.2 20.4 - - + +
934B GLU* 3.8 15.7 - - + -
937B LEU* 3.7 19.3 - - + +
956B GLN* 4.3 10.0 - - + +
987B ASP* 2.8 21.5 + - - +
989B PHE* 1.3 75.8 - - - +
991B MET* 1.3 90.5 + - - +
992B GLY 3.8 0.2 + - - -
1007B PHE 4.7 0.7 - - - +
1009B LEU* 4.0 9.9 - - - +
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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