Contacts of the strand formed by residues 938 - 946 (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 ARG 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897A TRP* 3.7 10.7 - - + +
900A LEU 3.6 23.3 - - - +
902A PRO 2.9 26.2 + - - -
903A GLN* 3.7 5.3 - - - +
904A GLU* 3.5 18.6 - - - +
905A ASN* 3.7 9.6 - - - +
920A LEU* 4.0 4.4 - - - +
924A ASP 3.2 19.4 + - - -
925A MET* 3.6 41.5 - - - +
927A THR* 5.1 1.4 + - - -
936A GLY* 2.8 41.6 + - - -
937A LEU* 1.3 75.8 - - - +
939A CYS* 1.3 63.4 + - - +
941A THR* 4.3 0.9 - - - +
956A GLN* 3.2 2.6 - - - -
957A PHE* 2.9 54.4 + - + -
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Residues in contact with CYS 939 (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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900A LEU* 3.2 23.3 + - + +
905A ASN* 2.8 35.0 + - - +
906A TYR* 3.8 3.4 - - - -
907A PRO* 3.8 24.2 - - - -
910A LEU* 3.8 17.5 - - + -
937A LEU* 3.7 20.0 - - - -
938A ARG* 1.3 72.1 - - - +
940A GLY* 1.3 68.0 + - - +
941A THR* 3.1 7.9 + - - -
956A GLN* 3.2 16.8 - - - +
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Residues in contact with GLY 940 (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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899A GLY* 3.4 13.7 - - - -
900A LEU* 4.0 11.5 + - - +
915A PHE* 3.7 14.7 - - - -
939A CYS* 1.3 76.6 - - - +
941A THR* 1.3 61.2 + - - +
942A ARG* 4.0 3.5 - - - -
954A ASP* 4.3 14.6 - - - -
955A PHE 4.0 0.7 - - - -
956A GLN* 3.0 11.6 + - - -
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Residues in contact with THR 941 (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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897A TRP* 3.4 21.7 + - + -
898A LEU 3.5 6.3 - - - +
899A GLY* 3.8 0.5 - - - -
938A ARG 4.0 1.0 + - - -
939A CYS 3.2 11.6 + - - -
940A GLY* 1.3 75.2 - - - +
942A ARG* 1.3 64.2 + - - +
943A GLU 3.5 21.5 - - - +
944A LEU* 4.6 0.4 - - + +
954A ASP* 3.4 5.2 - - - -
955A PHE* 2.9 62.5 + - + -
957A PHE* 3.4 24.0 - - + -
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Residues in contact with ARG 942 (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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693A GLN* 6.3 0.8 - - - +
721A ARG* 6.0 1.8 - - - +
724A GLU* 5.3 5.3 + - - -
898A LEU* 2.8 21.2 + - + +
915A PHE* 3.8 27.1 - - + -
940A GLY 4.0 4.9 - - - -
941A THR* 1.3 81.0 - - - +
943A GLU* 1.3 61.7 + - - +
952A ARG* 3.4 6.6 - - - +
953A GLY 2.9 48.8 + - - +
954A ASP* 3.8 15.7 - - - +
955A PHE* 4.4 1.8 - - - -
871B GLU* 5.8 1.8 + - - -
1013B ARG* 3.7 46.0 - - - +
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Residues in contact with GLU 943 (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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897A TRP* 3.3 5.8 - - - +
898A LEU* 2.9 41.9 + - + +
917A ARG* 2.7 39.7 + - - -
941A THR* 3.5 4.3 - - - +
942A ARG* 1.3 82.4 - - + +
944A LEU* 1.3 63.3 + - - +
945A ASN* 3.0 11.7 + - - +
950A GLN* 3.4 37.0 + - + +
951A TRP 3.2 6.5 - - - +
952A ARG* 4.2 9.3 - - + +
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Residues in contact with LEU 944 (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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895A VAL* 3.6 22.4 - - + -
896A ASN 3.7 4.9 - - - +
897A TRP* 4.0 1.8 - - + -
941A THR* 4.6 1.6 - - + -
943A GLU* 1.3 75.1 - - - +
945A ASN* 1.3 65.5 + - - +
950A GLN* 3.2 4.9 - - - -
951A TRP* 2.8 60.0 + - + +
955A PHE* 3.9 15.3 - - + -
957A PHE* 3.6 42.4 - - + -
959A ILE* 4.8 5.4 - - + -
984A LEU* 3.8 25.6 - - + -
986A ILE* 4.4 7.6 - - + -
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Residues in contact with ASN 945 (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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894A ARG 4.6 0.5 - - - +
895A VAL* 4.0 6.8 - - - +
896A ASN* 2.7 64.1 + - + +
917A ARG* 3.5 1.8 - - - +
943A GLU* 3.0 22.8 + - - +
944A LEU* 1.3 76.4 - - - +
946A TYR* 1.3 62.2 + - - +
949A HIS 3.3 3.8 - - - -
950A GLN* 2.7 33.7 + - - +
1023A LYS* 3.6 18.7 + - - +
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Residues in contact with TYR 946 (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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888A LEU* 3.9 16.6 - - + -
890A GLN* 3.9 15.9 - - + -
891A VAL* 3.5 0.9 - - - -
892A ALA* 2.9 38.7 + - + -
894A ARG 3.3 21.1 - - - -
895A VAL* 3.9 14.4 - - + -
922A LEU* 3.6 12.7 - - + +
944A LEU* 5.3 0.7 - - + -
945A ASN* 1.3 74.9 - - - +
947A GLY* 1.3 67.8 - - - +
948A PRO 3.2 0.3 - - - -
949A HIS* 3.0 30.1 + + - +
951A TRP* 3.9 15.9 - - + -
959A ILE* 3.6 21.8 - - + -
982A THR* 2.7 46.7 + - + +
1023A LYS* 4.2 0.8 - - - +
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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