Contacts of the strand formed by residues 1013 - 1022 (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 ARG1013 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870A VAL 3.3 4.0 - - - +
871A GLU* 4.2 25.9 + - + +
1011A ALA* 3.0 26.9 + - - +
1012A GLY* 1.3 88.4 - - - +
1014A TYR* 1.3 69.3 + - - +
721B ARG* 6.0 2.0 - - - +
724B GLU* 5.0 9.1 + - - -
942B ARG* 3.4 38.6 - - - +
954B ASP* 3.0 36.0 + - - +
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Residues in contact with TYR1014 (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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868A VAL 3.8 0.9 - - - +
869A ASP* 3.3 6.2 - - - +
870A VAL* 2.8 35.8 + - + +
872A VAL* 4.4 9.9 - - + -
882A ILE* 3.3 35.7 - - + -
989A PHE* 3.5 52.3 - + + -
1008A GLN 4.3 0.7 + - - -
1009A LEU* 2.9 35.8 - - + +
1010A SER 3.0 0.7 + - - -
1011A ALA* 2.9 44.0 + - + +
1012A GLY 3.9 7.0 - - - -
1013A ARG* 1.3 79.2 - - - +
1015A HIS* 1.3 60.0 + - - +
1016A TYR* 5.2 1.3 - - - -
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Residues in contact with HIS1015 (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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867A THR* 3.4 29.9 - - + +
868A VAL 3.4 5.0 + - - -
869A ASP* 2.6 26.9 + - - +
989A PHE* 3.3 19.8 - - - -
1014A TYR* 1.3 76.1 - - - +
1016A TYR* 1.3 75.8 + - - +
1017A GLN* 4.4 7.8 - - + +
867B THR* 5.7 0.4 - - + -
869B ASP* 3.5 14.8 + - - -
1015B HIS* 3.1 52.5 - + + -
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Residues in contact with TYR1016 (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* 4.7 0.9 + - - -
867A THR* 3.8 0.5 - - - -
868A VAL* 2.8 71.4 + - + +
870A VAL* 4.8 1.4 - - + +
882A ILE* 3.8 24.2 - - + +
883A GLY* 3.3 29.7 + - - -
884A LEU* 3.3 23.2 - - + +
954A ASP 5.3 6.1 - - - +
955A PHE* 6.0 1.3 - - + -
986A ILE 4.8 2.9 - - - -
987A ASP 5.0 0.4 - - - -
988A GLY* 3.7 32.1 - - - +
989A PHE* 4.2 8.1 - + + -
1014A TYR 5.2 1.6 - - - -
1015A HIS* 1.3 85.5 + - - +
1017A GLN* 1.3 66.1 + - - +
1018A LEU* 4.3 22.4 - - + -
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Residues in contact with GLN1017 (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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865A ALA* 4.3 13.7 - - - +
866A ILE 3.3 15.5 + - - +
867A THR* 3.5 22.5 + - + +
868A VAL* 5.8 0.2 - - - -
952A ARG 5.5 0.7 - - - +
953A GLY* 3.8 17.6 - - - -
954A ASP 4.3 4.0 + - - +
1015A HIS* 4.4 11.4 + - - +
1016A TYR* 1.3 80.0 - - - +
1018A LEU* 1.3 78.7 + - - +
1019A VAL* 4.6 8.0 - - - +
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Residues in contact with LEU1018 (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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864A MET 3.7 0.5 - - - +
865A ALA* 3.5 1.7 - - - -
866A ILE* 2.6 53.9 + - + +
868A VAL* 5.8 0.2 - - + -
884A LEU* 4.0 26.7 - - + -
951A TRP* 5.2 9.6 - - + -
952A ARG 3.2 7.9 - - - +
955A PHE* 3.5 38.6 - - + -
986A ILE* 3.9 26.7 - - + -
1016A TYR* 4.3 18.2 - - + -
1017A GLN* 1.3 84.1 + - - +
1019A VAL* 1.3 67.5 + - - +
1020A TRP* 6.1 0.2 - - + -
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Residues in contact with VAL1019 (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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863A GLN* 3.9 29.4 - - + +
864A MET 3.4 7.2 - - - +
865A ALA* 3.9 17.9 - - + -
950A GLN 3.6 1.2 - - - +
951A TRP* 3.2 5.7 - - - -
952A ARG* 2.8 67.6 + - + +
1017A GLN* 4.6 11.9 - - - +
1018A LEU* 1.3 78.3 - - - +
1020A TRP* 1.3 64.8 + - - +
1021A CYS* 4.0 0.7 + - - -
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Residues in contact with TRP1020 (chain A).
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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765A LEU* 4.8 1.3 - - + -
768A MET* 2.9 37.5 - - + +
776A LEU* 4.1 7.6 - - + -
780A LEU* 4.3 30.1 - - + -
862A GLY 4.6 0.9 - - - +
863A GLN* 3.9 0.3 - - - -
864A MET* 2.9 57.5 + - + +
866A ILE* 4.9 8.0 - - + +
886A CYS* 4.3 4.7 - - - -
888A LEU* 3.9 18.8 - - + -
949A HIS* 3.0 38.2 + + - +
950A GLN 3.5 6.3 - - - -
951A TRP* 3.1 38.7 - + + +
984A LEU* 5.5 0.7 - - + -
1018A LEU 4.2 0.6 - - - -
1019A VAL* 1.3 71.7 - - - +
1021A CYS* 1.3 74.9 + - - +
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Residues in contact with CYS1021 (chain A).
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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862A GLY 4.8 4.7 - - - +
863A GLN* 3.9 30.7 - - + +
949A HIS* 3.7 2.1 + - - -
950A GLN* 2.9 50.8 + - - +
952A ARG* 3.4 26.0 - - - +
1019A VAL* 4.7 0.9 - - + -
1020A TRP* 1.3 87.0 + - - +
1022A GLN* 1.3 70.1 + - - +
1023A LYS* 5.1 0.2 - - - -
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Residues in contact with GLN1022 (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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753A ASN* 4.3 5.4 + - - +
754A LYS* 3.7 32.3 - - + +
770A ILE* 3.8 34.5 - - + +
862A GLY 5.3 1.6 + - - -
948A PRO* 3.2 29.1 - - + +
949A HIS* 6.1 0.4 - - - +
1021A CYS* 1.3 86.5 - - - +
1023A LYS* 1.3 96.5 + - - +
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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