Contacts of the strand formed by residues 864 - 872 (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 MET 864 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756A TRP* 3.7 24.7 - - + +
758A PHE* 4.3 10.1 - - - -
765A LEU* 4.0 9.4 - - + -
768A MET* 3.9 24.2 - - - -
856A TYR* 3.9 26.9 - - + -
857A ARG 3.5 3.6 - - - +
858A ILE* 3.7 18.4 - - + -
862A GLY 4.0 0.2 + - - -
863A GLN* 1.3 75.5 - - - +
865A ALA* 1.3 60.5 + - - +
866A ILE* 3.7 16.6 + - + +
1018A LEU 3.7 0.2 - - - +
1019A VAL* 3.4 4.3 - - - -
1020A TRP* 2.9 72.5 + - + +
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Residues in contact with ALA 865 (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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855A THR* 3.5 2.4 + - - +
856A TYR* 3.3 3.6 - - - -
857A ARG* 2.9 46.9 + - + +
863A GLN* 4.0 1.6 - - + +
864A MET* 1.3 72.5 - - - +
866A ILE* 1.3 59.5 + - - +
867A THR* 4.1 1.4 + - - +
1017A GLN* 4.3 11.7 - - - +
1018A LEU 3.5 5.6 - - - -
1019A VAL* 3.9 14.8 - - + -
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Residues in contact with ILE 866 (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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780A LEU* 4.2 24.0 - - + -
854A LYS* 4.6 2.2 - - + -
855A THR 3.3 9.2 - - - +
856A TYR* 3.8 30.5 - - + -
864A MET* 4.1 23.1 - - + +
865A ALA* 1.3 77.1 - - - +
867A THR* 1.3 62.3 + - - +
868A VAL* 3.8 22.2 - - + +
884A LEU* 4.6 12.6 - - + -
951A TRP* 6.3 0.7 - - + -
1017A GLN* 3.3 6.1 + - - -
1018A LEU* 2.6 51.4 + - + +
1020A TRP* 4.9 9.4 - - + -
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Residues in contact with THR 867 (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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854A LYS* 3.0 27.5 - - - +
855A THR* 2.9 26.1 + - - -
865A ALA* 4.1 2.5 + - - +
866A ILE* 1.3 71.8 - - - +
868A VAL* 1.3 63.3 + - - +
869A ASP* 4.0 8.2 - - - +
1015A HIS* 3.4 30.5 - - + +
1016A TYR 3.8 3.1 - - - +
1017A GLN* 3.5 17.3 + - + +
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Residues in contact with VAL 868 (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* 4.4 3.4 - - - +
852A SER* 4.0 14.4 - - - +
853A ARG 3.5 2.7 - - - -
854A LYS* 4.0 13.9 - - + -
866A ILE* 3.8 21.5 - - + -
867A THR* 1.3 80.1 - - - +
869A ASP* 1.3 65.7 + - - +
870A VAL* 3.9 16.8 - - + -
884A LEU* 4.7 2.9 - - + -
1014A TYR 3.8 0.7 - - - +
1015A HIS* 3.4 4.2 + - - -
1016A TYR* 2.8 86.4 + - + +
1017A GLN* 5.8 0.2 - - - -
1018A LEU* 5.8 0.4 - - + -
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Residues in contact with ASP 869 (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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851A ILE 3.8 1.0 - - - +
852A SER* 3.7 0.5 - - - -
853A ARG* 2.8 54.9 + - + +
867A THR* 4.0 8.1 - - - +
868A VAL* 1.3 70.2 - - - +
870A VAL* 1.3 63.5 + - - +
871A GLU* 5.9 0.4 - - - -
1014A TYR 3.3 3.6 - - - +
1015A HIS* 2.6 44.4 + - - +
1015B HIS* 3.4 9.0 + - - -
1017B GLN* 3.5 20.8 - - - +
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Residues in contact with VAL 870 (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* 4.8 1.3 - - - +
784A PHE* 3.9 27.8 - - + -
850A PHE* 4.7 0.9 - - + -
851A ILE 3.1 11.7 - - - +
852A SER* 4.2 11.0 - - - +
868A VAL* 3.9 21.5 - - + -
869A ASP* 1.3 78.0 - - - +
871A GLU* 1.3 75.7 + - - +
872A VAL* 4.0 12.6 - - + -
882A ILE* 4.1 24.0 - - + -
1012A GLY 3.9 0.5 - - - +
1013A ARG* 3.3 6.1 - - - +
1014A TYR* 2.8 37.7 + - + +
1016A TYR* 4.8 0.7 - - + +
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Residues in contact with GLU 871 (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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850A PHE* 3.0 8.3 - - - +
851A ILE* 2.8 50.4 + - + +
853A ARG* 2.7 39.7 + - - +
869A ASP 5.6 0.4 - - - +
870A VAL* 1.3 75.4 - - - +
872A VAL* 1.3 61.1 + - - +
873A ALA 4.2 0.4 - - - -
1012A GLY 3.4 5.8 - - - +
1013A ARG* 4.2 22.2 + - + -
726B LEU* 3.3 30.9 - - + +
727B SER 4.9 2.1 + - - +
942B ARG* 5.8 1.0 + - - -
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Residues in contact with VAL 872 (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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849A LEU 3.6 3.1 - - - -
850A PHE* 4.1 14.8 - - + -
870A VAL* 4.0 16.4 - - + -
871A GLU* 1.3 79.5 - - - +
873A ALA* 1.3 76.5 + - - +
874A SER* 3.2 4.4 + - - -
876A THR* 3.9 15.3 - - + +
878A HIS* 5.5 3.8 - - + -
879A PRO* 4.1 18.4 - - + -
882A ILE* 4.1 19.7 - - + -
1009A LEU 5.3 3.4 - - - +
1012A GLY* 2.8 32.9 + - - +
1014A TYR* 4.4 7.0 - - + -
724B GLU* 4.2 3.3 - - - +
726B LEU* 4.2 3.2 - - - +
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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