Contacts of the strand formed by residues 864 - 872 (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 MET 864 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756B TRP* 3.8 35.0 - - + +
758B PHE* 4.2 11.0 - - - -
765B LEU* 3.9 17.3 - - + -
768B MET* 5.9 1.1 - - + -
856B TYR* 4.0 23.8 - - + -
857B ARG 3.6 4.3 - - - +
858B ILE* 3.9 16.6 - - + -
862B GLY 3.7 0.6 + - - -
863B GLN* 1.3 73.6 - - - +
865B ALA* 1.3 60.8 + - - +
866B ILE* 3.8 18.9 + - + +
1019B VAL* 3.4 3.2 - - - -
1020B TRP* 2.8 78.2 + - + +
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Residues in contact with ALA 865 (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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855B THR* 3.4 2.6 + - - +
856B TYR* 3.2 4.7 - - - -
857B ARG* 2.8 53.9 + - + +
863B GLN* 3.9 2.3 + - + -
864B MET* 1.3 70.3 - - - +
866B ILE* 1.3 60.7 + - - +
867B THR* 4.0 4.7 + - - +
1018B LEU 3.5 4.3 - - - +
1019B VAL* 4.2 16.8 - - + -
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Residues in contact with ILE 866 (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* 3.9 26.7 - - + -
854B LYS* 4.6 2.5 - - + -
855B THR 3.4 5.8 - - - +
856B TYR* 3.9 29.8 - - + -
864B MET* 4.0 27.8 - - + +
865B ALA* 1.3 73.6 - - - +
867B THR* 1.3 67.8 + - - +
868B VAL* 4.0 21.2 - - + +
884B LEU* 4.5 12.3 - - + -
951B TRP* 6.3 0.2 - - + -
1017B GLN* 3.2 5.5 - - - +
1018B LEU* 2.6 57.6 + - + +
1020B TRP* 4.8 9.2 - - + +
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Residues in contact with THR 867 (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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1015A HIS* 5.7 0.2 - - + -
853B ARG 4.5 0.2 - - - -
854B LYS* 3.1 29.1 - - - +
855B THR* 2.9 27.0 + - + +
865B ALA* 4.0 4.5 + - - +
866B ILE* 1.3 76.1 + - - +
868B VAL* 1.3 63.5 + - - +
869B ASP* 3.8 10.5 - - - +
1015B HIS* 3.7 26.2 - - + -
1016B TYR 3.8 2.7 - - - -
1017B GLN* 4.1 10.6 + - + +
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Residues in contact with VAL 868 (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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782B ASP* 4.2 4.0 - - - +
852B SER* 4.0 13.0 - - - +
853B ARG 3.5 2.9 - - - +
854B LYS* 4.1 11.7 - - + -
866B ILE* 4.0 20.0 - - + +
867B THR* 1.3 79.1 - - - +
869B ASP* 1.3 66.8 - - - +
870B VAL* 3.8 18.6 - - + -
884B LEU* 4.5 5.6 - - + -
1014B TYR 3.8 0.5 - - - +
1015B HIS* 3.3 5.0 + - - -
1016B TYR* 2.8 85.7 + - + +
1018B LEU* 6.1 0.4 - - + -
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Residues in contact with ASP 869 (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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1015A HIS* 3.5 13.9 + - - -
851B ILE 3.8 0.9 - - - +
852B SER* 3.7 0.3 - - - -
853B ARG* 2.7 52.8 + - + +
867B THR* 3.8 13.3 - - - +
868B VAL* 1.3 71.2 - - - +
870B VAL* 1.3 61.2 + - - +
871B GLU* 5.7 0.4 - - - +
1014B TYR 3.3 3.1 - - - +
1015B HIS* 2.6 41.9 + - - +
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Residues in contact with VAL 870 (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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782B ASP* 4.4 2.0 - - - +
784B PHE* 4.0 23.8 - - + -
850B PHE* 4.8 0.9 - - + -
851B ILE 3.1 9.2 - - - +
852B SER* 4.1 11.4 - - - +
868B VAL* 3.8 21.8 - - + -
869B ASP* 1.3 78.6 - - - +
871B GLU* 1.3 76.5 + - - +
872B VAL* 3.9 15.3 - - + -
882B ILE* 4.0 25.6 - - + -
1012B GLY 3.8 0.2 - - - +
1013B ARG* 3.3 6.1 - - - +
1014B TYR* 2.8 39.8 + - + +
1016B TYR* 4.9 0.7 - - + +
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Residues in contact with GLU 871 (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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726A LEU* 3.5 28.4 - - + +
727A SER 4.9 1.6 + - - +
942A ARG* 5.8 1.4 + - - -
850B PHE* 3.2 5.2 - - - -
851B ILE* 2.8 47.2 + - + +
853B ARG* 2.6 40.9 + - - +
869B ASP 5.7 0.7 - - - +
870B VAL* 1.3 79.0 - - - +
872B VAL* 1.3 61.4 + - - +
873B ALA 4.2 0.2 - - - -
1012B GLY 3.4 6.1 - - - +
1013B ARG* 4.2 21.4 + - + +
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Residues in contact with VAL 872 (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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724A GLU* 4.0 2.8 - - - +
726A LEU* 4.3 2.6 - - - +
849B LEU 3.6 3.1 - - - -
850B PHE* 4.0 13.5 - - + -
870B VAL* 3.9 17.0 - - + -
871B GLU* 1.3 77.5 - - - +
873B ALA* 1.3 78.9 + - - +
874B SER* 3.2 3.5 + - - -
876B THR* 3.8 16.6 - - + +
878B HIS* 5.5 2.9 - - + -
879B PRO* 3.9 22.2 - - + -
882B ILE* 4.1 19.3 - - + -
1009B LEU 5.2 3.1 - - - +
1012B GLY* 2.9 32.3 + - - +
1014B TYR* 4.4 7.0 - - + -
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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