Contacts of the strand formed by residues 1013 - 1022 (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 ARG1013 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721A ARG* 5.8 4.8 - - - +
724A GLU* 5.1 7.9 + - - -
726A LEU* 6.3 0.6 - - - +
942A ARG* 3.7 38.1 - - - +
954A ASP* 2.9 39.1 + - - +
870B VAL 3.3 8.5 - - - +
871B GLU* 4.2 22.6 + - + -
1011B ALA* 3.1 24.2 + - - +
1012B GLY* 1.3 89.1 + - - +
1014B TYR* 1.3 66.2 + - - +
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Residues in contact with TYR1014 (chain B).
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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868B VAL 3.8 0.3 - - - +
869B ASP* 3.3 4.8 - - - +
870B VAL* 2.8 38.5 + - + +
872B VAL* 4.4 9.6 - - + -
882B ILE* 3.1 36.1 - - + -
989B PHE* 3.5 50.7 - + + -
1008B GLN 4.5 0.7 + - - -
1009B LEU* 3.0 33.9 - - + +
1010B SER 3.2 0.3 + - - -
1011B ALA* 2.9 42.4 + - + +
1012B GLY 3.9 8.5 - - - -
1013B ARG* 1.3 78.6 - - - +
1015B HIS* 1.3 61.1 + - - +
1016B TYR* 5.3 1.3 - - + -
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Residues in contact with HIS1015 (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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869A ASP* 3.4 5.8 + - - -
1015A HIS* 3.1 52.6 - + + -
867B THR* 3.7 24.5 - - + -
868B VAL 3.3 5.1 + - - -
869B ASP* 2.6 27.3 + - - +
989B PHE* 3.2 20.6 - - - -
1014B TYR* 1.3 76.3 - - - +
1016B TYR* 1.3 70.2 + - - +
1017B GLN* 2.7 33.3 + - + +
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Residues in contact with TYR1016 (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* 4.6 0.9 + - - -
866B ILE 4.1 0.2 - - - +
867B THR* 3.8 0.3 - - - -
868B VAL* 2.8 70.4 + - + +
870B VAL* 4.9 0.8 - - + +
882B ILE* 4.0 23.1 - - + +
883B GLY* 3.3 31.2 + - - -
884B LEU* 3.4 25.2 - - + +
954B ASP 5.4 5.8 - - - +
955B PHE* 5.9 0.9 - - + -
986B ILE 4.8 2.7 - - - -
987B ASP 4.9 0.4 - - - -
988B GLY* 3.5 33.0 - - - -
989B PHE* 4.0 10.5 - + + -
1014B TYR 5.3 1.1 - - - -
1015B HIS* 1.3 85.0 + - - +
1017B GLN* 1.3 66.7 + - - +
1018B LEU* 4.6 19.7 - - + -
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Residues in contact with GLN1017 (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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853A ARG* 6.4 0.2 - - - +
869A ASP* 3.5 20.0 - - - +
866B ILE 3.2 11.2 - - - +
867B THR* 4.1 13.1 + - - +
953B GLY* 3.7 17.8 - - - -
954B ASP 4.4 3.3 + - - -
1015B HIS* 2.7 28.7 + - + +
1016B TYR* 1.3 81.0 - - - +
1018B LEU* 1.3 67.4 + - - +
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Residues in contact with LEU1018 (chain B).
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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864B MET 3.8 0.2 - - - +
865B ALA* 3.5 1.9 - - - +
866B ILE* 2.6 54.8 + - + +
868B VAL* 6.3 0.2 - - + -
884B LEU* 3.9 21.5 - - + -
951B TRP* 5.2 9.9 - - + -
952B ARG 3.2 6.1 - - - +
955B PHE* 3.4 44.0 - - + -
986B ILE* 3.9 33.7 - - + -
1016B TYR* 4.6 15.0 - - + -
1017B GLN* 1.3 79.8 - - - +
1019B VAL* 1.3 65.0 + - - +
1020B TRP* 6.3 0.2 - - + -
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Residues in contact with VAL1019 (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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863B GLN* 3.8 30.7 - - + +
864B MET 3.4 8.3 - - - +
865B ALA* 4.2 16.2 - - + -
950B GLN 3.7 0.9 - - - +
951B TRP* 3.2 5.2 - - - -
952B ARG* 2.8 73.2 + - + +
1018B LEU* 1.3 81.6 - - - +
1020B TRP* 1.3 62.3 + - - +
1021B CYS* 5.3 0.2 - - - -
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Residues in contact with TRP1020 (chain B).
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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756B TRP* 5.7 1.1 + - - -
765B LEU* 4.7 8.5 - - + -
768B MET* 5.8 15.6 - - + +
775B GLN* 5.8 1.6 - - + -
776B LEU* 4.2 16.2 - - + -
780B LEU* 4.1 31.9 - - + -
862B GLY 4.3 1.0 - - - +
864B MET* 2.8 63.5 + - + +
866B ILE* 4.8 7.5 - - + +
886B CYS* 4.2 5.8 - - - -
888B LEU* 4.1 21.8 - - + -
949B HIS* 3.0 36.2 + + + +
950B GLN 3.4 8.1 - - - -
951B TRP* 3.1 38.8 - + + -
984B LEU* 5.7 0.2 - - + -
1018B LEU* 4.2 1.0 - - + +
1019B VAL* 1.3 70.1 - - - +
1021B CYS* 1.3 78.0 + - - +
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Residues in contact with CYS1021 (chain B).
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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768B MET* 6.4 1.1 - - - -
861B SER 5.9 0.2 - - - +
862B GLY 4.4 5.6 - - - +
863B GLN* 3.4 29.2 - - + +
949B HIS* 3.8 1.8 + - - -
950B GLN* 2.8 59.7 + - - +
952B ARG* 3.8 15.5 - - - -
1019B VAL* 4.6 0.9 - - + -
1020B TRP* 1.3 87.6 + - - +
1022B GLN* 1.3 69.2 + - - +
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Residues in contact with GLN1022 (chain B).
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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753B ASN* 5.1 1.0 - - - +
754B LYS* 3.0 48.5 + - + +
768B MET* 5.7 4.2 - - + +
770B ILE* 3.9 33.0 - - + +
862B GLY 5.0 2.4 + - - -
948B PRO* 3.4 23.8 - - + +
949B HIS* 4.8 1.8 - - - +
1021B CYS* 1.3 85.1 - - - +
1023B LYS* 1.3 88.1 + - - +
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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