Contacts of the strand formed by residues 1013 - 1022 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721C ARG* 5.7 5.1 - - - +
724C GLU* 5.2 7.7 + - - -
942C ARG* 3.6 37.5 - - - +
954C ASP* 2.8 35.8 + - - +
870D VAL 3.3 7.6 - - - +
871D GLU* 4.2 21.9 + - + -
1011D ALA* 2.9 25.1 + - - +
1012D GLY* 1.3 87.8 - - - +
1014D TYR* 1.3 68.4 + - - +
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Residues in contact with TYR1014 (chain D).
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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868D VAL 3.8 0.5 - - - +
869D ASP* 3.3 5.0 - - - +
870D VAL* 2.8 36.2 + - + +
872D VAL* 4.4 7.0 - - + -
882D ILE* 3.2 34.8 - - + -
989D PHE* 3.6 51.1 - + + -
1008D GLN 4.3 0.7 + - - -
1009D LEU* 3.0 35.0 - - + +
1010D SER 3.1 0.7 + - - -
1011D ALA* 2.9 44.1 + - + +
1012D GLY 3.9 8.1 - - - -
1013D ARG* 1.3 79.9 - - - +
1015D HIS* 1.3 61.7 + - - +
1016D TYR* 5.3 0.8 - - - -
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Residues in contact with HIS1015 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869C ASP* 3.6 2.2 + - - -
1015C HIS* 3.4 53.2 + + + -
867D THR* 3.5 29.6 - - + -
868D VAL 3.3 5.8 + - - -
869D ASP* 2.6 26.9 + - - +
989D PHE* 3.2 19.6 - - - -
1014D TYR* 1.3 75.7 - - - +
1016D TYR* 1.3 71.7 + - - +
1017D GLN* 2.7 29.8 + - + +
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Residues in contact with TYR1016 (chain D).
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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782D ASP* 4.7 0.9 + - - -
867D THR* 3.8 0.2 - - - -
868D VAL* 2.7 74.0 + - + +
870D VAL* 5.1 0.8 - - + +
882D ILE* 3.9 24.4 - - + +
883D GLY* 3.3 19.7 + - - -
884D LEU* 3.3 29.6 - - + +
954D ASP 5.3 6.1 - - - +
955D PHE* 5.9 2.2 - - + -
986D ILE 4.9 2.5 - - - -
987D ASP 4.9 0.7 - - - -
988D GLY* 3.5 31.0 - - - -
989D PHE* 4.1 9.4 - + + -
1014D TYR 5.3 0.9 - - - -
1015D HIS* 1.3 88.4 - - - +
1017D GLN* 1.3 62.5 + - - +
1018D LEU* 4.3 26.0 - - + -
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Residues in contact with GLN1017 (chain D).
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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869C ASP* 3.7 18.6 + - - +
866D ILE 3.2 13.0 - - - +
867D THR* 4.0 15.8 + - - +
953D GLY* 3.8 17.7 - - - -
954D ASP 4.4 3.1 + - - -
955D PHE* 6.1 0.2 - - - +
1015D HIS* 2.7 29.0 + - + +
1016D TYR* 1.3 79.7 - - - +
1018D LEU* 1.3 69.0 + - - +
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Residues in contact with LEU1018 (chain D).
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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864D MET 3.8 0.3 - - - +
865D ALA* 3.5 1.9 - - - +
866D ILE* 2.6 51.7 + - + +
868D VAL* 5.9 0.2 - - + -
884D LEU* 4.0 27.6 - - + -
951D TRP* 4.7 10.5 - - + -
952D ARG 3.3 8.5 - - - +
955D PHE* 3.3 42.8 - - + -
986D ILE* 4.1 26.5 - - + -
1016D TYR* 4.3 16.2 - - + -
1017D GLN* 1.3 82.2 - - - +
1019D VAL* 1.4 63.1 + - - +
1020D TRP 4.2 0.2 - - - -
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Residues in contact with VAL1019 (chain D).
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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863D GLN* 3.8 26.7 - - + +
864D MET 3.4 6.5 - - - +
865D ALA* 4.3 15.3 - - + -
950D GLN 3.6 1.6 - - - +
951D TRP* 3.2 5.8 - - - -
952D ARG* 2.9 73.5 + - + +
1018D LEU* 1.4 75.8 - - - +
1020D TRP* 1.3 64.3 + - - +
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Residues in contact with TRP1020 (chain D).
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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756D TRP* 6.0 0.2 - - - -
765D LEU* 4.8 2.2 - - + -
768D MET* 3.2 30.5 - - + +
776D LEU* 4.0 7.6 - - + -
780D LEU* 4.1 33.0 - - + -
862D GLY 4.3 0.9 - - - +
863D GLN* 3.6 0.2 - - - -
864D MET* 2.8 69.9 + - + +
866D ILE* 4.8 8.5 - - + +
886D CYS* 4.1 6.1 - - - -
888D LEU* 4.0 24.0 - - + -
949D HIS* 3.2 26.9 + + - -
950D GLN 3.6 7.6 - - - -
951D TRP* 3.2 40.4 - + + +
984D LEU* 5.7 0.4 - - + -
1018D LEU* 4.2 0.4 - - + -
1019D VAL* 1.3 72.1 - - - +
1021D CYS* 1.3 83.4 + - - +
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Residues in contact with CYS1021 (chain D).
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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862D GLY 4.5 5.6 - - - +
863D GLN* 4.0 35.0 - - + +
949D HIS* 3.8 1.6 + - - -
950D GLN* 2.9 45.8 + - - -
952D ARG* 3.5 26.9 - - - +
1019D VAL* 4.0 0.4 - - + -
1020D TRP* 1.3 87.8 - - - +
1022D GLN* 1.3 62.0 + - - +
1023D LYS 4.0 12.8 - - - -
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Residues in contact with GLN1022 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D ASN* 5.6 0.7 + - - -
754D LYS* 3.7 34.6 + - + +
770D ILE* 3.9 39.5 - - + +
862D GLY 5.2 2.0 + - - -
948D PRO* 3.2 20.7 + - - +
949D HIS* 4.7 2.5 - - - +
1021D CYS* 1.3 77.3 - - - +
1023D LYS* 1.3 106.7 + - + +
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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