Contacts of the strand formed by residues 914 - 921 (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 CYS 914 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697D THR* 4.7 8.1 - - + -
699D ARG* 5.7 6.5 - - - +
717D TRP* 3.6 32.5 - - - -
719D GLN* 3.4 31.4 - - - +
900D LEU* 3.8 3.8 - - - -
901D GLY 2.9 30.4 + - - +
912D ALA 3.7 0.9 + - - -
913D ALA* 1.3 77.3 - - - +
915D PHE* 1.3 61.4 + - - +
916D ASP* 5.5 0.2 - - + -
918D TRP* 3.1 23.4 + - + -
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Residues in contact with PHE 915 (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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659D ASP* 4.6 13.5 - - - -
660D GLY 5.0 0.9 - - - -
693D GLN* 6.4 0.2 - - + -
695D TRP* 3.1 57.1 - + + +
719D GLN* 2.8 32.3 + - - +
721D ARG* 6.0 0.2 - - - -
898D LEU* 3.8 32.8 - - + -
899D GLY* 3.2 26.0 - - - -
900D LEU* 3.6 14.8 - - + +
914D CYS* 1.3 70.5 - - - +
916D ASP* 1.3 70.0 + - - +
940D GLY 3.5 20.2 - - - -
942D ARG* 3.9 20.9 - - + -
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Residues in contact with ASP 916 (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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655D MET* 6.1 0.5 - - - +
657D ALA* 4.8 10.5 - - - +
660D GLY* 3.6 24.7 - - - +
697D THR* 5.0 6.8 + - - -
719D GLN* 5.0 1.1 + - - +
898D LEU* 3.4 10.1 - - - -
899D GLY 3.0 29.1 + - - +
914D CYS* 3.5 1.7 + - + -
915D PHE* 1.3 85.0 - - - +
917D ARG* 1.3 76.6 + - - +
918D TRP* 3.4 30.6 - - + +
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Residues in contact with ARG 917 (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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659D ASP 4.9 5.5 + - - -
660D GLY* 4.2 11.6 - - - +
896D ASN* 2.8 41.7 + - - +
897D TRP 3.4 5.2 - - - -
898D LEU* 4.0 36.2 - - + +
916D ASP* 1.3 88.8 + - - +
918D TRP* 1.4 66.6 + - - +
919D ASP* 5.8 0.7 - - + -
943D GLU* 2.8 40.6 + - - -
945D ASN* 3.5 2.0 - - - +
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Residues in contact with TRP 918 (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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699D ARG* 4.7 16.4 - - - -
896D ASN* 3.2 5.7 - - - -
897D TRP* 2.8 75.5 + + + +
899D GLY 3.1 23.5 + - - -
901D GLY* 3.3 23.1 - - - +
902D PRO* 3.7 32.3 - - + -
914D CYS* 3.1 23.0 + - + -
916D ASP* 3.4 31.9 + - + +
917D ARG* 1.4 79.1 - - - +
919D ASP* 1.3 65.5 + - - +
920D LEU* 5.3 0.7 - - + -
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Residues in contact with ASP 919 (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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894D ARG* 2.7 59.2 + - - +
895D VAL 3.3 8.5 - - - -
896D ASN* 3.0 29.0 + - - +
917D ARG* 5.8 0.9 - - + -
918D TRP* 1.3 79.6 - - - +
920D LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 920 (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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894D ARG* 3.4 7.8 - - - +
895D VAL* 2.9 29.0 + - - +
897D TRP* 3.8 16.6 - - + -
902D PRO* 3.8 35.4 - - + +
918D TRP* 6.0 0.2 - - + -
919D ASP* 1.3 85.9 - - - +
921D PRO* 1.3 87.6 - - + +
924D ASP* 3.9 21.3 - - + +
925D MET* 3.9 16.8 - - - -
938D ARG* 4.0 3.8 - - - +
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Residues in contact with PRO 921 (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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893D GLU 3.4 11.4 - - - +
894D ARG* 3.6 25.1 - - - +
920D LEU* 1.3 99.8 - - + +
922D LEU* 1.3 66.4 + - - +
923D SER* 4.4 10.3 - - - +
924D ASP* 3.0 41.0 + - - +
925D MET* 3.8 2.4 + - - +
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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