Contacts of the strand formed by residues 909 - 916 (chain A) in PDB entry 3NZ0
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 GLY 909 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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905A GLU* 3.9 0.5 - - - -
906A GLY* 2.7 34.3 + - - +
907A HIS 3.6 0.4 - - - -
908A PHE* 1.3 82.3 - - - +
910A LYS* 1.3 58.5 + - - -
911A VAL 4.1 0.3 + - - -
930A LYS* 3.7 21.3 - - - +
931A ALA 2.9 17.0 - - - -
932A LEU* 4.3 0.2 - - - -
933A LYS* 4.1 6.5 - - - -
944A TRP* 4.7 1.6 - - - -
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Residues in contact with LYS 910 (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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899A LYS* 3.8 11.6 - - - +
902A ASP* 3.0 39.6 + - + +
904A GLY 3.5 9.4 - - - +
905A GLU* 3.5 30.1 - - + +
909A GLY* 1.3 73.6 - - - -
911A VAL* 1.3 70.9 + - - +
912A SER* 4.0 6.6 + - - +
929A VAL 3.7 1.9 - - - +
930A LYS* 3.4 1.7 - - - -
931A ALA* 3.0 31.4 + - + +
933A LYS* 4.3 8.1 - - + +
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Residues in contact with VAL 911 (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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1A IZA 3.7 52.7 - - + +
902A ASP* 3.7 0.7 - - - -
903A LEU* 2.7 35.7 + - + -
904A GLY 2.7 26.0 + - - +
910A LYS* 1.3 74.8 - - - +
912A SER* 1.3 60.1 + - - +
928A ALA* 3.9 22.2 - - + -
929A VAL 3.5 7.4 - - - +
930A LYS* 3.8 27.4 - - + +
978A MET* 4.4 4.7 - - + -
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Residues in contact with SER 912 (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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899A LYS* 3.7 11.3 + - - -
901A ARG 3.3 12.8 - - - -
902A ASP* 2.6 23.1 + - - -
903A LEU* 3.7 8.1 - - - +
910A LYS* 4.1 9.7 + - - +
911A VAL* 1.3 74.7 + - - +
913A LEU* 1.3 61.1 + - - +
914A TYR* 3.8 22.5 - - - -
928A ALA* 3.5 4.3 - - - -
929A VAL 2.9 32.8 + - - +
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Residues in contact with LEU 913 (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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899A LYS* 3.7 1.6 - - - +
900A ILE* 2.8 55.3 + - + -
901A ARG* 2.6 32.3 + - + +
903A LEU* 3.7 15.9 - - + +
912A SER* 1.3 71.0 - - - +
914A TYR* 1.3 65.3 + - - +
926A MET* 3.7 22.9 - - + -
927A VAL 3.7 11.2 - - - +
980A TYR* 3.7 49.4 - - + +
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Residues in contact with TYR 914 (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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894A LYS* 5.5 3.2 + - - -
897A LEU* 3.6 29.2 - - + -
898A LYS 3.3 8.7 - - - +
899A LYS* 3.4 49.7 + - + +
900A ILE* 4.3 0.2 - - - -
912A SER* 3.8 21.7 - - - -
913A LEU* 1.3 77.4 - - - +
915A CYS* 1.3 62.1 + - - +
926A MET* 3.4 12.2 - - - +
927A VAL* 2.9 46.1 + - + +
929A VAL* 3.5 36.1 - - + -
975A GLN* 3.9 17.5 + - - -
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Residues in contact with CYS 915 (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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896A TYR 3.2 4.3 - - - +
898A LYS* 2.9 42.0 + - + +
900A ILE* 3.7 7.9 - - + +
914A TYR* 1.3 72.8 - - - +
916A TYR* 1.3 59.9 + - - +
917A ASP* 3.3 14.6 + - - -
922A GLY* 4.5 11.0 - - - -
924A GLY* 3.5 40.4 - - - -
925A GLU 3.6 3.1 - - - -
926A MET* 3.7 17.9 - - + -
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Residues in contact with TYR 916 (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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891A VAL 4.0 4.4 + - - -
892A PHE* 3.6 36.0 - + + -
893A HIS* 3.0 42.3 + - - -
896A TYR* 3.6 19.1 - + + -
897A LEU* 3.2 36.6 - - + +
914A TYR 3.9 1.6 - - - -
915A CYS* 1.3 67.9 - - - +
917A ASP* 1.3 59.0 + - - +
918A PRO* 3.3 24.4 - - + +
924A GLY* 3.1 19.3 - - - -
925A GLU* 2.8 25.0 + - + +
927A VAL* 4.3 16.5 - - + +
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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