Contacts of the strand formed by residues 973 - 979 (chain A) in PDB entry 3NYX
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 SER 973 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910A LYS* 5.3 5.8 - - - -
932A LEU 3.2 19.3 - - - -
933A LYS* 4.4 4.3 - - - -
934A ALA* 4.1 2.7 - - - +
941A ARG* 4.5 1.3 - - - +
967A GLU* 3.8 6.1 - - - +
968A ASP* 2.8 38.9 + - - +
971A GLU* 3.2 22.2 + - - -
972A LYS* 1.3 76.4 - - - +
974A LEU* 1.3 58.5 + - - +
975A GLN* 3.7 17.2 + - - -
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Residues in contact with LEU 974 (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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930A LYS 3.4 2.9 - - - +
931A ALA* 3.8 1.4 - - - -
932A LEU* 2.8 45.6 + - + +
934A ALA* 4.4 2.5 - - + -
941A ARG* 4.2 13.9 - - + +
944A TRP* 3.7 32.5 - - + -
945A LYS* 4.1 25.8 - - + +
948A ILE* 4.1 17.0 - - + -
965A CYS* 4.0 17.5 - - - -
966A CYS 3.5 11.9 - - - +
967A GLU* 4.0 24.7 - - + +
973A SER* 1.3 75.4 - - - +
975A GLN* 1.3 63.1 + - - +
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Residues in contact with GLN 975 (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* 6.3 2.9 - - + -
897A LEU* 6.5 0.7 - - + -
914A TYR* 5.5 2.1 + - - -
929A VAL* 3.4 26.2 - - + +
930A LYS 3.6 0.2 - - - -
931A ALA* 3.7 28.7 - - - +
964A GLY 3.8 0.3 - - - +
965A CYS* 3.4 3.8 - - - -
966A CYS* 2.5 62.3 + - - +
967A GLU 5.5 0.4 - - - -
968A ASP* 4.7 17.3 + - + +
971A GLU* 5.2 1.4 + - - -
973A SER* 3.7 20.2 + - - -
974A LEU* 1.3 74.7 + - - +
976A LEU* 1.3 59.7 + - - +
977A VAL* 4.0 2.0 + - + -
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Residues in contact with LEU 976 (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 TZ1 3.5 52.5 - - + -
928A ALA 3.7 1.2 - - - +
929A VAL* 3.1 4.7 - - - -
930A LYS* 2.7 50.2 + - + +
932A LEU* 3.9 16.2 - - + -
948A ILE* 4.0 23.8 - - + -
962A TYR* 3.6 28.3 - - + -
964A GLY 3.6 11.2 - - - +
965A CYS* 4.5 4.9 - - + +
974A LEU 3.9 0.4 + - - -
975A GLN* 1.3 72.3 - - - +
977A VAL* 1.3 67.1 + - - +
978A MET* 4.9 3.1 - - - +
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Residues in contact with VAL 977 (chain A).
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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892A PHE* 4.2 42.4 - - + -
897A LEU* 5.3 5.8 - - + -
927A VAL* 3.9 34.8 - - + -
928A ALA 3.5 4.3 - - - +
929A VAL* 4.4 13.5 - - + +
962A TYR* 3.7 1.6 - - - -
963A LYS* 2.7 32.0 + - + -
964A GLY 2.8 24.1 + - - +
966A CYS* 4.5 7.0 - - - -
975A GLN* 4.4 8.7 - - + +
976A LEU* 1.3 77.8 - - - +
978A MET* 1.3 59.5 + - - +
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Residues in contact with MET 978 (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 TZ1 3.0 48.2 - - - +
911A VAL* 5.2 1.6 - - - -
927A VAL* 3.5 9.9 - - - +
928A ALA* 2.9 42.9 + - + +
930A LYS* 5.0 7.2 - - - -
960A ILE* 3.4 14.6 - - + -
961A LYS 3.4 13.0 - - - +
962A TYR* 2.8 43.1 - - + -
963A LYS* 4.0 8.3 - - - +
976A LEU* 4.9 7.9 - - - +
977A VAL* 1.3 75.1 - - - +
979A GLU* 1.3 76.0 + - - +
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Residues in contact with GLU 979 (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 TZ1 3.2 20.6 - - - -
926A MET 5.1 0.7 - - - -
927A VAL* 5.1 0.9 - - - +
928A ALA* 4.0 0.6 - - - +
960A ILE* 3.8 8.5 - - + +
961A LYS* 3.0 60.6 + - + +
963A LYS* 4.2 17.8 - - - +
978A MET* 1.3 79.4 - - - +
980A TYR* 1.3 63.2 + - - +
981A VAL* 4.0 14.7 - - + +
1038A LYS* 3.7 28.1 + - - +
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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