Contacts of the strand formed by residues 976 - 980 (chain B) in PDB entry 1ATZ
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 THR 976 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932B LEU* 4.1 12.6 - - + -
970B LEU* 4.0 12.3 - - + -
971B GLN 3.3 11.2 - - - +
972B TYR* 3.4 5.2 - - - +
975B ILE* 1.3 78.4 - - - +
977B THR* 1.3 65.1 + - - +
1006B GLN* 5.0 0.3 + - - +
1009B ASP* 4.1 8.0 + - - -
1010B ALA* 3.2 30.3 + - - +
1013B PHE* 3.5 54.4 - - + -
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Residues in contact with THR 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970B LEU* 3.1 8.4 - - - +
971B GLN* 2.9 51.7 + - - +
975B ILE* 3.7 25.4 - - + +
976B THR* 1.3 79.8 - - - +
978B ILE* 1.3 64.6 + - - +
979B ASP* 3.4 12.1 + - - +
1001B GLU* 3.7 17.4 + - + +
1013B PHE* 5.2 0.4 - - - -
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Residues in contact with ILE 978 (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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970B LEU* 3.8 23.6 - - + -
977B THR* 1.3 71.2 - - - +
979B ASP* 1.3 63.0 + - - +
980B VAL 3.9 0.7 - - - -
981B PRO* 3.6 39.2 - - + +
1013B PHE* 3.5 35.6 - - + -
1017B TYR* 3.6 32.1 - - + +
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Residues in contact with ASP 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969B VAL 2.8 11.1 + - - +
971B GLN* 2.9 39.8 + - - +
977B THR* 3.4 9.9 + - - +
978B ILE* 1.3 77.0 - - - +
980B VAL* 1.3 65.8 + - - +
981B PRO* 3.9 5.8 - - - +
994B LEU* 4.9 7.4 - - - +
997B VAL* 6.1 0.5 - - - +
998B MET* 3.5 35.8 - - + +
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Residues in contact with VAL 980 (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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955B ILE* 6.2 0.2 - - + -
967B VAL 4.3 7.4 - - - +
968B SER* 2.9 21.7 + - - -
969B VAL* 3.0 37.1 + - + +
978B ILE* 3.9 2.0 - - - -
979B ASP* 1.3 86.9 - - + +
981B PRO* 1.3 63.0 - - - +
984B VAL* 4.0 14.6 - - + -
991B LEU* 3.8 30.5 - - + +
994B LEU* 3.9 33.0 - - + +
995B VAL* 4.5 7.2 - - + +
998B MET* 4.8 0.2 - - - -
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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
------------------------------------------------------------
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