Contacts of the helix formed by residues 924 - 929 (chain A) in PDB entry 6MZL
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 ASP 924 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A TYR* 3.4 39.4 - - + +
907A SER* 4.1 12.1 + - - -
922A LYS 4.3 1.9 + - - +
923A ILE* 1.3 82.8 - - - +
925A ASP* 1.3 66.3 + - - +
926A GLU 3.4 0.4 - - - -
927A VAL* 3.3 17.6 + - + +
928A ARG* 3.1 22.1 + - - +
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Residues in contact with ASP 925 (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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903A TYR* 5.0 0.8 + - - -
923A ILE 4.7 1.9 - - - +
924A ASP* 1.3 74.3 - - - +
926A GLU* 1.3 62.3 + - - +
928A ARG* 3.3 29.8 + - - +
929A THR* 3.5 11.8 - - - +
953A VAL* 3.9 34.4 - - + +
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Residues in contact with GLU 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A LEU* 3.9 24.2 - - + +
901A ALA* 5.5 0.9 - - + -
903A TYR* 3.6 22.7 + - + +
924A ASP* 3.4 1.0 - - - +
925A ASP* 1.3 75.4 - - - +
927A VAL* 1.3 61.0 + - - +
929A THR* 2.4 41.7 + - - -
930A ALA* 3.6 2.9 + - - -
149J ARG* 2.4 39.7 + - - +
151J THR* 4.0 35.3 + - + +
152J ALA* 4.1 12.7 + - + +
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Residues in contact with VAL 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A LEU* 4.8 8.5 - - + -
903A TYR* 3.7 28.9 - - + -
907A SER* 3.8 23.1 - - - +
908A PHE* 4.0 17.7 - - + -
923A ILE* 3.7 25.4 - - + -
924A ASP* 3.3 24.0 + - + +
925A ASP 3.3 0.6 - - - -
926A GLU* 1.3 77.0 - - - +
928A ARG* 1.3 54.4 + - - +
930A ALA* 3.3 10.8 + - - +
932A TRP* 4.8 5.4 - - + +
933A ASN* 2.3 33.7 + - - +
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Residues in contact with ARG 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A LYS 4.8 8.1 - - - +
923A ILE* 3.5 41.1 + - + +
924A ASP 3.1 13.2 + - - +
925A ASP* 3.3 16.5 + - - +
926A GLU 3.2 0.4 - - - -
927A VAL* 1.3 77.9 - - - +
929A THR* 1.3 58.3 + - + +
930A ALA 3.2 1.5 + - - -
933A ASN* 3.5 20.8 - - - +
934A THR* 3.6 10.6 - - - +
949A GLU* 5.5 2.9 + - - -
953A VAL* 4.2 21.8 - - + -
954A ALA* 4.3 4.8 - - + +
965A TYR 4.6 3.3 - - - +
966A VAL* 3.4 41.8 - - + +
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Residues in contact with THR 929 (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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925A ASP 3.5 14.8 - - - +
926A GLU* 2.4 41.6 + - - -
928A ARG* 1.3 73.2 - - - +
930A ALA* 1.3 65.2 + - - +
931A PRO* 3.7 3.3 - - - +
934A THR* 3.9 11.6 - - - +
953A VAL* 4.2 3.8 - - + +
954A ALA* 3.8 28.5 - - - -
149J ARG* 3.3 33.0 + - - +
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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