Contacts of the helix formed by residues 109 - 114 (chain J) in PDB entry 7C97
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 109 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56I ASN* 5.3 9.2 + - - +
105J ARG* 2.8 32.5 + - - +
108J LYS* 1.3 84.3 - - - +
110J TRP* 1.3 76.6 + - + +
112J THR* 4.9 0.2 - - - -
113J LEU* 3.0 28.7 + - - +
135J GLU* 5.2 4.4 - - - +
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Residues in contact with TRP 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J ARG* 5.9 3.3 - - - +
106J ILE* 3.4 23.4 + - + +
109J ASP* 1.3 93.3 + - + +
111J TYR* 1.3 72.2 + - + +
113J LEU* 3.0 22.4 + - + +
114J MET* 3.0 17.0 + - + +
132J LEU* 3.9 17.2 - - + +
135J GLU* 3.0 38.6 + - + -
136J LEU* 3.4 39.3 - - + -
139J ILE* 4.5 18.4 - - + -
161J LEU* 4.6 10.5 - - + -
164J LEU* 3.4 33.0 - - + -
165J LEU* 6.2 2.7 - - + -
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Residues in contact with TYR 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ILE* 3.0 44.3 - - + +
21J TYR* 4.0 18.8 - + + +
24J GLN* 3.2 31.3 + - - -
106J ILE* 3.2 39.3 + - + +
107J GLU* 3.0 28.7 - - - +
109J ASP 3.6 0.2 - - - -
110J TRP* 1.3 80.6 - - + +
112J THR* 1.3 63.1 + - - +
114J MET* 3.1 30.3 + - + +
115J ASN* 3.7 4.3 + - - -
160J TYR* 2.5 28.2 + - + -
164J LEU* 4.5 8.1 - - + -
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Residues in contact with THR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 5.7 0.9 + - - -
107J GLU 4.1 7.8 + - - -
108J LYS* 4.0 17.9 + - - -
109J ASP 4.3 1.0 + - - -
110J TRP 3.4 0.2 - - - -
111J TYR* 1.3 74.6 - - - +
113J LEU* 1.3 65.4 + - - +
114J MET 3.2 0.2 - - - -
115J ASN* 3.1 39.9 + - + +
116J THR* 4.5 1.2 + - - -
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Residues in contact with LEU 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J ASP 3.0 24.7 + - - +
110J TRP* 3.0 10.7 + - + +
112J THR* 1.3 79.1 - - - +
114J MET* 1.3 55.7 + - - +
115J ASN 3.1 4.2 + - - -
116J THR* 3.7 9.4 + - - +
117J ILE* 3.8 1.6 - - + +
128J ALA* 3.5 38.4 - - + +
131J GLN* 5.4 4.7 - - + +
132J LEU* 3.3 49.4 - - + +
135J GLU* 4.7 7.9 - - - +
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Residues in contact with MET 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ILE* 4.8 18.8 - - + -
110J TRP* 3.0 14.3 + - + +
111J TYR* 3.1 22.6 + - + +
113J LEU* 1.3 74.8 - - + +
115J ASN* 1.3 65.0 + - - +
116J THR 3.5 0.2 - - - -
117J ILE* 3.5 20.3 + - + +
118J ILE* 3.4 31.8 + - + +
132J LEU* 5.6 9.9 - - + -
164J LEU* 3.4 34.3 - - + -
167J ARG* 5.5 7.9 - - + -
171J LEU* 4.9 16.6 - - + -
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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