Contacts of the helix formed by residues 123 - 133 (chain C) in PDB entry 3WBR
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C GLN* 5.2 5.0 + - - -
121C ILE* 3.7 3.4 - - - +
122C ASN* 1.3 89.9 - - + +
124C ARG* 1.3 59.3 + - - +
125C GLU* 3.6 16.6 + - - +
126C GLU* 3.1 25.0 + - - +
127C GLN* 3.0 26.7 + - - +
165G VAL* 3.9 7.2 - - - +
167G PHE* 4.3 6.3 - - - -
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C THR* 1.3 72.0 - - - +
125C GLU* 1.3 64.8 + - - +
127C GLN* 3.3 11.9 + - - +
128C ASP* 2.8 60.9 + - - +
131C ILE* 5.1 5.1 - - - +
165G VAL* 4.3 3.9 - - + +
167G PHE* 3.5 41.1 - - + -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.8 17.3 - - + -
91C GLN* 4.9 7.0 - - - +
123C THR* 3.8 18.2 - - - +
124C ARG* 1.3 85.9 + - - +
126C GLU* 1.3 57.3 + - - +
128C ASP* 3.3 10.8 + - - +
129C PHE* 2.8 29.1 + - - +
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.7 16.0 - - + -
91C GLN* 5.4 1.8 - - - +
95C TYR* 2.4 32.8 + - + +
120C VAL 3.4 7.9 - - - +
121C ILE* 4.0 3.4 - - + -
122C ASN* 2.8 29.7 + - - +
123C THR* 3.1 21.6 + - - +
125C GLU* 1.3 72.8 - - - +
127C GLN* 1.3 66.2 + - - +
129C PHE* 3.2 2.6 + - - +
130C ILE* 2.9 40.0 + - + +
207C LYS* 2.7 29.1 + - - +
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 3.5 19.4 - - + +
123C THR 3.0 6.0 + - - +
124C ARG* 3.4 20.1 - - - +
126C GLU* 1.3 76.8 - - - +
128C ASP* 1.3 62.6 + - - +
130C ILE* 3.2 5.8 + - - +
131C ILE* 3.1 40.4 + - + +
183C ILE* 3.7 22.4 - - - +
191C TRP 4.7 2.4 + - - -
192C GLY* 4.5 7.5 - - - -
193C TRP* 3.2 19.4 + - - +
167G PHE* 3.5 52.0 - - + +
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Residues in contact with ASP 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ARG* 2.8 62.6 + - - +
125C GLU* 3.4 10.2 - - - +
126C GLU 3.2 0.2 - - - -
127C GLN* 1.3 74.8 - - - +
129C PHE* 1.3 62.3 + - - +
131C ILE* 3.3 11.7 + - - +
132C GLN* 3.3 30.3 + - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C THR* 3.5 25.4 - - + -
89C SER 3.6 14.8 - - - -
90C PHE* 3.5 50.3 - + + -
95C TYR* 3.5 28.5 - + + -
125C GLU 2.8 20.0 + - - +
126C GLU 3.2 3.1 + - - +
128C ASP* 1.3 74.0 - - - +
130C ILE* 1.3 72.0 + - + +
132C GLN* 3.2 29.8 + - - +
133C ASN* 3.0 43.0 + - - -
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TYR* 4.1 20.4 - - + -
97C ILE* 5.6 0.6 - - + +
119C VAL* 3.7 17.9 - - + -
121C ILE* 3.6 35.0 - - + -
126C GLU* 2.9 32.5 + - + +
127C GLN* 3.2 5.1 + - - +
129C PHE* 1.3 79.4 - - + +
131C ILE* 1.3 63.8 + - - +
133C ASN* 2.9 18.0 + - - +
134C LEU* 3.3 33.6 + - + +
183C ILE* 4.8 8.1 - - + -
205C ILE* 4.0 21.1 - - + -
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Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ARG* 5.1 3.8 - - - +
127C GLN* 3.1 36.5 + - + +
128C ASP* 3.6 16.8 - - - +
129C PHE 3.3 0.2 - - - -
130C ILE* 1.3 75.0 - - - +
132C GLN* 1.3 65.1 + - + +
134C LEU* 2.9 28.1 + - - +
183C ILE* 4.3 12.1 - - + -
191C TRP* 3.5 58.2 + - + +
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Residues in contact with GLN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ASP* 3.3 20.5 + - - +
129C PHE* 3.2 27.3 + - - +
131C ILE* 1.3 78.3 - - + +
133C ASN* 1.3 63.8 + - - +
134C LEU 3.9 2.8 + - - +
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Residues in contact with ASN 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C THR* 4.1 19.7 + - - +
95C TYR* 6.1 0.2 - - - +
97C ILE* 4.2 25.8 - - + +
129C PHE* 3.0 56.0 + - - -
130C ILE* 2.9 9.6 + - - +
132C GLN* 1.3 82.0 - - - +
134C LEU* 1.3 64.5 + - - +
135C LYS* 4.9 4.7 + - - +
140C TYR* 4.9 0.5 + - - -
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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