Contacts of the helix formed by residues 130 - 137 (chain C) in PDB entry 1TAD
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 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C GLY* 3.3 18.9 - - - -
128C LYS 3.6 2.4 + - - -
129C ASP* 1.3 70.1 + - - +
131C GLY* 1.3 62.8 + - - +
133C GLN* 3.4 8.4 + - - +
134C ALA* 2.9 28.8 + - - +
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Residues in contact with GLY 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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84C MET* 3.7 7.2 - - - -
89C ILE* 3.7 7.8 - - - +
90C GLN 3.5 23.1 - - - -
92C GLY* 3.8 2.1 - - - +
129C ASP* 2.8 10.9 + - - -
130C SER* 1.3 80.9 + - - +
132C ILE* 1.3 63.2 + - - +
134C ALA* 3.1 6.6 + - - +
135C CYS* 3.0 21.7 + - - +
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Residues in contact with ILE 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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77C ILE* 4.5 7.9 - - + -
80C ILE* 3.8 19.9 - - + +
81C VAL* 4.5 10.8 - - + -
84C MET* 3.8 18.7 - - + +
91C TYR* 3.7 27.1 - - + -
126C LEU* 3.2 45.3 - - + +
127C TRP* 4.1 19.3 - - + +
129C ASP* 3.1 16.5 + - + +
131C GLY* 1.3 74.6 - - - +
133C GLN* 1.3 57.6 + - - +
135C CYS* 3.1 4.5 + - - +
136C PHE* 2.8 26.7 + - - +
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Residues in contact with GLN 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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127C TRP* 2.7 60.3 + - - +
128C LYS* 5.0 3.1 - - - +
129C ASP 2.9 20.7 + - - +
130C SER* 3.6 8.5 - - - +
131C GLY 3.2 0.2 - - - -
132C ILE* 1.3 76.8 - - - +
134C ALA* 1.3 61.4 + - - +
136C PHE* 3.1 22.2 + - - +
137C ASP* 2.9 32.6 + - - +
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Residues in contact with ALA 134 (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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89C ILE* 4.4 13.2 - - + -
130C SER 2.9 14.0 + - - +
131C GLY* 3.5 11.2 - - - +
133C GLN* 1.3 74.8 - - - +
135C CYS* 1.3 63.0 + - - +
137C ASP* 3.4 19.0 + - - +
138C ARG* 3.4 20.4 + - - +
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Residues in contact with CYS 135 (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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80C ILE* 3.5 15.9 - - + -
83C ALA* 3.3 42.6 - - - -
84C MET* 3.6 21.5 - - - -
87C LEU* 4.2 5.6 - - - -
89C ILE* 3.6 14.1 - - + +
131C GLY 3.0 5.6 + - - +
132C ILE 3.3 7.9 - - - +
134C ALA* 1.3 74.9 - - - +
136C PHE* 1.3 60.2 + - - +
138C ARG* 2.8 24.2 + - - +
142C TYR* 3.0 18.8 + - - -
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Residues in contact with PHE 136 (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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80C ILE* 4.1 9.4 - - + +
127C TRP* 3.8 30.5 - + + -
132C ILE 2.8 12.9 + - - +
133C GLN* 3.1 28.2 + - - +
135C CYS* 1.3 76.0 - - - +
137C ASP* 1.3 70.8 + - - +
139C ALA* 3.1 23.6 + - + +
142C TYR* 3.7 6.5 + - - -
144C LEU* 3.9 24.2 - - + -
148C ALA* 4.4 0.9 - - + -
149C GLY* 3.7 32.1 - - - -
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Residues in contact with ASP 137 (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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133C GLN* 2.9 25.0 + - - +
134C ALA* 3.6 15.3 - - - +
135C CYS 3.2 0.2 - - - -
136C PHE* 1.3 90.0 - - - +
138C ARG* 1.3 59.9 + - + +
139C ALA* 3.3 3.4 + - - +
140C SER* 5.0 1.7 + - - -
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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