Contacts of the helix formed by residues 129 - 139 (chain C) in PDB entry 5TF6
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C SER 3.7 10.3 - - - +
128C TYR* 1.3 78.7 - - - +
130C GLN* 1.3 66.4 + - - +
131C ARG* 3.2 11.9 + - - +
132C ASN* 2.8 44.0 + - - +
133C ILE* 3.2 18.4 + - - +
149C LEU* 5.6 0.7 - - - -
327C LEU* 4.3 19.5 - - + -
330C GLN* 3.9 12.1 - - - +
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Residues in contact with GLN 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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129C THR* 1.3 73.5 - - - +
131C ARG* 1.3 64.6 + - - +
133C ILE* 3.1 14.5 + - - +
134C ARG* 3.0 34.4 + - - +
147C ILE* 3.8 39.2 + - + +
149C LEU* 4.3 27.8 - - + +
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Residues in contact with ARG 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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129C THR* 3.2 10.3 + - - +
130C GLN* 1.3 80.0 - - - +
132C ASN* 1.3 60.0 + - - +
134C ARG* 3.2 30.3 + - - +
135C ASP* 2.9 63.5 + - - +
138C GLN* 3.5 23.8 + - - +
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Residues in contact with ASN 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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127C SER 4.0 2.1 - - - +
128C TYR* 3.5 40.0 + - + -
129C THR* 2.8 42.1 + - - +
131C ARG* 1.3 78.8 - - - +
133C ILE* 1.4 58.1 + - - +
135C ASP* 3.3 11.9 + - - +
136C LEU* 2.8 28.6 + - - +
330C GLN* 5.4 2.3 + - - -
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Residues in contact with ILE 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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121C MET* 4.4 11.2 - - - -
124C PHE* 4.3 27.4 - - + -
128C TYR* 3.8 19.3 - - + -
129C THR 3.2 15.2 + - - +
130C GLN* 3.1 11.0 + - - +
132C ASN* 1.4 73.3 - - - +
134C ARG* 1.3 68.2 + - - +
136C LEU* 3.2 9.0 + - + +
137C LEU* 3.2 27.6 + - + +
147C ILE* 4.0 25.8 - - + -
149C LEU* 4.8 3.6 - - + -
161C ALA* 4.3 8.5 - - + -
163C ILE* 3.5 30.5 - - + -
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Residues in contact with ARG 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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73C ALA* 4.7 11.3 - - - +
130C GLN* 3.0 24.8 + - - +
131C ARG* 3.2 38.7 + - - +
133C ILE* 1.3 79.0 - - - +
135C ASP* 1.3 57.3 + - - +
137C LEU* 3.2 2.8 + - - +
138C GLN* 2.8 40.7 + - + +
142C VAL 5.0 0.3 - - - +
143C VAL* 5.5 0.4 - - - +
144C ALA* 2.8 44.4 + - + +
145C LEU 4.4 8.9 + - - -
146C SER* 4.7 2.2 - - - +
147C ILE* 3.8 27.1 - - + +
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Residues in contact with ASP 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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131C ARG* 2.9 58.9 + - - +
132C ASN* 3.7 11.1 + - - +
134C ARG* 1.3 75.6 - - - +
136C LEU* 1.3 65.6 + - - +
138C GLN* 3.1 9.8 + - - +
139C ASP* 2.9 34.6 + - - +
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Residues in contact with LEU 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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121C MET* 4.5 9.9 - - + -
128C TYR* 3.6 25.4 - - + +
132C ASN 2.8 14.5 + - - +
133C ILE* 3.2 11.0 - - - +
135C ASP* 1.3 80.1 - - - +
137C LEU* 1.3 62.9 + - + +
139C ASP* 3.5 21.2 + - + +
140C ILE* 3.8 10.6 + - - +
178C LEU* 4.1 21.4 - - + +
181C LEU* 4.2 20.6 - - + -
183C ILE* 4.3 6.3 - - + -
188C LEU* 4.1 26.7 - - + -
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Residues in contact with LEU 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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119C LEU* 4.7 2.7 - - + -
121C MET* 4.4 9.0 - - + -
133C ILE* 3.2 26.9 + - + +
134C ARG 3.8 5.2 - - - +
136C LEU* 1.3 78.7 - - + +
138C GLN* 1.3 67.6 + - - +
140C ILE* 3.0 16.8 + - - +
142C VAL* 2.9 36.6 + - + +
144C ALA* 3.9 15.5 - - + -
163C ILE* 3.7 29.4 - - + -
165C VAL* 4.0 17.0 - - + -
174C CYS* 4.1 16.6 - - - -
178C LEU* 3.7 22.9 - - + -
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Residues in contact with GLN 138 (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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76C LEU* 4.0 31.2 - - + +
131C ARG* 3.5 26.3 + - - +
134C ARG* 2.8 25.5 + - + +
135C ASP* 3.4 10.9 + - - +
137C LEU* 1.3 78.1 - - - +
139C ASP* 1.3 58.2 + - - +
141C ASN* 2.9 22.5 + - - +
142C VAL 3.6 7.8 + - - +
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Residues in contact with ASP 139 (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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135C ASP* 2.9 26.5 + - - +
136C LEU* 3.7 15.6 - - + +
137C LEU 3.2 0.2 - - - -
138C GLN* 1.3 76.1 - - - +
140C ILE* 1.4 64.5 + - + +
141C ASN* 3.4 5.3 + - - +
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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