Contacts of the helix formed by residues 129 - 139 (chain C) in PDB entry 1O94
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C ALA* 3.9 19.5 - - - -
98C ILE* 5.3 1.3 - - - -
127C TYR* 3.0 20.3 + - - +
128C ALA* 1.3 73.5 + - - +
130C THR* 1.3 57.9 + - - -
131C GLY 3.5 2.2 - - - +
132C ILE* 3.5 3.3 + - - +
133C SER* 3.0 16.8 + - - -
1236C AMP 2.7 9.9 + - - -
104D SER* 2.7 34.0 + - - -
114D PHE* 3.3 24.3 - - - -
116D THR* 3.5 6.4 - - - +
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Residues in contact with THR 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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97C ALA* 3.3 33.7 - - - +
100C VAL* 4.1 8.3 - - + -
101C GLY* 4.3 2.1 - - - +
104C LEU* 4.0 18.4 - - + -
127C TYR* 4.7 0.5 - - - -
129C SER* 1.3 69.7 - - - +
131C GLY* 1.3 65.3 + - - +
133C SER* 3.2 4.0 + - - -
134C VAL* 3.0 22.4 + - - +
1236C AMP 2.7 72.6 + - + +
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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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104C LEU* 6.3 0.2 - - - -
118C ALA* 3.7 28.0 - - - +
119C GLY 5.2 1.8 + - - -
129C SER 3.5 0.4 - - - -
130C THR* 1.3 79.5 - - - +
132C ILE* 1.3 60.1 + - - +
134C VAL* 3.2 12.4 - - - +
135C ALA 3.1 20.4 + - - -
179C VAL* 3.5 13.1 - - - +
181C THR* 4.2 7.4 - - - +
1236C AMP 4.2 5.7 + - - -
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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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128C ALA 5.8 1.8 - - - +
129C SER* 3.5 3.8 + - - -
130C THR 3.3 0.6 - - - -
131C GLY* 1.3 73.5 - - - +
133C SER* 1.3 65.0 + - - +
135C ALA* 3.4 4.3 + - + +
136C SER* 3.2 20.6 + - - -
142C HIS* 3.8 33.4 - - + -
143C ALA 4.3 6.1 - - - +
144C ALA* 4.1 13.2 - - + +
179C VAL* 4.9 2.9 - - + +
181C THR* 3.9 24.9 - - + +
100D LEU 3.4 22.0 - - - +
101D GLY 3.8 18.6 - - - +
102D TYR* 4.2 4.0 - - - -
104D SER* 3.5 17.0 - - - +
105D SER* 4.1 16.4 - - - +
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Residues in contact with SER 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ALA 4.1 11.4 - - - -
98C ILE* 3.6 19.5 + - - -
101C GLY* 3.7 1.8 - - - -
129C SER 3.0 18.1 + - - -
130C THR 3.5 4.9 - - - -
132C ILE* 1.3 78.3 - - - +
134C VAL* 1.4 61.4 + - - +
136C SER* 3.2 4.4 + - - -
137C TYR* 3.1 38.7 + - - -
104D SER* 3.5 6.6 + - - -
108D SER* 2.9 23.4 + - - -
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Residues in contact with VAL 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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101C GLY* 3.6 23.5 - - - +
104C LEU* 3.7 24.9 - - + -
105C THR* 3.5 11.9 + - - +
108C ILE* 3.6 27.4 - - + -
116C VAL* 4.6 4.5 - - + -
130C THR 3.0 18.5 + - - +
131C GLY* 3.2 11.9 + - - +
133C SER* 1.4 75.4 + - - +
135C ALA* 1.3 63.9 + - - +
136C SER 3.2 0.2 + - - -
137C TYR 3.3 1.2 + - - -
138C LEU* 2.9 33.7 + - + +
179C VAL* 4.2 6.5 - - + -
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Residues in contact with ALA 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 GLY 3.1 9.6 + - - +
132C ILE* 3.5 11.0 - - - +
133C SER 3.3 0.2 - - - -
134C VAL* 1.3 76.6 - - - +
136C SER* 1.3 57.1 + - - +
138C LEU* 4.5 1.3 - - - -
139C ASN* 2.9 22.9 + - - -
140C TRP 3.0 16.0 + - - +
142C HIS* 3.5 41.7 + - + +
179C VAL* 3.8 22.6 - - + +
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Residues in contact with SER 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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132C ILE 3.2 2.3 + - - -
133C SER 3.2 9.9 + - - -
135C ALA* 1.3 79.7 - - - +
137C TYR* 1.3 64.8 + - - +
139C ASN* 3.1 14.7 + - - +
142C HIS* 5.2 2.9 + - - -
105D SER* 3.6 26.6 + - - -
108D SER* 3.6 9.8 - - - -
109D LYS* 2.7 48.9 + - - +
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Residues in contact with TYR 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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98C ILE* 3.4 20.1 + - - +
99C VAL* 5.5 0.2 - - - -
101C GLY 3.8 2.2 - - - -
102C ARG* 3.5 57.5 - - + +
105C THR* 3.2 26.1 - - + +
133C SER* 3.1 38.6 + - - -
134C VAL 3.9 0.2 - - - +
136C SER* 1.3 78.3 - - - +
138C LEU* 1.3 59.4 + - - +
139C ASN* 3.5 1.0 + - - +
108D SER* 3.4 31.8 + - - -
109D LYS* 5.7 0.7 - - - -
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Residues in contact with LEU 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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105C THR* 3.8 21.8 - - + +
108C ILE* 3.9 31.6 - - + -
109C LYS* 4.3 11.7 - - + -
116C VAL* 4.3 0.2 - - + -
134C VAL* 2.9 27.4 + - + +
135C ALA 4.0 2.2 - - - +
137C TYR* 1.3 74.6 - - - +
139C ASN* 1.3 68.9 + - - +
140C TRP* 3.2 56.7 + - + +
179C VAL* 3.8 16.8 - - + -
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Residues in contact with ASN 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 ALA 2.9 10.8 + - - -
136C SER* 3.1 13.0 + - - +
137C TYR 4.9 1.1 - - - +
138C LEU* 1.3 80.8 - - - +
140C TRP* 1.3 60.5 + - - +
141C PRO* 4.4 1.0 - - - +
109D LYS* 5.9 3.1 - - - -
182D ARG* 3.0 27.6 + - - +
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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