Contacts of the helix formed by residues 129 - 138 (chain E) in PDB entry 1O95
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E ALA* 4.1 20.2 - - - -
98E ILE* 5.2 2.0 - - - -
120E VAL 4.6 0.2 + - - -
127E TYR* 3.1 18.4 + - - +
128E ALA* 1.4 76.2 + - - +
130E THR* 1.3 68.7 + - - +
131E GLY 3.2 2.7 - - - -
132E ILE* 3.3 3.1 + - - +
133E SER* 3.1 21.1 + - - -
1237E AMP 3.0 1.2 + - - -
104F SER* 3.4 21.9 + - - -
114F PHE* 3.1 27.6 - - - -
116F THR* 4.0 1.9 - - - +
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Residues in contact with THR 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ALA* 6.2 0.2 - - + -
97E ALA* 3.4 31.5 + - - +
100E VAL* 3.6 9.3 - - + +
101E GLY* 4.1 2.0 - - - +
104E LEU* 3.6 29.8 - - + -
129E SER* 1.3 77.3 - - - +
131E GLY* 1.3 62.6 + - - +
133E SER* 3.4 2.6 + - - -
134E VAL* 3.1 19.9 + - - +
1237E AMP 3.1 56.5 + - - +
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Residues in contact with GLY 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ALA* 3.7 27.8 - - - +
119E GLY 5.4 0.4 + - - -
129E SER 3.2 0.8 - - - +
130E THR* 1.3 82.9 - - - +
132E ILE* 1.3 65.0 + - - +
134E VAL* 3.2 11.1 + - - +
135E ALA 3.0 16.8 + - - -
179E VAL* 3.6 11.8 - - - +
181E THR* 4.3 6.5 - - - +
1237E AMP 4.2 5.3 + - - -
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Residues in contact with ILE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ALA 5.3 3.1 - - - +
129E SER 3.3 3.0 + - - -
131E GLY* 1.3 77.1 - - - +
133E SER* 1.3 56.5 + - - +
135E ALA* 3.3 3.7 + - + -
136E SER 2.9 21.8 + - - -
142E HIS* 3.9 34.3 - - + -
143E ALA 4.8 1.3 - - - +
144E ALA* 4.4 11.7 - - + +
179E VAL 5.0 1.6 - - - +
181E THR* 3.9 24.6 - - + +
100F LEU* 3.2 24.7 - - + +
101F GLY* 4.4 3.4 - - - +
102F TYR* 4.2 5.4 - - - -
104F SER* 2.7 23.3 - - - +
105F SER* 3.5 29.7 - - - +
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Residues in contact with SER 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA 3.7 17.7 - - - -
98E ILE* 3.5 13.3 + - - +
101E GLY* 3.9 3.8 - - - -
129E SER 3.1 8.4 + - - -
130E THR 3.5 8.7 - - - -
131E GLY 3.0 0.4 - - - -
132E ILE* 1.3 72.8 - - - +
134E VAL* 1.3 68.1 + - - +
135E ALA 2.9 2.2 + - - -
136E SER* 3.1 2.6 + - - -
137E TYR* 3.0 44.6 + - - -
104F SER* 4.3 0.4 + - - -
108F SER* 2.9 25.3 + - - -
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E GLY* 3.7 6.2 - - - +
104E LEU* 3.6 38.4 - - + -
105E THR* 3.2 10.9 + - - +
108E ILE* 3.7 16.4 - - + -
116E VAL* 4.2 4.9 - - + -
130E THR* 3.1 16.4 + - + +
131E GLY* 3.4 11.7 - - - +
133E SER* 1.3 79.5 - - - +
135E ALA* 1.3 52.6 + - - +
138E LEU* 2.9 54.8 + - + +
179E VAL* 4.0 9.2 - - + -
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Residues in contact with ALA 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLY 3.0 12.3 + - - +
132E ILE* 3.6 10.1 - - - +
133E SER 2.9 2.2 + - - -
134E VAL* 1.3 74.4 - - - +
136E SER* 1.3 60.0 - - - +
138E LEU* 4.4 2.2 - - - -
139E ASN* 3.2 2.0 + - - -
140E TRP* 3.1 30.8 + - + +
142E HIS* 3.7 30.9 + - + +
179E VAL* 3.6 27.6 - - + -
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Residues in contact with SER 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ILE 2.9 11.3 + - - -
133E SER 3.1 0.4 + - - -
135E ALA* 1.3 71.9 - - - +
137E TYR* 1.4 62.1 + - - +
139E ASN* 2.8 24.8 + - - +
142E HIS* 5.6 0.7 - - - -
76F GLU* 5.1 4.3 - - - -
105F SER* 3.8 25.0 + - - -
108F SER* 3.5 30.3 - - - -
109F LYS* 3.7 18.1 + - - +
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Residues in contact with TYR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ILE* 3.5 19.4 + - + +
99E VAL* 5.8 0.2 - - - -
101E GLY 4.1 0.2 - - - -
102E ARG* 3.3 54.5 - - + +
105E THR* 3.5 26.3 - - + +
109E LYS* 5.0 6.6 + - - -
133E SER* 3.0 39.0 + - - +
136E SER* 1.4 79.3 + - - +
138E LEU* 1.3 59.4 + - - +
139E ASN* 5.1 0.5 - - - +
226E MET* 5.8 1.2 - - - -
108F SER* 3.2 28.0 + - - -
109F LYS* 5.6 1.1 - - - -
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Residues in contact with LEU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E THR* 3.8 18.2 - - + -
108E ILE* 3.9 28.3 - - + -
109E LYS* 4.6 16.6 - - + +
134E VAL* 2.9 44.9 + - + +
135E ALA 4.3 0.2 - - - +
137E TYR* 1.3 75.3 - - - +
139E ASN* 1.3 65.1 + - - +
140E TRP* 3.4 44.2 + - + +
179E VAL* 3.9 13.9 - - + -
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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