Contacts of the helix formed by residues 113 - 123 (chain E) in PDB entry 1O1F
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 LYS 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E SER 3.9 1.9 + - - +
112E ILE* 1.3 73.9 - - + +
114E LYS* 1.3 65.7 + - - +
115E SER* 3.3 21.2 + - - +
116E PHE* 3.1 27.0 + - + +
117E LEU* 3.2 5.2 + - - +
146E GLY 2.9 4.0 - - - -
147E ASN* 3.0 11.3 - - - +
148E VAL* 4.4 6.5 - - + -
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Residues in contact with LYS 114 (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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113E LYS* 1.3 65.8 - - - +
115E SER* 1.3 62.9 + - - +
118E GLU* 3.1 36.7 + - - +
137E TRP* 3.3 29.2 - - + +
146E GLY* 1.8 32.4 + - - +
147E ASN* 2.4 19.4 + - - -
148E VAL* 4.3 6.3 - - + +
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Residues in contact with SER 115 (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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113E LYS* 3.3 22.2 + - - +
114E LYS* 1.3 79.5 - - - +
116E PHE* 1.3 59.4 + - - +
118E GLU* 3.2 15.8 + - - +
119E GLU* 3.0 48.9 + - - +
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Residues in contact with PHE 116 (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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104E LEU* 5.0 5.2 - - + -
112E ILE* 3.5 31.6 - - + -
113E LYS* 3.1 26.0 + - + +
115E SER* 1.3 79.0 + - - +
117E LEU* 1.3 60.4 + - + +
119E GLU* 3.3 13.0 + - - +
120E LEU* 2.9 58.7 + - + +
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Residues in contact with LEU 117 (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 PHE* 5.2 11.9 - - + -
104E LEU* 4.2 20.0 - - + -
112E ILE* 3.5 32.3 - - + -
113E LYS 3.2 2.5 + - - +
114E LYS 3.3 0.2 + - - -
116E PHE* 1.3 81.0 - - + +
118E GLU* 1.3 55.8 + - - +
120E LEU* 4.6 6.3 - - + -
121E LEU* 3.0 34.1 + - - +
144E VAL 5.0 0.7 - - - +
147E ASN* 1.7 87.9 - - + +
150E TYR* 5.7 1.1 - - + -
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Residues in contact with GLU 118 (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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114E LYS* 3.1 33.1 + - - +
115E SER* 3.2 22.5 - - - +
116E PHE 3.3 0.2 - - - -
117E LEU* 1.3 76.3 - - - +
119E GLU* 1.3 63.9 + - + +
122E THR* 3.0 30.2 + - - -
133E ILE* 3.5 32.9 - - + +
137E TRP* 3.1 24.6 + - - +
147E ASN* 4.1 3.6 - - - +
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Residues in contact with GLU 119 (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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115E SER* 3.0 33.2 + - - +
116E PHE* 3.7 11.8 - - - +
118E GLU* 1.3 79.9 - - + +
120E LEU* 1.3 57.5 + - - +
122E THR* 3.8 1.9 - - - -
123E THR* 2.8 44.3 + - + +
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Residues in contact with LEU 120 (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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809D ARG* 4.0 19.9 + - - +
104E LEU* 3.7 31.4 - - + -
116E PHE* 2.9 40.6 + - + +
117E LEU* 4.2 6.7 - - + +
119E GLU* 1.3 73.9 - - - +
121E LEU* 1.3 64.4 + - - +
123E THR* 3.7 7.4 - - - +
124E GLY* 3.6 14.6 + - - -
128E PHE* 4.5 2.5 - - - -
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Residues in contact with LEU 121 (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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117E LEU 3.0 18.9 + - - +
118E GLU 3.9 2.0 - - - +
120E LEU* 1.3 74.3 - - - +
122E THR* 1.3 61.5 + - - +
125E GLY 2.9 13.2 + - - +
127E ARG 4.3 5.4 - - - +
128E PHE* 0.6 159.4 - - + +
132E GLU* 5.9 1.3 - - + -
133E ILE* 4.0 16.4 - - + -
136E MET* 5.2 13.7 - - + -
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Residues in contact with THR 122 (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 GLU 3.0 16.4 + - - -
119E GLU* 3.8 3.1 - - - -
121E LEU* 1.3 77.4 - - - +
123E THR* 1.3 63.6 + - + +
124E GLY 3.0 3.5 + - - -
125E GLY 2.6 20.8 + - - +
128E PHE 2.9 20.1 + - - -
129E THR* 4.4 3.4 - - - -
130E PRO* 3.9 22.8 - - + +
133E ILE* 3.3 8.5 - - - +
19F ARG* 4.3 13.8 + - - +
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Residues in contact with THR 123 (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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802D GLU* 4.5 5.2 - - - +
809D ARG* 3.5 7.4 + - - -
119E GLU* 2.8 39.0 + - + +
120E LEU* 3.7 11.4 - - - +
122E THR* 1.3 76.8 - - + +
124E GLY* 1.2 58.0 + - - +
19F ARG* 5.5 7.1 + - - +
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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