Contacts of the helix formed by residues 150 - 159 (chain E) in PDB entry 1RFU
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 ASN 150 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E GLY 2.6 28.4 - - - +
118E ASP* 3.9 6.2 - - - +
119E GLN* 3.7 14.4 - - - +
127E TYR* 5.2 0.5 + - - -
149E PRO* 1.3 73.6 - - - +
151E GLN* 1.3 73.4 + - - +
152E PHE* 2.9 6.2 + - - +
153E GLU* 2.7 33.9 + - + +
154E ALA* 2.5 25.4 + - - +
185E ILE* 4.5 0.4 - - - -
186E THR* 4.3 3.3 + - - -
4402E ADP 3.6 41.3 + - - -
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Residues in contact with GLN 151 (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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119E GLN* 3.0 27.3 - - - +
150E ASN* 1.3 77.6 - - - +
152E PHE* 1.3 52.5 + - - +
154E ALA* 3.3 3.1 - - - +
155E GLU* 2.6 61.6 + - - +
162E ILE* 3.9 28.4 + - + +
185E ILE* 3.8 12.2 - - + +
187E SER 3.1 14.3 + - - +
188E SER* 2.8 30.5 - - - -
189E ASN* 3.0 36.9 + - - +
190E LEU* 4.8 1.0 + - - +
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Residues in contact with PHE 152 (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 GLY* 3.5 39.3 - - - -
118E ASP 3.6 4.0 - - - -
119E GLN* 3.5 25.4 - - + +
124E GLY 3.5 28.7 - - - -
125E ALA* 3.6 28.3 - - - -
126E MET* 3.7 11.4 - - + -
150E ASN* 3.9 4.7 - - - +
151E GLN* 1.3 78.9 - - - +
153E GLU* 1.3 67.8 + - - +
155E GLU* 2.9 22.1 + - - +
156E LEU* 2.8 44.7 + - + +
161E LYS* 5.7 4.7 - - - -
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Residues in contact with GLU 153 (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 ASP* 4.6 2.6 - - - +
114E PRO* 2.7 27.9 - - + +
115E VAL* 3.0 8.4 - - - +
116E MET* 2.7 33.5 + - + +
117E GLY 3.5 20.7 + - - +
127E TYR* 4.8 0.3 + - - -
148E THR 4.4 2.3 - - - +
149E PRO* 3.8 4.0 - - - +
150E ASN* 2.7 46.1 + - + +
152E PHE* 1.3 75.1 - - + +
154E ALA* 1.3 56.2 + - - +
156E LEU* 2.7 30.5 + - - +
157E LEU* 2.7 18.2 + - - +
4402E ADP 5.2 4.1 + - - -
4403E ZN 4.3 5.0 - - - -
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Residues in contact with ALA 154 (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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149E PRO* 3.8 12.4 - - + +
150E ASN 2.5 21.6 + - - +
151E GLN* 3.3 5.6 - - - +
153E GLU* 1.3 72.1 - - - +
155E GLU* 1.3 64.5 + - - +
157E LEU* 3.2 7.6 + - - +
158E THR* 2.9 24.5 + - - +
162E ILE* 5.8 2.7 - - + -
171E VAL* 3.9 13.2 - - + +
175E LEU* 4.6 1.8 - - + -
185E ILE* 3.5 31.2 - - + -
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Residues in contact with GLU 155 (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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123E GLU* 6.2 0.3 - - - +
151E GLN* 2.6 62.2 + - - +
152E PHE* 3.2 18.6 - - + +
154E ALA* 1.3 72.7 - - - +
156E LEU* 1.3 57.3 + - - +
157E LEU 2.9 0.7 + - - -
158E THR* 3.1 5.3 + - - -
159E GLY* 2.7 31.5 + - - -
160E ARG 3.2 24.7 + - - +
161E LYS* 3.3 29.8 + - - +
162E ILE* 3.2 33.2 + - + +
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Residues in contact with LEU 156 (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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116E MET* 3.5 23.8 - - + -
126E MET* 4.0 24.0 - - + -
133E LEU* 3.2 54.9 - - + +
137E ARG* 4.5 3.3 + - - -
152E PHE* 2.8 35.7 + - + +
153E GLU* 2.7 18.3 + - - +
155E GLU* 1.3 73.6 - - - +
157E LEU* 1.3 59.9 + - - +
159E GLY* 3.6 8.6 + - - +
161E LYS* 6.4 0.4 - - - +
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Residues in contact with LEU 157 (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 PRO* 4.0 26.5 - - + -
116E MET* 3.7 21.3 - - + -
133E LEU* 4.3 2.7 - - + -
136E TYR* 4.1 15.3 - - + -
137E ARG* 3.2 39.1 - - + +
141E VAL* 3.9 27.6 - - + -
147E ILE* 5.2 3.6 - - + -
149E PRO* 4.3 9.0 - - + -
153E GLU 2.7 19.7 + - - +
154E ALA* 3.8 3.6 - - - +
155E GLU 3.1 0.2 - - - -
156E LEU* 1.3 70.7 - - - +
158E THR* 1.3 59.7 + - - +
159E GLY 2.9 9.2 + - - -
175E LEU* 4.1 23.1 - - + -
178E MET* 4.5 7.7 - - + +
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Residues in contact with THR 158 (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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154E ALA 2.9 12.0 + - - -
155E GLU* 3.4 4.0 + - - -
157E LEU* 1.3 75.0 - - - +
159E GLY* 1.3 54.4 + - - +
160E ARG* 3.1 13.9 + - - +
171E VAL* 3.1 43.1 - - + +
174E MET* 3.3 42.5 - - + +
175E LEU* 3.4 26.5 - - + +
178E MET* 4.6 6.5 - - - -
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Residues in contact with GLY 159 (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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137E ARG* 5.9 2.0 - - - -
155E GLU 2.7 10.4 + - - -
156E LEU* 4.0 7.4 - - - -
157E LEU 2.9 6.4 + - - -
158E THR* 1.3 78.1 - - - +
160E ARG* 1.3 60.4 + - - +
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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