Contacts of the helix formed by residues 138 - 153 (chain E) in PDB entry 7RDB
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 ASP 138 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134E ASN* 3.2 13.6 + - + +
135E TYR 3.7 3.8 - - - +
136E TYR 3.4 2.0 - - - -
137E ASP* 1.3 83.2 - - + +
139E LEU* 1.3 65.1 + - - +
140E ASP* 2.9 28.7 + - - +
141E PHE* 3.3 17.5 + - + +
142E LYS* 3.1 20.3 + - - +
193J VAL* 3.8 20.6 - - + +
194J VAL 3.4 4.2 + - - +
195J ASN* 4.5 0.2 - - - +
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Residues in contact with LEU 139 (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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136E TYR 6.2 0.2 - - - -
138E ASP* 1.3 74.3 + - - +
140E ASP* 1.3 58.2 + - - +
142E LYS* 4.1 7.6 - - + -
143E ASN* 2.8 35.9 + - - +
183J TYR* 3.5 48.5 - - + +
186J CYS* 4.7 0.2 - - + -
188J ARG* 3.0 37.7 - - - +
194J VAL* 2.8 48.1 + - + +
195J ASN 4.1 8.7 - - - +
196J THR* 4.1 17.3 - - + -
198J CYS* 4.2 1.6 - - - -
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Residues in contact with ASP 140 (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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138E ASP* 2.9 17.8 + - - +
139E LEU* 1.3 78.7 - - - +
141E PHE* 1.3 63.5 + - - +
143E ASN* 3.2 4.2 + - - +
144E ILE* 3.2 29.8 + - + +
188J ARG* 2.8 21.2 + - - +
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Residues in contact with PHE 141 (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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127E ASN 5.5 0.2 - - - -
128E ILE* 4.1 21.1 - - + -
131E GLY* 3.0 50.3 - - - -
132E ILE* 3.4 6.1 - - - -
134E ASN* 4.7 3.4 - - + +
135E TYR* 4.3 10.8 - + - -
138E ASP* 3.3 20.4 + - + +
140E ASP* 1.3 78.8 - - - +
142E LYS* 1.3 64.7 + - - +
144E ILE* 3.1 16.9 + - + -
145E MET* 2.9 61.4 + - + +
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Residues in contact with LYS 142 (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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135E TYR* 3.0 74.2 + - + +
136E TYR* 4.5 6.9 - - + -
138E ASP 3.1 12.0 + - - +
139E LEU* 3.6 9.9 - - + +
140E ASP 3.2 0.4 - - - -
141E PHE* 1.3 77.3 - - - +
143E ASN* 1.3 55.2 + - - +
144E ILE 3.1 0.2 + - - -
145E MET* 3.8 0.5 - - - +
146E ASP* 2.7 53.5 + - - +
183E TYR* 5.8 6.3 + - - -
183J TYR* 3.1 40.3 + - + +
196J THR* 3.8 18.6 - - + -
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Residues in contact with ASN 143 (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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139E LEU* 2.8 25.9 + - - +
140E ASP* 3.6 5.9 - - - +
142E LYS* 1.3 73.5 - - - +
144E ILE* 1.3 58.5 + - + +
146E ASP* 3.9 4.8 + - - +
147E PHE* 2.8 31.6 + - - +
150J LYS* 4.3 16.9 - - - +
183J TYR* 4.3 21.8 + - - -
184J THR* 6.1 0.6 - - - +
188J ARG* 2.8 31.5 + - - +
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Residues in contact with ILE 144 (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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140E ASP* 3.2 20.4 + - + +
141E PHE* 3.1 20.2 + - + +
143E ASN* 1.3 75.5 - - + +
145E MET* 1.3 67.9 + - - +
147E PHE* 3.2 6.7 + - + +
148E VAL* 2.8 37.1 + - + +
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Residues in contact with MET 145 (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 ILE* 4.7 16.4 - - - -
132E ILE* 4.8 5.6 - - + -
135E TYR* 4.0 17.3 - - + -
141E PHE* 2.9 58.0 + - + +
142E LYS 3.8 2.5 - - - +
144E ILE* 1.3 73.9 - - - +
146E ASP* 1.3 64.1 + - - +
148E VAL* 3.9 6.6 - - - +
149E GLN* 2.9 67.3 + - + +
156E GLY* 4.2 18.8 - - - +
163E TRP* 3.8 11.4 - - + -
219E CYS* 5.1 3.8 - - + -
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Residues in contact with ASP 146 (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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135E TYR* 2.4 32.8 + - - -
142E LYS* 2.7 44.9 + - - +
143E ASN* 3.9 5.0 + - - +
145E MET* 1.3 73.2 - - - +
147E PHE* 1.3 62.0 + - - +
149E GLN* 4.0 0.9 + - - -
150E LYS* 3.2 24.4 + - - +
183E TYR* 6.1 1.3 - - - -
184E THR* 2.9 38.8 + - + +
183J TYR* 3.9 5.4 + - - -
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Residues in contact with PHE 147 (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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143E ASN 2.8 19.6 + - - +
144E ILE* 3.6 7.2 - - + +
146E ASP* 1.3 77.2 - - - +
148E VAL* 1.3 73.6 + - + +
150E LYS* 3.3 4.1 + - - +
151E LYS* 2.9 56.7 + - + +
152E PHE* 4.6 9.0 - + - -
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Residues in contact with VAL 148 (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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144E ILE* 2.8 34.9 + - + +
145E MET* 3.9 8.1 - - - +
147E PHE* 1.3 82.6 - - + +
149E GLN* 1.3 65.2 + - - +
150E LYS 3.1 0.2 + - - -
152E PHE* 2.9 50.3 + - + +
154E CYS* 4.1 0.2 - - - -
219E CYS* 3.7 29.6 - - + -
223E VAL* 4.1 11.4 - - + -
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Residues in contact with GLN 149 (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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145E MET* 2.9 41.8 + - + +
146E ASP* 4.0 4.2 + - - +
148E VAL* 1.3 71.3 - - - +
150E LYS* 1.3 61.3 + - - +
153E LYS* 3.1 19.2 + - - -
154E CYS 3.4 26.0 + - - +
156E GLY 2.9 23.9 + - - -
163E TRP* 3.1 26.2 + - - -
182E PRO* 4.4 0.8 - - - +
184E THR* 2.7 45.8 + - - +
185E CYS* 3.2 14.9 - - - -
215E TYR* 4.2 1.6 - - - -
219E CYS* 3.8 10.3 - - - -
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Residues in contact with LYS 150 (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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146E ASP 3.2 17.7 + - - +
147E PHE* 3.8 3.8 - - + +
148E VAL 3.1 0.8 - - - -
149E GLN* 1.3 78.6 - - - +
151E LYS* 1.3 62.3 + - - +
153E LYS* 3.8 15.6 + - - +
184E THR* 4.0 18.3 + - + +
188E ARG* 3.8 26.8 - - + +
215E TYR* 4.9 5.4 + - + -
143J ASN* 3.3 34.5 + - - +
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Residues in contact with LYS 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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147E PHE* 2.9 43.9 + - + +
150E LYS* 1.3 80.2 - - - +
152E PHE* 1.3 90.7 + - + +
153E LYS* 3.7 9.9 + - - +
226E TRP* 4.4 25.8 - - - +
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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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147E PHE* 4.6 7.2 - + - -
148E VAL* 2.9 41.5 + - + +
151E LYS* 1.3 105.5 - - + +
153E LYS* 1.3 61.8 + - - +
154E CYS* 3.4 14.3 + - - +
217E ARG* 2.6 32.5 + - - +
222E ALA* 3.9 10.0 - - + +
223E VAL* 3.9 26.9 - - + -
226E TRP* 3.8 53.8 - + + -
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Residues in contact with LYS 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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149E GLN 3.1 12.4 + - - -
150E LYS 3.9 13.0 - - - +
151E LYS 3.4 7.8 - - - +
152E PHE* 1.3 81.0 - - - +
154E CYS* 1.3 56.4 + - - +
189E ASP* 5.0 11.7 + - - +
215E TYR* 3.5 52.6 - - + +
217E ARG* 3.1 22.3 + - - +
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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