Contacts of the helix formed by residues 218 - 230 (chain J) 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 GLY 218 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154J CYS* 3.8 1.6 - - - -
155J CYS 3.7 5.4 - - - -
157J GLY 3.0 17.9 - - - -
158J GLU 3.2 19.8 + - - -
217J ARG* 1.3 79.3 - - - +
219J CYS* 1.3 64.0 + - - -
220J THR 3.3 3.3 + - - -
221J ASN* 3.5 9.3 + - - +
222J ALA* 3.4 19.9 + - - +
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Residues in contact with CYS 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J ILE* 4.9 5.6 - - + -
145J MET* 5.4 2.0 - - + -
148J VAL* 3.7 21.5 - - + -
149J GLN* 3.9 12.3 - - - -
154J CYS* 2.1 60.6 - - - -
155J CYS 3.4 2.9 - - - -
156J GLY 3.0 20.9 + - - +
218J GLY* 1.3 70.7 - - - -
220J THR* 1.3 59.2 + - - +
222J ALA* 3.9 0.6 - - - +
223J VAL* 2.8 37.8 + - + +
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Residues in contact with THR 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ILE* 3.7 30.5 - - + +
124J LEU* 4.0 27.9 - - + +
125J ASN* 2.3 37.0 + - - +
128J ILE* 3.9 8.2 - - - +
156J GLY 4.3 0.2 + - - -
157J GLY* 3.5 16.1 + - - -
158J GLU* 5.5 0.4 - - - -
218J GLY 3.3 0.4 - - - -
219J CYS* 1.3 79.9 - - - +
221J ASN* 1.3 63.1 + - + +
223J VAL* 3.6 3.5 + - - +
224J ILE* 3.4 25.1 + - + +
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Residues in contact with ASN 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ILE* 6.4 0.2 - - - -
157J GLY 4.8 0.2 + - - -
218J GLY* 3.5 9.3 + - - +
219J CYS 3.3 0.4 - - - -
220J THR* 1.3 82.1 - - + +
222J ALA* 1.3 63.3 + - - +
224J ILE* 3.4 8.4 + - - +
225J ILE* 3.1 30.3 + - + +
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Residues in contact with ALA 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J PHE* 3.9 21.7 - - + +
154J CYS* 4.3 3.6 - - + -
217J ARG* 3.7 36.1 - - - +
218J GLY 3.4 14.1 + - - +
219J CYS* 3.2 4.3 + - - +
221J ASN* 1.3 74.9 - - - +
223J VAL* 1.3 67.1 + - - +
225J ILE* 3.6 8.4 + - - +
226J TRP* 3.3 21.5 + - - +
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Residues in contact with VAL 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J LEU* 5.3 10.3 - - + -
148J VAL* 4.3 23.3 - - + -
152J PHE* 4.4 23.5 - - + -
219J CYS* 2.8 23.7 + - + +
220J THR* 3.8 6.3 - - - +
222J ALA* 1.3 76.9 - - - +
224J ILE* 1.3 68.6 + - + +
226J TRP* 3.2 10.8 + - + +
227J PHE* 3.0 24.6 + - + +
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Residues in contact with ILE 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J ARG* 4.0 26.2 - - + +
120J THR* 5.5 1.6 - - - +
121J ILE* 3.6 34.3 - - + -
124J LEU* 5.6 5.8 - - + -
220J THR* 3.4 20.4 + - + +
221J ASN* 3.4 11.5 + - - +
222J ALA 3.3 0.8 - - - -
223J VAL* 1.3 82.3 - - + +
225J ILE* 1.3 61.3 + - + +
227J PHE* 3.2 6.3 + - + +
228J MET* 2.8 60.5 + - + +
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Residues in contact with ILE 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J ARG* 5.2 7.4 - - - +
217J ARG* 5.3 9.4 - - - +
221J ASN* 3.1 18.6 + - + +
222J ALA* 3.8 9.6 - - - +
224J ILE* 1.3 82.0 - - + +
226J TRP* 1.3 62.3 + - + +
228J MET* 4.1 6.2 - - - +
229J ASP* 2.9 32.7 + - + +
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Residues in contact with TRP 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J PHE* 3.5 40.6 - + + -
222J ALA 3.3 10.2 + - - +
223J VAL* 3.2 14.1 + - + +
224J ILE 3.2 0.6 - - - -
225J ILE* 1.3 81.1 - - + +
227J PHE* 1.3 91.8 + + + +
229J ASP* 3.4 3.3 + - - +
230J ASN* 3.1 49.2 + - + +
234J LEU* 4.9 18.4 - - + -
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Residues in contact with PHE 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J VAL* 3.0 15.7 + - + +
224J ILE* 3.5 8.1 - - - +
226J TRP* 1.3 92.6 - + + +
228J MET* 1.3 105.8 + - + +
230J ASN 3.0 12.6 + - - -
231J LEU* 3.3 42.1 + - + -
234J LEU* 3.5 20.0 - - + -
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Residues in contact with MET 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J ARG* 4.6 15.9 - - - +
224J ILE* 2.8 49.2 + - + +
225J ILE* 4.1 5.6 - - - +
227J PHE* 1.3 105.7 - - + +
229J ASP* 1.3 63.9 + - - +
231J LEU* 3.4 20.2 + - - +
232J GLU* 5.1 2.3 - - - +
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Residues in contact with ASP 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J ILE* 2.9 21.3 + - + +
226J TRP* 3.9 5.2 - - - +
227J PHE 3.1 0.2 - - - -
228J MET* 1.3 77.7 - - - +
230J ASN* 1.3 69.7 + - - +
231J LEU 3.6 0.7 + - - -
232J GLU* 3.8 10.7 - - - +
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Residues in contact with ASN 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J TRP* 3.1 42.8 + - + +
227J PHE 3.0 6.6 + - - +
229J ASP* 1.3 88.2 + - - +
231J LEU* 1.3 61.9 + - - +
232J GLU* 3.5 3.6 - - - -
233J VAL* 3.5 20.8 + - + +
234J LEU* 3.0 28.1 - - + +
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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