Contacts of the helix formed by residues 218 - 230 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B CYS* 3.8 0.6 - - - +
155B CYS 3.5 11.4 - - - -
157B GLY 3.3 6.5 - - - -
158B GLU 3.3 28.5 + - - -
216B VAL 3.5 0.8 + - - -
217B ARG* 1.3 78.0 - - - +
219B CYS* 1.3 65.1 + - - -
220B THR 3.3 2.5 - - - -
221B ASN* 4.0 5.3 + - - +
222B ALA* 3.5 19.2 + - - +
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Residues in contact with CYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 4.6 9.2 - - + -
145B MET* 4.9 3.1 - - + -
148B VAL* 3.7 20.6 - - + -
149B GLN* 3.8 13.5 - - - -
154B CYS* 2.1 59.0 - - - -
155B CYS 3.6 0.4 - - - -
156B GLY 2.7 23.4 + - - +
157B GLY 3.3 0.2 + - - -
218B GLY* 1.3 72.8 - - - -
220B THR* 1.3 65.9 + - - +
222B ALA* 4.1 0.7 - - - -
223B VAL* 2.9 28.9 + - + +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.9 26.7 - - + +
124B LEU* 3.4 38.1 - - + +
125B ASN* 2.3 33.6 + - - +
128B ILE* 3.4 14.4 - - - +
157B GLY 3.0 12.2 + - - -
219B CYS* 1.3 79.7 - - - +
221B ASN* 1.3 63.4 + - - +
223B VAL* 3.9 0.3 - - - +
224B ILE* 3.3 27.3 + - + +
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Residues in contact with ASN 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 6.1 1.3 - - - +
157B GLY 4.7 0.4 + - - -
218B GLY* 4.0 6.3 + - - +
220B THR* 1.3 78.5 - - - +
222B ALA* 1.3 67.7 + - - +
224B ILE* 3.0 23.3 + - - +
225B ILE* 3.2 30.3 + - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 4.1 18.1 - - + +
154B CYS* 4.1 18.6 - - + -
217B ARG* 4.2 20.6 - - - +
218B GLY 3.5 17.8 + - - +
219B CYS* 3.2 5.2 + - - +
221B ASN* 1.3 81.3 + - - +
223B VAL* 1.3 62.5 + - - +
225B ILE* 3.7 8.6 + - - +
226B TRP* 3.3 22.2 + - - +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 5.0 11.0 - - + -
148B VAL* 4.1 15.7 - - + -
152B PHE* 3.9 42.8 - - + -
219B CYS* 2.9 20.4 + - + +
220B THR* 3.9 5.2 - - - +
222B ALA* 1.3 74.1 - - - +
224B ILE* 1.3 66.6 + - + +
226B TRP* 3.5 6.1 + - + +
227B PHE* 3.0 24.1 + - + +
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B THR* 5.5 4.0 - - + -
121B ILE* 3.3 34.3 - - + -
124B LEU* 4.2 19.3 - - + -
220B THR 3.4 17.3 - - - +
221B ASN* 3.0 16.2 + - - +
223B VAL* 1.3 75.8 - - + +
225B ILE* 1.3 70.9 + - + +
227B PHE* 3.0 9.0 + - + +
228B MET* 2.9 36.5 + - + +
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ARG* 5.3 11.0 - - - +
221B ASN* 3.2 31.9 + - - +
222B ALA* 3.8 11.4 - - - +
224B ILE* 1.3 78.2 - - + +
226B TRP* 1.3 63.4 + - - +
228B MET* 3.2 7.4 + - - +
229B ASP* 2.8 32.9 + - + +
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Residues in contact with TRP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LYS* 4.1 23.8 - - - +
152B PHE* 3.4 39.2 - + + -
222B ALA 3.3 15.1 + - - +
223B VAL* 3.7 9.4 - - + +
224B ILE 3.1 0.6 - - - -
225B ILE* 1.3 85.1 - - + +
227B PHE* 1.3 88.5 + + + +
229B ASP* 4.6 3.6 - - - -
230B ASN* 3.0 57.6 + - + +
234B LEU* 4.7 20.2 - - + -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B VAL* 3.0 16.7 + - + +
224B ILE* 3.0 11.4 + - + +
226B TRP* 1.3 92.6 - + + +
228B MET* 1.3 76.4 + - + +
230B ASN* 3.4 2.5 + - - -
231B LEU* 3.0 50.9 + - + -
234B LEU* 3.8 27.1 - - + +
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Residues in contact with MET 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ILE* 2.9 33.6 + - + +
225B ILE* 3.7 6.5 - - - +
227B PHE* 1.3 95.5 - - + +
229B ASP* 1.3 63.4 + - - +
230B ASN 3.4 0.3 + - - -
231B LEU* 3.6 29.8 + - - +
232B GLU* 4.2 4.9 - - - +
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Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 2.8 18.2 + - + +
226B TRP* 3.8 2.7 - - - +
228B MET* 1.3 78.0 - - - +
230B ASN* 1.3 70.2 + - - +
231B LEU 3.4 1.0 + - - -
232B GLU* 3.9 8.4 - - - +
233B VAL* 5.1 2.6 - - - +
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Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TRP* 3.0 52.1 + - + +
227B PHE* 3.5 3.4 - - - +
229B ASP* 1.3 88.0 - - - +
231B LEU* 1.3 64.9 + - - +
232B GLU 3.3 2.2 - - - -
233B VAL* 3.2 25.7 + - + +
234B LEU* 3.0 30.5 + - + +
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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