Contacts of the helix formed by residues 221 - 232 (chain B) in PDB entry 1YRP
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 THR 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.5 3.8 - - - -
57A SER* 4.9 0.2 - - - -
59A GLU* 3.2 31.0 - - + +
60A GLU* 3.6 19.5 - - + +
63A ARG* 5.3 4.5 - - - +
166A HIS* 6.0 3.1 - - - +
219B GLY 4.0 1.9 - - - -
220B GLU* 1.3 81.1 - - + +
222B LYS* 1.3 65.5 + - - +
223B GLN* 3.6 14.7 + - - +
224B GLU* 3.1 25.2 + - - +
225B THR* 3.1 25.2 + - - -
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Residues in contact with LYS 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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23A GLN* 4.4 17.0 - - - +
24A PHE* 4.8 11.4 - - - -
47A ARG* 5.4 9.2 - - - +
60A GLU* 2.7 23.0 + - - +
176A ASN* 4.5 10.1 - - - +
177A ILE 5.0 10.5 + - - +
178A PHE* 5.8 6.1 - - + +
181B PRO* 3.8 35.2 - - + -
221B THR* 1.3 70.1 - - - +
223B GLN* 1.3 67.9 + - - +
225B THR* 3.1 7.6 + - - -
226B LEU* 3.1 34.9 + - + +
278B DTT 4.9 14.0 + - - +
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Residues in contact with GLN 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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166A HIS* 4.2 8.7 + - - +
173A GLU 3.8 16.8 + - - -
174A PHE* 3.2 37.6 - - + +
175A LYS 3.4 15.7 + - - +
176A ASN* 3.8 26.9 - - - +
191A TYR* 4.7 0.2 + - - -
221B THR* 3.6 12.1 + - - +
222B LYS* 1.3 78.6 - - - +
224B GLU* 1.3 59.2 + - - +
226B LEU* 3.3 3.5 + - - +
227B THR* 3.0 35.7 + - - +
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Residues in contact with GLU 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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59A GLU* 5.6 0.2 - - - +
219B GLY* 4.1 6.7 - - - -
220B GLU* 3.2 31.5 + - - +
221B THR* 3.1 20.1 + - - +
223B GLN* 1.3 78.5 - - + +
225B THR* 1.3 66.7 + - - +
227B THR* 3.2 9.8 + - + -
228B ASN* 2.9 43.7 + - - +
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Residues in contact with THR 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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47A ARG* 5.0 2.8 + - - -
181B PRO* 4.1 18.8 - - + +
182B GLU* 4.2 16.8 - - + +
217B PHE 3.5 22.2 - - - +
218B LEU* 3.8 11.7 - - + +
219B GLY 3.2 18.0 + - - +
221B THR 3.1 15.7 + - - -
222B LYS* 3.5 11.6 - - - -
224B GLU* 1.3 78.1 - - - +
226B LEU* 1.3 61.2 + - - +
228B ASN 3.4 0.7 + - - -
229B ILE* 3.3 35.9 + - + +
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Residues in contact with LEU 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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176A ASN* 3.7 14.6 - - + -
177A ILE* 3.7 42.0 - - + +
191A TYR* 3.6 16.1 + - + +
181B PRO* 4.2 28.3 - - + -
184B VAL* 4.7 2.2 - - + -
189B VAL* 3.9 28.9 - - + +
222B LYS* 3.1 18.6 + - + +
223B GLN 3.7 4.9 - - - +
225B THR* 1.3 74.2 - - - +
227B THR* 1.3 64.8 + - - +
229B ILE* 3.2 9.0 + - + +
230B SER* 3.1 21.8 + - - -
278B DTT 5.1 8.3 - - - -
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Residues in contact with THR 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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175A LYS* 5.2 1.2 + - - +
191A TYR* 3.5 13.1 + - - -
223B GLN* 3.0 23.9 + - - +
224B GLU* 3.5 15.8 - - + +
226B LEU* 1.3 75.5 - - - +
228B ASN* 1.3 62.6 + - - +
230B SER* 4.0 1.7 - - - -
231B ALA* 2.9 38.2 + - + +
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Residues in contact with ASN 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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217B PHE* 3.3 29.6 + - + +
218B LEU 4.6 1.6 + - - -
219B GLY* 4.4 5.1 - - - +
224B GLU* 2.9 41.5 + - - +
225B THR* 3.6 6.2 - - - +
227B THR* 1.3 80.1 - - - +
229B ILE* 1.3 53.2 + - - +
231B ALA* 4.4 0.2 - - - -
232B VAL* 2.7 27.5 + - - -
233B ASN* 2.7 55.6 + - - +
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Residues in contact with ILE 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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181B PRO 2.9 30.7 - - - +
182B GLU 4.3 5.2 - - - +
184B VAL* 3.3 28.0 - - + +
186B PRO* 3.4 25.6 - - - +
189B VAL* 3.6 16.4 - - + -
201B TRP* 3.8 8.2 - - + -
217B PHE* 3.7 26.2 - - + -
225B THR* 3.3 24.2 + - + +
226B LEU* 3.2 10.7 + - + +
227B THR 3.2 0.6 - - - -
228B ASN* 1.3 74.1 - - - +
230B SER* 1.3 65.4 + - - +
232B VAL* 3.1 13.7 + - - +
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Residues in contact with SER 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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191A TYR* 4.0 16.5 - - - -
186B PRO* 4.2 6.5 - - - -
189B VAL* 4.5 3.1 - - - -
190B ASN* 2.9 32.1 + - - -
226B LEU 3.1 15.0 + - - -
227B THR* 4.0 2.9 - - - -
229B ILE* 1.3 78.2 - - - +
231B ALA* 1.3 60.6 + - - +
232B VAL 3.6 0.2 + - - -
258B LYS* 3.1 39.1 + - - +
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Residues in contact with ALA 231 (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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227B THR* 2.9 25.4 + - + +
228B ASN* 4.0 2.9 - - - +
230B SER* 1.3 74.6 - - - +
232B VAL* 1.3 70.5 + - - +
233B ASN* 4.2 13.0 - - + +
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Residues in contact with VAL 232 (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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201B TRP* 4.2 12.3 - - + -
217B PHE* 4.0 6.3 - - + -
228B ASN 2.7 13.5 + - - -
229B ILE 3.1 14.6 + - - +
231B ALA* 1.3 79.4 - - - +
233B ASN* 1.3 57.9 + - - +
234B TYR* 3.3 25.8 + - + +
256B LEU 3.6 22.7 - - - +
257B VAL* 5.3 0.2 - - - -
258B LYS* 3.7 38.8 - - + +
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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