Contacts of the helix formed by residues 218 - 225 (chain B) in PDB entry 1URP
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 PRO 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B PRO* 6.0 5.6 - - + -
216B GLY 4.6 0.9 - - - +
217B THR* 1.3 89.7 - - + +
219B ASP* 1.3 60.5 + - - +
221B GLU* 4.1 3.8 - - + +
222B LYS* 2.9 31.1 + - - +
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Residues in contact with ASP 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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166B ARG* 3.3 20.9 + - - +
192B GLU* 4.7 3.5 - - - +
195B LEU* 3.8 22.1 - - + +
217B THR* 3.2 5.1 + - - +
218B PRO* 1.3 82.4 - - - +
220B GLY* 1.3 62.2 + - - +
222B LYS* 3.6 15.2 - - - +
223B ALA* 3.0 23.9 + - - +
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Residues in contact with GLY 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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191B ASP* 3.8 21.1 - - - -
195B LEU* 4.2 4.2 - - - +
217B THR* 3.0 19.3 + - - -
219B ASP* 1.3 76.3 - - - +
221B GLU* 1.3 61.7 + - - +
223B ALA* 3.1 14.4 + - - +
224B VAL* 3.1 17.2 + - - +
229B LEU* 3.6 11.3 - - - +
232B THR* 4.7 3.1 - - - -
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Residues in contact with GLU 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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216B GLY* 3.2 26.8 - - - +
217B THR 2.7 18.5 + - - +
218B PRO* 4.2 3.6 - - + +
220B GLY* 1.3 68.1 - - - -
222B LYS* 1.3 63.3 + - - +
224B VAL* 3.1 9.7 + - - +
225B ASN* 3.0 33.6 + - - +
232B THR* 4.1 10.5 - - + +
234B ALA* 3.8 21.1 - - - +
266B LYS* 5.6 1.2 + - - -
268B VAL* 4.1 16.4 - - + +
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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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218B PRO 2.9 20.7 + - - +
219B ASP* 3.6 17.3 - - - +
221B GLU* 1.3 76.4 - - - +
223B ALA* 1.3 63.3 + - - +
225B ASN* 3.1 12.3 + - - +
226B ASP* 3.0 47.4 + - - +
228B LYS* 5.3 3.8 - - - +
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Residues in contact with ALA 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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195B LEU* 3.6 24.7 - - + -
198B LEU* 4.6 0.2 - - + -
219B ASP 3.0 14.2 + - - +
220B GLY 3.1 9.6 + - - +
222B LYS* 1.3 76.0 - - - +
224B VAL* 1.3 59.0 + - - +
226B ASP* 3.5 1.1 + - - +
227B GLY 3.4 2.6 + - - -
228B LYS* 3.0 50.5 + - + +
229B LEU* 3.1 18.3 + - + +
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Residues in contact with VAL 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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220B GLY 3.1 13.3 + - - +
221B GLU* 3.1 8.7 + - - +
223B ALA* 1.3 76.8 - - - +
225B ASN* 1.3 64.8 + - - +
227B GLY* 3.1 13.9 + - - -
229B LEU* 3.3 36.9 - - + +
230B ALA 4.4 2.5 - - - +
231B ALA 3.9 15.9 - - - -
232B THR* 4.1 10.5 - - + +
268B VAL* 3.9 8.3 - - + +
269B VAL* 3.6 14.4 - - - +
270B LYS* 3.6 36.5 - - + +
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Residues in contact with ASN 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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221B GLU* 3.0 25.8 + - - +
222B LYS* 3.1 9.4 + - - +
224B VAL* 1.3 80.6 - - - +
226B ASP* 1.3 60.4 + - - +
268B VAL* 5.6 3.8 - - - +
269B VAL 5.2 3.1 - - - +
270B LYS* 3.2 31.4 + - - +
271B GLN 5.6 0.9 + - - -
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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