Contacts of the helix formed by residues 220 - 228 (chain B) in PDB entry 1UES
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 SER 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B VAL 4.2 0.4 - - - -
216B ALA* 4.7 10.8 - - - +
217B PRO* 4.3 3.3 + - - -
218B VAL 4.0 0.8 - - - -
219B ILE* 1.3 74.7 - - - +
221B LYS* 1.3 65.7 + - - +
222B GLU* 3.5 14.5 + - - +
223B THR* 3.1 28.8 + - - -
224B VAL* 2.9 26.2 + - - +
365B LEU* 4.8 2.8 - - - +
366B THR* 3.5 22.0 + - - -
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Residues in contact with LYS 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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212B VAL* 3.3 32.8 + - + +
213B ASP* 3.7 31.5 - - + +
216B ALA* 5.3 2.6 - - - +
220B SER* 1.3 73.9 - - - +
222B GLU* 1.3 84.0 + - - +
224B VAL* 3.3 2.3 + - - +
225B GLU* 3.0 50.3 + - - +
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER* 3.2 12.1 + - - +
221B LYS* 1.3 102.9 + - - +
223B THR* 1.3 58.9 + - - +
225B GLU* 3.3 14.7 + - - +
226B PHE* 2.9 46.6 + - + -
365B LEU* 4.2 14.6 - - + -
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ILE* 3.8 13.5 - - + -
220B SER* 3.1 27.8 + - - -
222B GLU* 1.3 75.1 - - - +
224B VAL* 1.3 56.0 + - - +
226B PHE* 4.8 1.6 - - - -
227B HIS* 2.6 48.4 + - + +
361B HIS 3.9 15.2 + - - +
362B ALA 3.7 24.4 - - - +
363B TYR* 5.4 1.7 - - - -
365B LEU* 3.7 27.4 + - - +
366B THR* 4.6 3.3 + - - -
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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
----------------------------------------------------------
208B LEU* 3.2 35.9 - - + -
210B TYR* 5.1 4.3 - - + -
212B VAL* 3.4 32.8 - - + +
215B LEU* 4.9 10.3 - - + -
219B ILE* 3.6 23.3 - - + +
220B SER 2.9 15.3 + - - +
221B LYS 3.7 2.0 - - - +
223B THR* 1.3 75.6 - - - +
225B GLU* 1.3 59.3 + - - +
227B HIS* 4.5 3.8 - - - -
228B HIS* 2.7 39.5 + - + +
278B PHE* 5.0 7.2 - - + -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B VAL* 4.3 19.9 - - + +
221B LYS* 3.0 44.6 + - - +
222B GLU* 3.5 21.4 + - - +
224B VAL* 1.3 77.0 - - - +
226B PHE* 1.3 61.6 + - + +
229B GLY* 2.9 28.8 + - - +
230B LYS* 3.5 5.1 + - - +
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Residues in contact with PHE 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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164A TYR* 3.5 16.8 - - + +
168A GLN* 3.6 43.7 - - + -
169A ASN* 3.6 23.6 - - - -
170A ARG* 6.3 0.4 - - - -
222B GLU* 2.9 45.7 + - + +
223B THR* 4.0 3.4 - - - +
225B GLU* 1.3 75.5 - - + +
227B HIS* 1.3 61.3 + - - +
230B LYS* 2.9 20.3 + - + +
231B HIS* 2.8 30.4 + - + -
365B LEU* 4.1 7.6 - - + -
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 4.8 0.4 + - - -
219B ILE* 5.6 1.6 - - - +
223B THR* 2.6 34.5 + - + +
224B VAL* 4.1 0.9 - - - +
226B PHE* 1.3 73.8 - - - +
228B HIS* 1.3 57.2 + - - +
231B HIS* 3.3 13.2 - - + +
232B LEU* 3.0 27.2 + - - +
274B HIS* 3.1 13.8 + + - -
277B TYR* 3.6 21.9 + + - -
278B PHE* 3.6 13.4 - + + -
357B ASP* 2.9 18.4 + - - -
361B HIS* 3.5 14.4 - + - +
362B ALA* 3.5 26.0 - - + -
392B MN 2.2 29.7 + - - -
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Residues in contact with HIS 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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205B LEU* 3.6 30.5 - - + +
206B ILE* 2.6 32.3 + - + +
207B SER* 5.1 0.4 - - - -
208B LEU* 3.5 45.8 - - + +
224B VAL* 2.7 18.2 + - + +
227B HIS* 1.3 74.4 - - - +
229B GLY* 1.3 66.8 + - - +
230B LYS 3.4 0.7 + - - -
232B LEU* 3.3 36.5 - - + +
233B LYS 3.5 5.0 + - - -
278B PHE* 3.7 20.1 - + + -
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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