Contacts of the helix formed by residues 225 - 235 (chain B) in PDB entry 3N1Z
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 VAL 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B LEU* 4.9 3.6 - - + -
220B THR* 3.0 14.3 + - + +
221B ALA 3.8 7.2 - - - +
224B LEU* 1.3 82.0 - - - +
226B THR* 1.3 68.4 + - - +
227B LYS 3.5 0.4 - - - -
228B PRO* 3.3 9.7 - - - +
229B ALA* 3.3 14.7 + - - +
289B VAL* 4.2 33.7 - - + +
292B TRP* 3.9 33.2 - - + +
293B GLU* 4.1 3.6 - - - +
296B ALA* 3.6 26.8 - - + +
321B SER* 5.5 0.2 - - - -
325B ARG* 3.7 10.8 + - - +
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Residues in contact with THR 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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131B LEU* 5.4 0.7 - - + -
135B LEU* 4.3 7.6 - - + -
202B PHE* 5.5 0.7 - - + -
205B LEU* 3.5 38.6 - - + +
206B ILE* 4.1 24.0 - - + -
209B ALA* 4.2 8.0 - - - +
221B ALA 2.8 23.3 + - - -
222B ILE* 3.7 7.6 - - - -
225B VAL* 1.3 77.0 - - - +
227B LYS* 1.3 59.9 + - - +
229B ALA* 3.1 5.6 + - - +
230B VAL* 2.8 41.5 + - + +
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Residues in contact with LYS 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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135B LEU* 3.4 21.5 - - + -
158B GLU* 3.5 11.9 - - - +
162B HIS* 2.9 31.1 - - + +
165B TRP* 3.8 7.1 - - - -
222B ILE* 3.0 22.1 + - + +
223B ASN* 3.4 27.6 - - - +
226B THR* 1.3 70.0 - - - +
228B PRO* 1.3 73.9 - - + +
230B VAL* 3.0 5.7 + - - +
231B GLU* 2.7 54.9 + - + +
264B HIS* 3.0 33.6 + - - -
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Residues in contact with PRO 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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223B ASN 3.3 17.5 - - - +
224B LEU 3.2 17.5 - - - +
225B VAL 3.3 14.8 - - - +
227B LYS* 1.3 93.3 - - + +
229B ALA* 1.3 55.8 + - - +
231B GLU* 3.5 12.5 - - - +
232B GLU* 2.9 35.2 + - - +
265B ARG* 3.9 6.1 - - + +
321B SER* 3.8 27.6 - - - +
324B VAL* 4.2 22.7 - - + -
325B ARG* 4.5 0.4 - - - +
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Residues in contact with ALA 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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202B PHE* 3.4 11.0 - - + -
205B LEU* 4.9 0.4 - - + -
225B VAL 3.3 10.8 + - - +
226B THR* 3.1 9.6 + - - +
227B LYS 3.1 0.2 - - - -
228B PRO* 1.3 76.9 - - - +
230B VAL* 1.3 65.1 + - - +
232B GLU* 4.0 1.5 - - - +
233B ALA* 3.0 27.4 + - - +
296B ALA* 4.4 17.5 - - + +
300B ILE* 4.0 27.0 - - + +
321B SER* 4.0 10.4 - - - +
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Residues in contact with VAL 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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131B LEU* 3.6 33.7 - - + -
132B PHE* 4.2 15.5 - - + -
135B LEU* 4.1 20.6 - - + -
165B TRP* 5.3 1.6 - - + -
202B PHE* 3.5 25.6 - - + -
226B THR* 2.8 37.3 + - + +
227B LYS* 3.7 6.3 - - - +
229B ALA* 1.3 71.5 - - - +
231B GLU* 1.3 60.3 + - + +
234B LEU* 2.8 36.1 + - + +
235B LEU* 6.1 0.2 - - + -
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Residues in contact with GLU 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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165B TRP* 4.1 15.5 - - + -
227B LYS* 2.7 61.7 + - + +
228B PRO* 3.5 3.3 - - - +
230B VAL* 1.3 74.6 - - + +
232B GLU* 1.3 58.5 + - - +
235B LEU* 3.0 38.8 + - + +
236B GLN* 3.0 9.9 + - - +
258B LYS* 4.7 4.0 + - - -
261B ALA* 3.3 30.3 - - + +
265B ARG* 2.6 46.0 + - - +
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Residues in contact with GLU 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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228B PRO 2.9 20.3 + - - +
229B ALA* 4.2 2.7 - - - +
231B GLU* 1.3 75.6 - - - +
233B ALA* 1.3 60.0 + - - +
236B GLN* 3.3 23.7 - - - +
237B GLN* 3.0 34.2 + - - +
258B LYS* 2.8 26.5 + - - -
265B ARG* 3.2 21.9 + - - +
317B ALA* 4.0 21.3 - - + +
320B ALA* 3.6 31.5 - - + +
321B SER* 4.0 12.3 - - - +
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Residues in contact with ALA 233 (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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202B PHE* 3.6 26.0 - - + -
229B ALA 3.0 18.8 + - - +
232B GLU* 1.3 78.3 - - - +
234B LEU* 1.3 63.0 + - + +
237B GLN* 3.3 25.9 - - - +
238B LEU 3.3 8.0 + - - -
300B ILE* 4.9 6.5 - - + -
303B TYR* 3.7 19.2 - - + -
304B CYS* 4.2 10.3 - - - -
317B ALA* 4.6 1.3 - - - +
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Residues in contact with LEU 234 (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 PHE 4.8 1.3 - - - +
128B ALA* 3.6 31.4 - - + -
131B LEU* 3.8 22.4 - - + -
132B PHE* 4.0 17.5 - - + -
199B TRP* 3.9 7.4 - - + -
202B PHE* 4.0 20.0 - - + -
230B VAL* 2.8 21.8 + - + +
233B ALA* 1.3 75.5 - - + +
235B LEU* 1.3 66.2 + - + +
238B LEU* 3.3 27.8 - - + +
239B GLY 4.3 0.5 + - - -
250B LEU* 5.8 1.2 - - - +
254B ALA* 4.9 2.6 - - - +
303B TYR* 3.5 37.7 - - + +
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Residues in contact with LEU 235 (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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132B PHE* 4.4 19.1 - - + -
165B TRP* 4.3 19.5 - - + -
230B VAL* 4.9 0.4 - - + +
231B GLU* 3.0 24.6 + - + +
234B LEU* 1.3 83.6 - - + +
236B GLN* 1.3 67.7 + - - +
239B GLY* 3.0 22.3 + - - -
254B ALA* 3.7 23.1 - - + +
257B GLN* 3.2 32.8 - - + +
258B LYS* 4.0 39.7 - - + +
261B ALA* 4.6 0.2 - - + -
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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