Contacts of the helix formed by residues 220 - 230 (chain B) in PDB entry 3NX4
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A VAL* 4.0 9.9 - - - -
217B ASP* 2.8 24.0 + - - -
219B VAL* 1.3 75.4 - - - +
221B ASP* 1.3 75.9 + - - +
223B VAL 3.4 4.3 + - - -
224B LEU* 3.1 20.1 + - - -
241B GLY 3.7 11.5 + - - -
245B GLY 3.9 4.0 - - - -
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Residues in contact with ASP 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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252A VAL* 4.5 1.0 - - - +
219B VAL* 5.3 0.7 - - + -
220B GLY* 1.3 75.9 - - - +
222B LYS* 1.3 98.4 + - - +
223B VAL 4.7 0.2 - - - +
224B LEU* 3.8 1.8 - - - +
225B ALA* 3.2 18.5 + - - +
244B GLY* 3.5 28.7 - - - +
245B GLY* 3.3 14.1 + - - +
247B ALA* 2.9 43.0 + - - +
248B LEU* 4.3 1.8 - - - +
249B PRO* 3.8 12.2 - - - +
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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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201B PHE 4.2 4.9 - - - +
202B ALA* 3.4 29.1 - - - +
203B GLU* 5.5 3.8 - - - +
204B SER* 5.2 0.3 + - - -
221B ASP* 1.3 102.0 + - - +
223B VAL* 1.3 65.0 + - + +
225B ALA* 3.3 8.9 + - - +
226B LYS* 3.0 24.4 + - - +
249B PRO* 4.6 11.9 - - + -
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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
----------------------------------------------------------
153B THR* 3.7 33.7 - - + -
177B VAL* 5.4 3.1 - - + -
198B ARG* 4.4 20.0 - - + -
201B PHE* 3.8 34.4 - - + +
217B ASP* 4.0 4.3 - - - +
219B VAL* 3.6 29.2 - - + -
221B ASP 3.3 0.8 - - - -
222B LYS* 1.3 77.2 - - + +
224B LEU* 1.3 62.8 + - - +
226B LYS* 3.2 4.3 + - - +
227B VAL* 3.0 23.5 + - + +
330B NAP 4.9 1.6 - - + -
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Residues in contact with LEU 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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252A VAL* 3.8 27.6 - - + -
217B ASP* 3.5 37.2 + - + +
220B GLY 3.1 14.0 + - - +
221B ASP 3.8 1.3 - - - +
223B VAL* 1.3 77.7 - - - +
225B ALA* 1.3 65.5 + - - +
227B VAL* 3.3 6.5 + - + +
228B LEU* 3.0 32.0 + - + +
237B VAL* 3.8 26.7 - - + -
239B ALA* 4.2 13.2 - - + -
248B LEU* 3.9 22.0 - - + -
262B LEU* 4.6 5.4 - - + -
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Residues in contact with ALA 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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204B SER* 4.0 9.5 + - - +
221B ASP 3.2 13.1 + - - +
222B LYS* 3.5 12.3 - - + +
223B VAL 3.2 0.2 - - - -
224B LEU* 1.3 79.4 - - - +
226B LYS* 1.3 61.8 + - - +
228B LEU* 3.4 8.6 + - - +
229B ALA* 3.2 20.3 + - - +
248B LEU* 4.4 6.3 - - + +
249B PRO* 3.5 31.2 - - + +
250B THR* 4.6 6.9 + - - -
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Residues in contact with LYS 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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200B GLU 2.9 20.5 + - - +
201B PHE* 3.5 31.3 - - + +
202B ALA 4.6 1.6 - - - +
203B GLU 3.4 27.5 + - - +
204B SER* 3.6 18.3 + - - +
208B GLU* 4.3 15.4 + - + -
222B LYS 3.0 15.4 + - - +
223B VAL 3.2 3.8 + - - +
225B ALA* 1.3 75.6 - - - +
227B VAL* 1.3 65.5 + - - +
229B ALA* 3.1 10.7 + - - +
230B GLN* 3.2 43.5 + - + +
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Residues in contact with VAL 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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151B VAL* 4.1 12.1 - - + -
153B THR* 4.2 23.8 - - + -
201B PHE* 4.2 17.7 - - + -
212B TRP* 4.2 1.8 - - + +
215B ALA* 3.5 31.4 - - + -
217B ASP* 5.2 2.5 - - + +
223B VAL 3.0 21.5 + - - +
224B LEU* 3.3 9.2 + - + +
226B LYS* 1.3 76.4 - - - +
228B LEU* 1.3 62.9 + - - +
230B GLN* 2.9 19.3 + - - +
231B MSE 3.3 21.4 + - - +
237B VAL* 4.2 7.6 - - + -
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Residues in contact with LEU 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 LEU* 3.0 35.1 + - + +
225B ALA 3.6 7.0 - - - +
227B VAL* 1.3 76.5 - - - +
229B ALA* 1.3 61.1 + - - +
230B GLN 3.0 1.6 + - - -
231B MSE 3.3 18.2 + - - +
237B VAL* 3.9 24.5 - - + -
248B LEU* 4.3 6.3 - - + -
250B THR* 3.8 29.8 - - + +
254B PRO* 3.5 22.4 - - + +
255B PHE* 3.9 33.2 - - + -
258B ARG* 5.2 0.5 + - - -
260B VAL* 4.3 10.1 - - + -
262B LEU* 4.4 13.9 - - + -
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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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204B SER* 4.3 2.7 - - - +
205B ARG 3.5 16.6 - - - +
206B PRO 3.5 24.7 - - - +
208B GLU* 2.8 38.4 + - + +
225B ALA 3.2 10.3 + - - +
226B LYS 3.1 10.8 + - - +
228B LEU* 1.3 78.0 - - - +
230B GLN* 1.3 56.5 + - - +
231B MSE 3.5 0.2 - - - -
254B PRO* 4.2 4.4 - - + +
258B ARG* 3.0 15.3 + - - +
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Residues in contact with GLN 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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200B GLU 5.5 0.4 + - - -
201B PHE* 3.4 20.3 - - - -
208B GLU* 3.7 21.3 + - + +
209B LYS 3.7 12.3 - - - +
210B GLN* 4.3 0.7 - - - -
211B LEU* 2.7 50.4 + - + +
212B TRP* 2.9 30.9 + - + +
226B LYS* 3.2 39.9 - - - +
227B VAL* 2.9 9.9 + - - +
229B ALA* 1.3 80.1 - - - +
231B MSE 1.3 58.4 + - - +
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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