Contacts of the helix formed by residues 245 - 256 (chain B) in PDB entry 3NZG
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 ASP 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B THR* 4.3 9.0 - - - +
219B TRP 5.6 0.5 + - - -
241B LEU* 3.8 17.8 - - + +
242B GLN* 2.9 26.2 + - + +
243B HIS 3.3 0.2 - - - -
244B ASP* 1.3 74.1 - - - +
246B LEU* 1.3 63.1 + - - +
247B SER* 3.3 8.7 + - - -
248B GLY* 2.9 30.7 + - - -
249B HIS* 2.8 23.7 + - - -
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Residues in contact with LEU 246 (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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243B HIS 3.5 22.9 - - - +
244B ASP* 3.0 16.2 + - - +
245B ASP* 1.3 71.4 - - - +
247B SER* 1.3 62.0 - - - +
249B HIS* 3.1 17.7 + - - +
250B ALA 3.1 9.7 + - - -
274B GLU* 3.2 58.1 - - + +
275B TRP* 3.6 36.8 - - + +
278B LYS* 3.9 16.7 - - + +
279B GLY* 3.5 14.0 - - - +
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ASP* 3.6 4.5 + - - -
246B LEU* 1.3 78.0 - - - +
248B GLY* 1.3 65.4 + - - +
250B ALA* 3.3 10.3 + - - +
251B LYS* 3.2 25.3 + - - +
278B LYS* 4.3 20.2 - - - +
501B MG 2.3 31.5 - - - -
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TRP* 3.8 7.3 - - - +
241B LEU* 3.3 17.5 - - - +
245B ASP* 2.9 32.0 + - - -
247B SER* 1.3 79.2 + - - +
249B HIS* 1.3 61.4 + - - +
251B LYS* 3.2 20.2 + - - +
252B LEU 3.2 8.8 + - - -
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Residues in contact with HIS 249 (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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214B TYR* 6.0 1.0 - - - -
239B ALA* 5.6 1.8 - - - -
240B THR* 4.0 16.4 + - - -
241B LEU* 3.6 25.2 + - + +
242B GLN 3.5 24.7 - - - -
243B HIS* 4.9 0.2 - - - -
245B ASP 2.8 24.0 + - - -
246B LEU* 3.1 9.5 + - - +
248B GLY* 1.3 74.8 - - - +
250B ALA* 1.3 65.1 + - - +
252B LEU* 3.1 8.1 + - + +
253B VAL* 3.0 25.1 + - - +
260B ILE* 3.9 13.6 - - + +
261B CYS 3.6 23.0 + - - -
262B GLY* 5.1 0.2 - - - -
275B TRP* 3.7 26.5 - + - -
279B GLY* 3.6 11.2 - - - +
281B VAL* 4.3 7.6 - - + -
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Residues in contact with ALA 250 (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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246B LEU 3.1 6.7 + - - +
247B SER* 3.5 11.4 - - - +
249B HIS* 1.3 76.4 - - - +
251B LYS* 1.3 58.3 + - - +
253B VAL* 3.2 2.0 + - - +
254B GLU* 2.9 43.1 + - - +
278B LYS 3.4 23.6 - - - +
279B GLY 3.3 10.9 + - - +
280B LYS* 4.0 18.4 - - + -
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Residues in contact with LYS 251 (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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219B TRP* 3.5 54.5 - - + +
247B SER* 3.2 17.0 + - - +
248B GLY* 3.3 10.8 - - - +
249B HIS 3.1 0.4 - - - -
250B ALA* 1.3 77.6 - - + +
252B LEU* 1.3 56.3 + - - +
254B GLU* 3.3 15.9 + - - +
255B ASN* 2.8 39.7 + - - +
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Residues in contact with LEU 252 (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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219B TRP* 3.3 29.4 - - + +
222B VAL* 3.7 25.6 - - + -
223B ALA* 3.8 12.6 - - + +
226B LEU* 4.9 0.4 - - + -
240B THR* 3.3 27.6 - - - +
241B LEU* 3.8 14.8 - - + -
248B GLY 3.2 10.3 + - - +
249B HIS* 3.1 9.9 + - - +
251B LYS* 1.3 79.2 - - - +
253B VAL* 1.3 60.6 + - - +
255B ASN* 5.1 0.2 - - - -
256B THR* 2.7 40.2 + - + +
260B ILE* 4.0 26.5 - - + -
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Residues in contact with VAL 253 (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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249B HIS 3.0 16.8 + - - +
250B ALA 3.5 7.0 - - - +
252B LEU* 1.3 74.6 - - - +
254B GLU* 1.3 64.8 + - + +
256B THR* 3.3 16.3 - - - +
260B ILE* 3.8 28.0 - - + -
279B GLY 3.9 2.0 - - - +
280B LYS* 3.3 46.7 - - + +
281B VAL* 4.3 0.4 - - - -
282B HIS* 4.1 20.1 - - + +
255C ASN* 5.7 0.9 - - - +
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Residues in contact with GLU 254 (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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250B ALA* 2.9 27.6 + - - +
251B LYS* 3.8 20.1 + - - +
253B VAL* 1.3 79.0 - - + +
255B ASN* 1.3 70.1 + - - +
256B THR 3.8 0.4 - - - -
280B LYS* 2.6 41.4 + - + +
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Residues in contact with ASN 255 (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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219B TRP* 3.6 34.6 - - + -
223B ALA* 4.7 5.2 - - + -
227B ASN* 3.1 21.5 + - - +
251B LYS* 2.8 33.2 + - - +
254B GLU* 1.3 96.0 + - - +
256B THR* 1.3 60.6 + - - +
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Residues in contact with THR 256 (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 ALA* 3.7 31.9 - - + +
226B LEU* 4.3 17.3 - - + -
227B ASN* 3.3 15.0 - - - +
252B LEU* 2.7 26.2 + - + +
253B VAL* 3.3 14.9 - - - +
254B GLU 3.8 0.9 - - - -
255B ASN* 1.3 83.1 - - - +
257B ARG* 1.3 66.8 + - - +
258B SER* 3.4 20.1 + - - +
260B ILE* 4.1 4.7 - - - +
282B HIS* 5.8 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