Contacts of the helix formed by residues 248 - 260 (chain B) in PDB entry 3NO1
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 ASN 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B GLU 4.0 2.9 + - - -
247B HIS* 1.3 86.0 + - - +
249B ASP* 1.3 64.3 + - - +
250B LYS* 3.2 3.7 + - - -
251B ARG* 3.4 26.7 + - - +
252B SER* 3.0 28.0 + - - +
310C SER 3.2 18.5 - - - +
311C TYR* 3.4 20.2 + - - +
312C ASP* 3.6 13.0 - - - +
274D SER* 4.4 0.2 - - - -
277D ARG* 2.8 29.7 + - - +
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Residues in contact with ASP 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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218B GLN* 4.0 14.4 + - + +
242B GLU* 5.3 4.0 - - - +
244B VAL* 3.7 15.5 - - + +
245B GLU 3.6 14.2 + - - +
246B TRP* 3.2 20.7 + - - +
247B HIS 4.8 1.4 - - - +
248B ASN* 1.3 76.0 - - - +
250B LYS* 1.3 80.1 + - - +
253B MSE 2.7 45.1 + - - +
266B ALA* 5.9 0.9 - - - +
269B THR* 5.4 4.7 - - - +
270B GLU* 4.4 11.7 - - - +
279B LEU* 5.0 5.4 - - - +
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Residues in contact with LYS 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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248B ASN 3.2 1.2 + - - -
249B ASP* 1.3 94.1 + - - +
251B ARG* 1.3 70.1 + - + +
253B MSE 4.2 0.9 - - - -
254B ARG* 3.2 17.3 + - - +
270B GLU* 4.4 14.5 + - - +
275B GLY* 5.8 0.4 - - - -
278B ASP* 3.9 38.3 + - + +
279B LEU* 3.9 22.0 - - + +
282B THR* 3.8 27.6 - - + +
284B ALA* 3.3 19.3 - - - +
250D LYS* 5.2 6.8 - - - +
278D ASP* 4.0 21.8 + - - -
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASN* 3.4 24.0 + - - +
250B LYS* 1.3 84.7 - - + +
252B SER* 1.3 66.0 + - - +
254B ARG* 3.3 31.9 + - - +
255B ASP* 3.1 28.6 + - - +
282B THR* 4.0 16.9 + - + -
280C MSE 5.4 0.4 - - - -
281C GLU* 3.1 40.3 + - - -
311C TYR* 3.6 20.4 - - + -
277D ARG* 3.4 14.5 - - - +
278D ASP* 2.9 32.8 + - - +
281D GLU* 4.1 11.7 - - - +
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Residues in contact with SER 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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222B PRO* 3.5 15.7 - - - +
244B VAL* 3.6 19.1 - - - -
248B ASN* 3.0 22.9 + - - +
251B ARG* 1.3 78.1 - - - +
253B MSE 1.3 57.5 + - - +
255B ASP* 3.2 11.8 + - - +
256B VAL* 3.0 27.6 + - - +
311C TYR 4.4 0.5 + - - -
312C ASP* 2.5 36.1 + - - +
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Residues in contact with MSE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLU* 4.8 2.2 - - - +
243B PRO* 3.7 24.5 - - + -
244B VAL* 3.7 5.5 - - + +
249B ASP* 2.7 34.8 + - - +
252B SER* 1.3 70.9 - - - +
254B ARG* 1.3 58.2 + - - +
256B VAL* 3.4 9.5 - - - +
257B ARG* 2.7 35.9 + - - +
264B VAL* 2.9 23.7 - - + +
265B CYS 4.2 0.4 - - - -
266B ALA* 3.5 23.1 - - + -
279B LEU* 4.1 10.5 - - - -
284B ALA* 2.7 44.0 - - + +
285B ILE* 2.8 29.4 - - + -
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Residues in contact with ARG 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 LYS 3.2 16.2 + - - +
251B ARG* 3.4 41.2 + - - +
252B SER 3.2 0.2 - - - -
253B MSE 1.3 77.0 - - - +
255B ASP* 1.3 95.9 + - - +
257B ARG* 3.2 5.2 + - - +
258B TYR* 2.9 49.7 + - + -
282B THR* 3.8 20.5 + - + +
283B GLY 3.7 21.5 - - - +
284B ALA* 3.9 5.4 - - - +
258C TYR* 3.4 18.2 + - - -
280C MSE 5.2 2.2 + - - -
281C GLU* 4.3 15.6 + - - -
282C THR 5.1 1.4 + - - -
283C GLY* 4.0 13.9 - - - -
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Residues in contact with ASP 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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222B PRO* 5.7 6.4 - - + +
226B VAL* 4.7 0.4 - - + -
251B ARG* 3.1 16.9 + - - +
252B SER* 3.5 9.9 - - - +
253B MSE 3.1 0.6 - - - -
254B ARG* 1.3 100.4 + - - +
256B VAL* 1.3 56.6 + - + +
258B TYR 4.3 0.2 - - - +
259B GLN* 2.7 55.5 + - - +
257C ARG* 3.1 25.0 + - - +
258C TYR* 2.9 22.8 + - - -
311C TYR 5.6 1.2 - - - +
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Residues in contact with VAL 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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222B PRO* 4.1 12.8 - - + +
225B ALA* 3.8 38.1 - - + +
226B VAL* 3.9 9.6 - - + +
229B SER* 4.8 3.5 + - - -
240B PHE* 4.2 15.3 - - + -
243B PRO* 4.2 14.4 - - + -
244B VAL* 3.8 15.9 - - + -
252B SER 3.0 18.4 + - - +
253B MSE 3.0 11.1 + - - +
255B ASP* 1.3 74.6 - - - +
257B ARG* 1.3 57.4 + - - +
260B GLY* 2.7 34.0 + - - -
262B VAL 5.1 1.8 - - - +
264B VAL* 4.5 5.6 - - + +
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B MSE 2.7 12.2 + - - +
254B ARG* 3.2 10.3 - - - +
256B VAL* 1.3 78.7 - - - +
258B TYR* 1.3 70.6 + - + +
260B GLY 4.1 9.0 + - - +
261B SER* 5.6 0.2 - - - -
262B VAL 4.6 6.3 + - - +
264B VAL* 3.5 16.8 - - + +
283B GLY* 2.9 35.6 + - - -
284B ALA 3.7 12.3 - - - -
285B ILE 3.6 14.4 + - - -
286B ASP* 2.8 45.0 + - - +
230E ARG* 5.7 1.4 + - - -
255E ASP* 2.9 38.9 + - - +
259E GLN* 3.4 27.7 + - - +
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Residues in contact with TYR 258 (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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254B ARG* 2.9 34.7 + - + +
255B ASP 4.1 0.2 - - - +
257B ARG* 1.3 103.4 + - + +
259B GLN* 1.3 62.5 + - - +
260B GLY 3.4 3.6 - - - +
282B THR 4.9 0.8 + - - -
283B GLY* 3.8 10.9 + - - -
258C TYR* 3.4 63.2 - + + +
254E ARG* 3.3 17.9 + - - -
255E ASP* 2.8 31.8 + - - -
258E TYR* 3.6 46.7 - + + +
259E GLN* 4.5 5.8 - - + -
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Residues in contact with GLN 259 (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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222B PRO* 6.0 1.4 - - - +
226B VAL* 3.9 25.9 - - + +
230B ARG* 2.8 39.4 + - - +
255B ASP* 2.7 36.2 + - - +
258B TYR* 1.3 72.6 - - - +
260B GLY* 1.3 66.1 + - - +
261B SER* 5.0 0.2 + - - -
257C ARG* 3.5 32.1 + - - +
258C TYR* 4.5 8.5 - - + -
262C VAL 5.5 1.2 + - - -
263C PRO* 4.6 8.5 - - - +
286C ASP* 2.8 37.4 + - - +
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Residues in contact with GLY 260 (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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226B VAL* 4.3 4.9 - - - +
229B SER* 3.4 15.5 - - - -
230B ARG* 4.5 6.3 - - - -
256B VAL 2.7 26.7 + - - -
257B ARG 4.3 6.4 - - - +
258B TYR 3.4 5.6 - - - +
259B GLN* 1.3 79.6 - - - +
261B SER* 1.3 66.4 + - - -
262B VAL 3.8 0.4 - - - -
230E ARG* 4.7 3.3 + - - -
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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