Contacts of the helix formed by residues 248 - 263 (chain A) in PDB entry 3OQN
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 THR 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PHE* 6.4 0.9 - - + -
197A LYS* 4.9 0.3 + - - -
222A TYR* 3.1 32.6 - - + -
246A SER* 2.5 25.1 + - - -
247A ALA* 1.3 83.1 + - - +
249A ASP* 1.3 65.2 + - + +
250A GLU* 3.4 27.6 - - + +
251A MET* 3.4 15.0 + - - +
252A ALA* 3.0 12.5 + - - +
275A PHE 3.6 10.5 - - - -
276A ASP* 3.8 15.4 + - - +
278A THR* 6.1 0.9 - - + -
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Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A THR* 1.3 73.3 - - + +
250A GLU* 1.3 71.5 + - + +
252A ALA* 2.9 13.9 + - - +
253A LEU* 2.9 17.9 + - - +
274A GLY* 3.7 0.7 - - - -
275A PHE 3.0 31.9 + - - +
277A ASN 3.3 1.8 + - - -
278A THR* 2.8 50.4 + - + +
280A LEU* 4.5 10.1 - - + -
281A SER* 3.2 11.0 + - - -
288A LEU* 3.9 7.7 - - + +
290A THR* 3.0 14.8 + - - +
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 4.3 12.9 + - + +
222A TYR* 2.9 22.6 - - + +
223A THR* 5.0 0.3 - - - -
224A TYR* 3.6 27.6 + - - +
248A THR* 3.3 14.3 - - + +
249A ASP* 1.3 81.9 - - + +
251A MET* 1.3 64.0 + - - +
253A LEU* 3.1 1.2 + - - +
254A GLY 3.1 13.9 + - - -
280A LEU* 4.3 14.4 - - + +
279C ARG* 2.9 36.1 + - - -
283C MET* 3.6 22.9 - - - +
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Residues in contact with MET 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 4.1 10.5 - - + +
185A SER 3.2 35.7 - - - +
220A GLY* 3.8 10.5 - - - -
222A TYR* 3.6 39.9 - - + -
223A THR 3.8 9.0 - - - +
226A SER* 3.9 2.9 - - - +
227A GLY* 3.7 13.8 - - - +
246A SER* 3.3 14.8 - - - +
247A ALA* 4.1 4.5 - - + +
248A THR* 3.4 39.3 + - - +
249A ASP 3.3 0.4 - - - -
250A GLU* 1.3 79.8 - - - +
252A ALA* 1.3 56.9 + - - +
254A GLY* 2.9 3.4 + - - +
255A ILE* 2.8 33.4 + - - +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A SER* 3.3 6.0 + - - -
248A THR 3.0 15.6 + - - +
249A ASP* 2.9 11.8 + - - +
251A MET* 1.3 75.9 - - - +
253A LEU* 1.3 56.3 + - - +
255A ILE* 2.7 31.3 + - - +
256A ILE* 2.8 17.3 + - - +
272A ILE* 4.9 3.1 - - + -
274A GLY* 4.0 13.9 - - - +
288A LEU* 3.4 28.9 - - + -
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 3.5 23.3 - - + -
249A ASP 2.9 18.8 + - - +
250A GLU 3.7 2.0 - - - +
252A ALA* 1.3 73.4 - - - +
254A GLY* 1.3 62.8 + - - +
256A ILE* 4.2 7.6 - - + -
257A HIS* 3.1 25.3 + - - +
280A LEU* 4.1 31.0 - - + -
283A MET 5.5 1.3 - - - +
284A VAL* 3.3 46.2 - - + -
288A LEU* 3.5 19.7 - - + -
283C MET* 4.1 22.4 - - + +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 3.2 29.8 - - - -
228A LEU* 2.8 37.7 - - - +
250A GLU 3.1 6.5 + - - -
251A MET 2.9 11.0 + - - -
253A LEU* 1.3 79.2 - - - +
255A ILE* 1.3 54.7 + - - +
258A ALA* 3.0 11.6 + - - +
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.9 28.3 - - + -
227A GLY* 3.4 22.0 - - - +
231A LEU* 3.2 33.9 - - + +
244A ILE* 4.2 15.5 - - + -
246A SER* 4.5 7.4 - - - -
251A MET 2.8 27.0 + - - +
252A ALA* 2.7 14.8 + - - +
254A GLY* 1.3 76.4 - - - +
256A ILE* 1.3 67.9 + - - +
258A ALA 3.3 1.0 + - - -
259A ALA* 3.0 17.3 + - - +
272A ILE* 3.3 31.2 - - + -
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Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA 2.8 17.1 + - - +
253A LEU* 3.9 10.3 - - + +
255A ILE* 1.3 77.2 - - - +
257A HIS* 1.3 70.0 + - + +
259A ALA* 3.0 3.6 + - - +
260A GLN* 2.9 56.9 + - + +
266A ILE* 4.3 11.2 - - + +
272A ILE* 3.3 41.5 - - + -
284A VAL* 4.8 8.1 - - + -
285A ARG 4.3 1.1 - - - +
286A PRO* 4.2 14.8 - - + +
288A LEU* 4.3 10.5 - - + -
331A SER* 3.7 15.3 - - - +
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Residues in contact with HIS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 3.1 23.1 + + - +
228A LEU* 4.3 1.3 - - + -
253A LEU* 3.1 13.8 + - + +
256A ILE* 1.3 90.7 - - + +
258A ALA* 1.3 63.6 + - - +
259A ALA 2.9 1.4 + - - -
260A GLN* 3.0 28.1 + - - -
261A ASP* 2.7 29.8 + - - +
284A VAL* 3.5 22.5 - - + +
285A ARG* 4.3 5.6 + - - +
283C MET 3.4 23.3 - - - -
284C VAL* 3.7 17.0 - - + -
285C ARG* 3.3 36.1 + - + +
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.2 38.3 - - + +
231A LEU* 3.1 15.2 - - + +
232A GLN* 5.0 4.8 - - + +
254A GLY 3.0 21.4 + - - +
255A ILE 3.3 1.6 + - - -
257A HIS* 1.3 77.0 - - - +
259A ALA* 1.3 57.9 + - - +
261A ASP* 3.8 7.3 - - - +
262A GLN* 3.1 28.6 + - - +
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.2 21.7 - - + +
255A ILE 3.0 13.0 + - - +
256A ILE 3.0 9.6 + - - +
257A HIS 3.0 0.4 - - - -
258A ALA* 1.3 74.5 - - - +
260A GLN* 1.3 55.7 + - - +
261A ASP 2.9 4.3 - - - -
262A GLN* 2.6 26.4 + - - +
263A GLY 3.1 7.6 + - - -
264A LEU* 3.6 24.8 + - + -
266A ILE* 3.8 18.4 - - + -
270A LEU* 4.8 1.3 - - + -
272A ILE* 5.2 0.2 - - + -
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Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 2.9 26.5 + - + +
257A HIS* 3.0 34.6 - - - +
259A ALA* 1.3 71.9 - - - +
261A ASP* 1.3 63.6 + - - +
263A GLY* 3.4 12.5 + - - +
264A LEU 3.4 15.6 + - - +
265A SER* 5.6 0.2 - - - -
266A ILE* 4.6 13.6 + - + +
285A ARG 3.0 24.7 + - - +
286A PRO* 3.5 15.4 - - - +
285C ARG* 4.8 8.8 - - + +
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Residues in contact with ASP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 5.4 0.9 - - - +
257A HIS 2.7 23.1 - - - +
258A ALA* 3.8 8.1 - - - +
259A ALA 2.8 1.6 + - - -
260A GLN* 1.3 76.9 - - - +
262A GLN* 1.3 58.3 + - + +
263A GLY* 2.9 9.9 + - - -
285C ARG* 2.7 42.7 + - - -
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Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.5 17.6 - - - +
232A GLN* 3.6 26.9 - - + +
235A MET* 3.6 27.8 - - - +
258A ALA 3.1 15.9 - - - +
259A ALA 2.6 10.9 + - - +
261A ASP* 1.3 70.7 - - + +
263A GLY* 1.3 56.9 + - - +
264A LEU* 3.5 20.3 + - + +
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ALA 3.1 1.4 + - - -
260A GLN 3.4 6.7 + - - +
261A ASP 2.9 8.5 + - - -
262A GLN* 1.3 79.7 - - - +
264A LEU* 1.3 71.2 + - - +
265A SER* 3.2 10.6 + - - -
269A ASP* 4.8 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