Contacts of the helix formed by residues 273 - 286 (chain A) in PDB entry 3F98
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 SER 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A HIS* 1.6 64.2 - - - +
274A PHE* 1.4 54.2 + - - -
276A GLY* 2.8 20.0 + - - +
277A ALA 3.2 3.3 + - - -
295A LEU 2.7 14.1 + - - -
296A ASP* 3.0 21.7 + - - -
298A TRP* 3.1 24.6 + - - +
322A PHE* 4.7 1.3 - - - -
351A HIS* 5.2 2.2 - - - -
473A NTJ 1.6 57.6 + - - -
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Residues in contact with PHE 274 (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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153A LEU* 3.7 16.2 - - + +
183A SER* 3.8 19.5 - - - -
218A ARG* 4.0 12.1 - - - -
221A GLN* 3.4 40.2 - - + -
222A VAL* 4.1 8.5 - - + -
225A ARG* 3.6 34.1 - - - -
272A HIS 3.3 0.4 + - - -
273A SER* 1.4 65.9 + - - -
275A GLY* 1.3 58.6 + - - +
277A ALA* 3.3 4.4 + - + +
278A THR* 2.9 28.3 + - - -
298A TRP* 3.7 31.2 - + + +
301A PRO* 3.5 26.9 - - + -
473A NTJ 2.7 21.7 + - - +
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Residues in contact with GLY 275 (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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150A SER* 3.3 32.2 - - - -
151A HIS 3.5 4.1 + - - -
271A GLY* 3.5 9.2 - - - -
272A HIS 2.8 15.0 + - - -
274A PHE* 1.3 77.5 - - - +
276A GLY* 1.3 58.3 + - - -
277A ALA 3.4 0.2 - - - -
278A THR* 3.3 3.9 + - - -
279A VAL* 2.9 30.0 + - - +
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLY 3.7 13.0 - - - -
272A HIS 3.4 5.9 - - - -
273A SER 2.8 10.1 + - - -
275A GLY* 1.3 73.5 - - - +
277A ALA* 1.3 63.2 + - - +
279A VAL* 3.2 13.1 + - - +
280A ILE* 3.3 17.2 + - - +
294A ALA* 3.9 17.9 - - - +
297A ALA* 3.9 13.7 - - - -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL* 3.8 10.8 - - + -
273A SER 3.2 5.5 + - - -
274A PHE 3.5 9.2 - - - +
276A GLY* 1.3 75.7 - - - +
278A THR* 1.3 57.6 + - - +
280A ILE* 3.1 3.8 + - - +
281A GLN* 2.9 24.4 + - - +
297A ALA* 4.2 2.0 - - - +
298A TRP 3.1 26.5 + - - +
299A MET* 5.3 0.2 - - - -
301A PRO* 4.3 9.9 - - + -
302A LEU* 3.5 34.0 - - + +
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Residues in contact with THR 278 (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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150A SER* 3.5 18.2 - - - +
222A VAL* 3.9 9.2 - - - +
225A ARG* 3.1 43.5 + - + +
226A ALA 4.1 0.2 - - - +
229A CYS* 3.6 25.6 - - - -
269A VAL* 5.7 0.2 - - + -
274A PHE 2.9 15.3 + - - -
275A GLY 3.3 9.2 - - - -
276A GLY 3.2 0.2 - - - -
277A ALA* 1.3 73.0 - - - +
279A VAL* 1.3 57.8 + - - +
281A GLN* 3.4 1.0 + - - +
282A THR* 2.7 41.9 + - - +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 3.9 16.1 - - + +
270A ILE* 3.4 13.0 - - - +
271A GLY* 3.3 24.7 - - - +
275A GLY 2.9 20.1 + - - +
276A GLY* 3.3 10.8 - - - +
278A THR* 1.3 75.6 - - - +
280A ILE* 1.3 58.1 + - - +
282A THR* 3.6 1.6 - - - -
283A LEU* 2.9 32.0 + - + +
292A GLY* 3.7 28.5 - - - -
293A ILE 3.5 12.3 - - - +
294A ALA* 4.6 1.3 - - + +
314A LEU* 4.0 16.4 - - + -
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Residues in contact with ILE 280 (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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276A GLY 3.6 13.0 - - - +
277A ALA 3.1 7.7 + - - +
279A VAL* 1.3 75.2 - - - +
281A GLN* 1.3 65.2 + - - +
283A LEU* 3.4 3.6 + - - +
284A SER* 3.1 22.2 + - - -
294A ALA* 4.9 0.2 - - + -
297A ALA* 4.8 0.7 - - + -
299A MET* 3.6 35.9 - - + -
302A LEU* 3.7 18.2 - - + -
306A VAL* 3.7 9.8 - - + +
307A TYR* 5.0 2.5 - - + -
310A ILE* 3.5 25.8 - - + +
314A LEU* 3.9 22.9 - - + -
316A PHE* 3.8 22.7 - - + -
334A CYS* 4.3 6.7 - - - -
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Residues in contact with GLN 281 (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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219A ASN* 4.8 2.8 + - - -
222A VAL* 3.7 32.7 - - + +
223A ARG* 4.2 23.0 - - - +
226A ALA* 3.5 20.2 - - + -
277A ALA 2.9 15.8 + - - +
278A THR 3.9 2.7 - - - +
280A ILE* 1.3 76.1 - - - +
282A THR* 1.3 62.7 + - - +
284A SER* 2.7 31.4 + - - -
285A GLU* 2.9 35.3 + - - +
302A LEU* 3.7 10.1 - - + +
305A GLU* 4.7 3.1 + - - +
306A VAL* 3.5 25.9 - - - +
309A ARG* 6.1 0.8 - - - +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 3.3 25.5 - - - +
229A CYS* 3.8 18.4 - - + +
230A SER* 4.3 8.5 - - - +
269A VAL* 4.4 9.0 - - + -
278A THR* 2.7 30.0 + - - +
279A VAL 3.6 4.0 - - - -
281A GLN* 1.3 73.2 - - - +
283A LEU* 1.3 63.7 + - - +
285A GLU* 3.0 3.6 + - - +
286A ASP* 2.9 23.7 + - - +
289A PHE* 3.3 38.8 - - + -
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Residues in contact with LEU 283 (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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269A VAL* 3.8 12.6 - - + -
279A VAL* 2.9 28.0 + - + +
280A ILE* 3.7 6.7 - - - +
282A THR* 1.3 75.8 - - - +
284A SER* 1.3 61.6 + - - +
285A GLU 3.2 1.0 + - - -
286A ASP 3.6 5.0 + - - -
287A GLN* 3.5 10.7 + - - -
289A PHE* 3.8 11.7 - - + +
291A CYS 3.8 24.0 - - - +
292A GLY* 3.9 20.4 - - - +
310A ILE* 3.8 27.1 - - + -
312A GLN* 3.0 38.8 + - + +
313A PRO 4.4 5.4 - - - +
314A LEU* 4.2 11.9 - - + -
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Residues in contact with SER 284 (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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280A ILE 3.1 5.8 + - - -
281A GLN* 2.7 23.3 + - - -
282A THR 3.2 0.2 - - - -
283A LEU* 1.3 76.8 - - - +
285A GLU* 1.3 63.1 + - - +
287A GLN* 5.2 2.2 + - - -
306A VAL* 3.2 40.6 - - - +
309A ARG* 3.6 37.2 + - - +
310A ILE* 3.8 8.3 - - - +
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Residues in contact with GLU 285 (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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223A ARG* 4.7 13.7 + - - +
226A ALA* 3.8 18.7 - - - +
227A LYS* 4.5 8.1 + - - +
230A SER* 5.2 4.0 + - - +
281A GLN* 2.9 39.5 + - - +
282A THR* 3.0 5.0 + - - +
284A SER* 1.3 85.9 - - - +
286A ASP* 1.3 60.4 + - + +
287A GLN* 4.2 2.2 + - - -
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Residues in contact with ASP 286 (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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230A SER* 2.7 29.4 + - - +
282A THR 2.9 14.6 + - - +
283A LEU 3.6 4.3 + - - -
284A SER 3.8 0.2 - - - -
285A GLU* 1.3 80.8 - - + +
287A GLN* 1.3 58.9 + - - +
288A ARG* 2.8 55.4 + - - +
289A PHE* 3.3 31.4 + - + +
312A GLN* 3.7 9.0 + - - -
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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