Contacts of the helix formed by residues 264 - 279 (chain A) in PDB entry 5K9S
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A CYS* 3.2 15.2 - - - -
227A ARG* 2.6 45.5 + - - -
262A HIS* 3.3 22.3 + - + +
263A ASN* 1.3 78.3 - - - +
265A PRO* 1.3 75.2 - - - +
266A GLU 3.1 19.1 + - - -
267A VAL* 3.3 16.7 + - + +
268A LEU* 3.0 24.1 + - - +
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Residues in contact with PRO 265 (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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227A ARG* 5.0 3.1 - - - +
263A ASN* 3.3 8.0 - - - +
264A ASP* 1.3 92.3 - - - +
266A GLU* 1.3 60.0 + - + +
268A LEU* 3.3 5.6 + - + +
269A ALA* 2.9 27.5 + - - +
306A GLU* 4.4 18.8 - - + +
309A ILE* 3.8 22.2 - - + +
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Residues in contact with GLU 266 (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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227A ARG* 3.5 47.5 + - + +
264A ASP* 3.1 9.5 + - - +
265A PRO* 1.3 76.9 - - + +
267A VAL* 1.3 67.1 + - - +
269A ALA* 3.2 7.7 + - - +
270A ASP* 3.0 32.7 + - - +
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Residues in contact with VAL 267 (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 CYS* 6.1 0.4 - - - -
226A LEU* 4.2 17.0 - - + -
227A ARG* 4.0 17.9 - - + +
230A THR* 3.6 30.4 - - - +
259A LEU* 3.6 33.2 - - + +
262A HIS* 4.0 13.2 - - + +
264A ASP* 3.3 27.9 + - + +
266A GLU* 1.3 77.4 - - - +
268A LEU* 1.3 62.4 + - - +
271A SER* 2.9 29.7 + - - +
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Residues in contact with LEU 268 (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 LEU 3.9 4.0 - - - +
260A LEU* 3.1 33.7 - - - +
262A HIS 3.3 24.5 - - - +
263A ASN* 4.0 10.1 - - - +
264A ASP 3.0 19.6 + - - +
265A PRO* 3.5 6.5 - - + +
266A GLU 3.2 0.2 - - - -
267A VAL* 1.3 76.2 - - - +
269A ALA* 1.3 64.2 + - - +
271A SER* 3.7 3.5 - - - -
272A CYS* 3.0 29.7 + - - -
297A GLN* 4.5 0.9 - - - +
301A LEU* 4.0 30.1 - - + -
309A ILE* 4.0 20.2 - - + -
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Residues in contact with ALA 269 (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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265A PRO 2.9 14.0 + - - +
266A GLU* 3.2 11.4 + - - +
268A LEU* 1.3 76.8 - - - +
270A ASP* 1.3 61.2 + - - +
272A CYS* 3.1 5.2 + - - +
273A TRP* 2.9 37.1 + - + +
308A PRO* 3.4 33.7 - - + +
309A ILE* 4.2 5.8 - - + +
312A PRO* 3.9 3.5 - - - +
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Residues in contact with ASP 270 (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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227A ARG* 4.3 4.9 - - - +
230A THR* 3.6 27.0 - - + +
231A TRP* 3.5 33.1 + - - +
234A SER* 3.7 8.8 - - - +
266A GLU* 3.0 20.8 + - - +
269A ALA* 1.3 79.6 - - - +
271A SER* 1.3 56.7 + - - +
273A TRP* 3.2 11.7 + - - +
274A ALA* 2.9 27.7 + - - +
13B THR 4.0 18.2 + - - -
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Residues in contact with SER 271 (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 THR* 3.6 7.5 - - - +
256A LEU* 4.5 10.1 - - - +
259A LEU* 3.2 28.7 - - - +
260A LEU* 3.7 30.5 - - - -
267A VAL 2.9 20.7 + - - -
268A LEU 3.7 2.2 - - - -
270A ASP* 1.3 75.3 - - - +
272A CYS* 1.3 57.7 + - - +
274A ALA* 3.2 8.8 + - - +
275A ILE* 3.0 31.5 + - - +
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Residues in contact with CYS 272 (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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260A LEU* 3.7 8.3 - - - -
268A LEU 3.0 18.1 + - - +
269A ALA 3.4 8.1 - - - +
271A SER* 1.3 71.9 - - - +
273A TRP* 1.3 67.0 + - - +
275A ILE* 3.3 6.4 + - - +
276A SER* 2.9 24.3 + - - -
298A LEU* 4.2 7.4 - - + -
301A LEU* 3.4 30.5 - - - -
309A ILE* 4.5 4.5 - - - -
312A PRO* 3.5 22.5 - - + +
313A ALA* 3.9 22.0 - - - +
316A ALA* 4.6 0.7 - - - +
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Residues in contact with TRP 273 (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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234A SER* 5.1 2.7 - - - +
269A ALA* 2.9 32.0 + - + +
270A ASP* 3.2 18.4 + - - +
272A CYS* 1.3 75.1 - - - +
274A ALA* 1.3 62.7 + - - +
276A SER* 2.8 32.9 + - - -
277A TYR* 2.9 40.7 + + + +
308A PRO 4.4 4.4 + - - -
311A THR* 4.3 15.9 - - + -
312A PRO* 3.5 31.8 - - + +
315A ARG* 4.3 33.0 - - + -
13B THR* 3.5 45.4 - - + +
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Residues in contact with ALA 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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234A SER* 3.9 17.5 - - - -
237A CYS* 4.1 6.7 - - - +
256A LEU* 3.7 29.8 - - + -
270A ASP 2.9 13.9 + - - +
271A SER 3.2 8.9 + - - +
273A TRP* 1.3 75.8 - - - +
275A ILE* 1.3 63.4 + - - +
277A TYR* 3.1 16.6 + - - +
278A LEU* 2.9 26.6 + - - +
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Residues in contact with ILE 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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253A LEU* 4.5 10.3 - - + -
256A LEU* 3.7 26.2 - - + +
257A VAL* 6.1 0.2 - - + -
260A LEU* 4.3 23.8 - - + -
271A SER 3.0 17.1 + - - +
272A CYS* 3.7 7.9 - - - +
274A ALA* 1.3 75.9 - - - +
276A SER* 1.3 60.8 + - - +
278A LEU* 3.2 5.3 + - + +
279A THR* 2.9 30.5 + - + +
289A VAL* 3.7 30.3 - - + -
294A VAL* 4.8 7.0 - - + -
298A LEU* 4.1 22.9 - - + -
316A ALA* 4.1 7.9 - - + -
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Residues in contact with SER 276 (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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272A CYS 2.9 14.4 + - - -
273A TRP* 2.8 31.1 + - - -
275A ILE* 1.3 76.9 - - - +
277A TYR* 1.3 65.5 + - - +
279A THR* 3.2 8.7 + - - -
280A ASP* 3.3 6.2 + - - +
312A PRO 3.8 4.3 - - - -
315A ARG* 3.8 27.2 + - - +
316A ALA* 3.8 14.8 - - - +
319A ASN* 2.9 22.0 + - - -
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Residues in contact with TYR 277 (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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234A SER* 3.5 31.2 + - - -
235A ASN* 5.2 0.4 - - - -
237A CYS 3.5 18.1 - - - +
238A ARG* 3.3 58.6 + - + -
239A ASN 5.1 2.0 - - - +
240A LYS* 5.8 1.9 - - - +
273A TRP* 2.9 52.4 + + + +
274A ALA* 3.1 9.8 + - - +
276A SER* 1.3 81.3 - - - +
278A LEU* 1.3 63.6 + - - +
280A ASP* 3.1 24.2 + - - +
285A ARG* 5.7 0.5 - - - -
13B THR* 3.7 13.9 + - - -
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Residues in contact with LEU 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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237A CYS* 3.6 35.0 - - + +
244A PRO* 4.8 3.6 - - + -
249A VAL* 3.8 43.5 - - + -
252A ILE* 5.9 1.1 - - + -
253A LEU* 4.1 15.7 - - + -
256A LEU* 3.9 28.5 - - + -
274A ALA 2.9 16.7 + - - +
275A ILE* 3.2 3.6 + - - +
277A TYR* 1.3 76.1 - - - +
279A THR* 1.3 60.3 + - - +
280A ASP 3.5 0.9 + - - -
285A ARG* 3.5 36.4 - - - +
289A VAL* 3.8 15.0 - - + -
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Residues in contact with THR 279 (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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275A ILE* 2.9 23.8 + - + +
276A SER* 3.2 3.5 + - - -
277A TYR 3.2 0.2 - - - -
278A LEU* 1.3 74.4 - - - +
280A ASP* 1.3 58.7 + - - +
281A GLY 3.2 7.3 + - - -
286A ILE* 3.6 29.9 - - - +
289A VAL* 3.9 32.3 - - + -
316A ALA* 3.9 3.8 + - - -
319A ASN* 3.2 38.2 + - - +
320A ILE* 3.9 21.8 - - + -
322A THR* 5.3 0.3 + - - -
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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