Contacts of the helix formed by residues 253 - 269 (chain A) in PDB entry 4CEJ
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 ARG 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PRO* 4.1 20.5 + - + +
251A ALA 3.2 2.2 + - - -
252A PRO* 1.3 77.1 - - - +
254A ALA* 1.3 64.8 + - - +
255A ASP 3.3 0.7 - - - -
256A ASN* 3.1 27.3 + - + +
257A PHE* 3.0 50.6 + - + -
289A ALA* 3.4 32.6 + - - +
290A LYS 3.0 25.7 + - - +
291A ALA* 4.2 6.1 - - - +
292A VAL* 3.9 10.4 - - - +
302A LEU* 3.6 28.1 + - - +
305A ALA* 5.7 1.8 - - - +
306A THR* 3.5 31.0 - - - +
309A ARG* 6.1 1.6 - - - +
40X T 5.6 5.3 - - - -
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Residues in contact with ALA 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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241A LEU* 4.1 14.1 - - + -
244A THR* 3.9 26.3 - - + +
251A ALA 3.3 15.7 + - - +
252A PRO 3.2 0.8 - - - -
253A ARG* 1.3 77.3 - - - +
255A ASP* 1.3 55.4 + - - +
257A PHE* 3.0 6.3 + - - +
258A LEU* 2.7 42.2 + - + +
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Residues in contact with ASP 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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252A PRO 3.8 2.3 + - - +
253A ARG 3.3 0.4 - - - -
254A ALA* 1.3 80.7 - - - +
256A ASN* 1.3 61.8 + - - +
258A LEU* 4.1 15.8 - - - +
259A ASP* 3.2 22.7 + - - +
287A LYS* 5.6 3.4 + - - +
290A LYS* 3.8 21.9 + - - +
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Residues in contact with ASN 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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253A ARG* 3.1 23.1 + - + +
255A ASP* 1.3 75.7 - - - +
257A PHE* 1.3 67.1 + - + +
259A ASP* 3.0 7.3 + - - +
260A ASP* 2.9 28.3 + - - +
287A LYS* 4.3 25.0 + - - +
288A ARG 3.7 15.7 + - - -
289A ALA* 4.8 1.1 - - - -
290A LYS* 3.1 46.0 + - - +
309A ARG* 3.9 18.4 - - - +
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Residues in contact with PHE 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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237A LEU* 4.4 16.4 - - + +
240A ALA* 3.4 43.7 - - + -
241A LEU* 3.7 9.2 - - + -
244A THR* 3.6 24.0 - - + -
250A PRO* 5.6 1.1 - - + -
253A ARG* 3.0 36.9 + - + -
254A ALA* 3.5 4.9 - - - +
256A ASN* 1.3 77.8 - - + +
258A LEU* 1.3 54.1 + - - +
260A ASP* 3.1 9.1 + - - +
261A LEU* 2.7 39.8 + - + +
305A ALA* 4.1 21.1 - - + -
306A THR* 5.8 0.4 - - - -
309A ARG* 3.7 39.0 - - + -
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Residues in contact with LEU 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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241A LEU* 4.0 31.9 - - + -
254A ALA* 2.7 25.0 + - + +
255A ASP* 4.1 18.4 - - - +
257A PHE* 1.3 73.3 - - - +
259A ASP* 1.3 61.2 + - - +
261A LEU* 3.8 14.3 - - + +
262A ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 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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255A ASP 3.2 14.5 + - - +
256A ASN* 3.0 11.9 + - - +
258A LEU* 1.3 74.5 - - - +
260A ASP* 1.3 67.3 + - - +
262A ALA* 3.1 8.6 + - - +
263A GLN* 2.9 41.9 + - - +
287A LYS* 4.1 32.0 + - + +
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Residues in contact with ASP 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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237A LEU* 3.6 18.8 - - + +
256A ASN 2.9 16.9 + - - +
257A PHE* 3.4 8.4 - - - +
259A ASP* 1.3 77.0 - - - +
261A LEU* 1.3 51.8 + - - +
263A GLN* 3.2 11.0 + - - +
264A ILE* 2.7 38.3 + - - +
286A PHE* 3.5 31.8 - - + +
287A LYS* 4.4 1.2 + - - +
309A ARG* 2.8 47.3 + - - +
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Residues in contact with LEU 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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234A LYS* 3.8 47.1 - - + +
237A LEU* 3.7 18.5 - - + +
238A LEU* 3.6 26.9 - - + +
241A LEU* 4.7 6.3 - - + -
257A PHE* 2.7 20.6 + - + +
258A LEU* 3.8 24.7 - - + +
260A ASP* 1.3 71.6 - - - +
262A ALA* 1.3 51.6 + - - +
264A ILE* 3.1 3.6 + - + +
265A ASP* 2.5 40.7 + - + +
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Residues in contact with ALA 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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258A LEU 3.1 13.2 + - - +
259A ASP* 3.1 12.8 + - - +
261A LEU* 1.3 76.6 - - - +
263A GLN* 1.3 53.0 + - + +
265A ASP* 3.2 7.9 + - - +
266A GLU* 2.6 36.9 + - - +
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Residues in contact with GLN 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 ASP* 2.9 37.4 + - - +
260A ASP* 3.4 10.5 + - - +
262A ALA* 1.3 74.3 - - + +
264A ILE* 1.3 63.7 + - - +
266A GLU* 3.1 18.4 + - - +
267A LEU* 3.1 25.5 + - - +
283A ALA 5.0 0.5 - - - +
284A VAL* 3.5 21.6 - - + +
285A SER 3.1 40.1 + - - +
286A PHE* 3.9 14.7 - - + +
287A LYS* 5.0 1.2 - - - +
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Residues in contact with ILE 264 (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 LEU* 3.7 28.0 - - + +
233A ALA* 3.6 25.6 - - + -
234A LYS* 4.3 8.5 - - + -
237A LEU* 3.6 24.7 - - + -
260A ASP 2.7 21.7 + - - +
261A LEU* 3.6 5.8 - - - +
263A GLN* 1.3 69.5 - - + +
265A ASP* 1.3 65.5 + - - +
267A LEU* 3.0 11.7 + - + +
268A ILE* 3.0 34.8 + - + +
284A VAL* 5.7 0.2 - - + -
286A PHE* 4.1 19.7 - - + -
312A ALA* 4.6 0.9 - - + -
316A LEU* 4.4 16.4 - - + -
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Residues in contact with ASP 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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234A LYS* 4.3 21.0 + - - +
261A LEU* 2.5 24.9 + - + +
262A ALA* 3.4 8.3 - - - +
264A ILE* 1.3 72.7 - - - +
266A GLU* 1.3 62.0 + - - +
268A ILE* 3.1 24.3 + - - +
269A GLN* 3.0 39.1 + - - +
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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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262A ALA 2.6 16.2 + - - +
263A GLN* 3.1 21.7 + - - +
265A ASP* 1.3 75.1 + - - +
267A LEU* 1.3 58.2 + - + +
269A GLN* 3.6 14.3 + - - +
270A HIS* 2.9 31.0 + - + +
280A ARG* 3.1 36.2 + - - +
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Residues in contact with LEU 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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230A LEU* 3.8 33.5 - - + +
263A GLN 3.1 15.6 + - - +
264A ILE* 3.0 12.6 + - - +
266A GLU* 1.3 76.1 - - + +
268A ILE* 1.3 59.3 + - - +
270A HIS* 2.9 20.5 + - - +
271A GLN* 3.1 11.6 + - - +
277A LEU* 3.8 10.0 - - + +
280A ARG* 3.6 34.1 - - + -
281A VAL* 3.9 26.2 - - + +
284A VAL* 3.9 20.0 - - + -
316A LEU* 4.3 15.9 - - + -
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Residues in contact with ILE 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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230A LEU* 4.3 14.4 - - + +
231A ASN* 4.8 3.4 - - + +
234A LYS* 3.9 40.4 - - + +
264A ILE* 3.0 24.8 + - + +
265A ASP* 3.1 21.0 + - - +
267A LEU* 1.3 70.5 - - - +
269A GLN* 1.3 61.7 + - + +
270A HIS 3.0 6.3 + - - -
271A GLN* 3.3 46.4 + - - +
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Residues in contact with GLN 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 ASP* 3.0 38.7 + - - +
266A GLU* 3.9 14.8 - - - +
267A LEU 3.2 0.4 - - - -
268A ILE* 1.3 76.3 - - + +
270A HIS* 1.3 72.7 + - + +
271A GLN 3.7 0.7 - - - -
272A ASP* 5.4 1.2 + - - +
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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