Contacts of the helix formed by residues 248 - 261 (chain E) in PDB entry 4CEV
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 TYR 248 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E LEU* 4.3 8.5 - - + -
234E ASP* 3.8 22.7 + - + +
247E THR* 1.3 73.5 - - - +
249E ARG* 1.3 59.7 + - + +
251E SER* 3.2 5.2 + - - -
252E HIS* 3.0 65.7 + + - -
285E VAL* 4.0 40.4 - - + -
288E ALA* 3.9 11.0 - - + +
289E LEU* 5.5 0.4 - - + -
243F ILE* 3.4 34.4 - - + +
244F GLY* 4.1 25.4 - - - -
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Residues in contact with ARG 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E THR* 3.3 7.1 + - - +
248E TYR* 1.3 79.9 - - + +
250E GLU* 1.3 60.1 + - - +
252E HIS* 3.2 2.1 + - - +
253E LEU* 2.9 26.5 + - - +
195F MET* 3.2 21.4 - - - +
198F VAL* 3.9 8.7 - - - +
199F ASP* 2.8 47.4 + - - +
244F GLY* 4.2 17.3 - - - +
245F GLY 2.8 34.8 + - - -
247F THR* 3.7 14.3 - - - +
250F GLU* 2.8 39.8 + - - -
411F GAI 3.8 14.8 - - - +
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Residues in contact with GLU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ARG* 2.8 45.8 + - - -
121E TYR* 4.1 1.6 - - - -
198E VAL* 3.9 9.6 - - - +
202E GLY* 5.9 0.2 - - - -
203E MET* 3.6 33.5 + - + +
246E LEU* 3.4 12.1 - - + +
247E THR* 3.0 31.0 + - - +
249E ARG* 1.3 76.5 - - + +
251E SER* 1.3 58.2 + - - +
253E LEU* 3.4 6.2 + - + +
254E ALA* 2.9 29.3 + - - +
199F ASP* 5.5 1.3 - - - +
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Residues in contact with SER 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TYR* 2.8 25.3 + - - -
230E LEU* 3.3 22.7 - - - +
246E LEU* 4.3 1.6 - - - +
247E THR 3.1 13.0 + - - -
248E TYR 3.5 9.0 - - - -
249E ARG 3.2 0.2 - - - -
250E GLU* 1.3 75.1 - - - +
252E HIS* 1.3 63.7 + - - +
254E ALA* 3.5 1.6 + - - +
255E MET* 3.1 29.9 + - - +
289E LEU* 3.5 27.8 - - - -
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Residues in contact with HIS 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ARG* 5.4 1.8 - - - -
248E TYR* 3.0 68.6 + + - -
249E ARG 3.2 3.5 + - - +
251E SER* 1.3 73.2 - - - +
253E LEU* 1.3 60.8 + - - +
255E MET* 3.2 4.2 + - - +
256E GLU* 2.7 35.2 + - - +
288E ALA* 3.5 36.7 - - + +
289E LEU* 3.9 10.1 - - + +
292E SER* 3.0 19.4 + - - +
411F GAI 3.6 28.3 + - - +
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Residues in contact with LEU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E MET* 4.3 12.3 - - + -
204E THR* 3.5 37.7 - - - +
249E ARG 2.9 16.3 + - - +
250E GLU* 3.6 5.6 - - - +
252E HIS* 1.3 76.7 - - - +
254E ALA* 1.3 57.0 + - - +
256E GLU* 3.1 8.9 + - - +
257E MET* 2.8 45.0 + - - +
196F HIS* 3.6 32.5 - - + +
199F ASP* 3.7 20.9 - - + +
200F ARG* 3.7 22.7 - - + +
411F GAI 4.0 0.6 + - - -
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Residues in contact with ALA 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TYR* 4.0 15.0 - - + +
203E MET* 4.4 3.3 - - - +
207E MET* 3.9 33.8 - - + +
250E GLU 2.9 17.9 + - - +
251E SER 3.7 5.2 - - - +
252E HIS 3.2 0.2 - - - -
253E LEU* 1.3 76.9 - - - +
255E MET* 1.3 77.1 + - + +
257E MET* 3.2 2.9 + - - +
258E LEU* 3.0 26.9 + - - +
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Residues in contact with MET 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TYR* 4.5 8.5 - - + -
223E LEU* 3.8 19.5 - - + -
225E LEU* 3.6 33.0 - - + -
251E SER 3.1 17.3 + - - +
252E HIS 3.6 3.4 - - - +
254E ALA* 1.3 88.0 - - + +
256E GLU* 1.3 57.3 + - - +
258E LEU* 3.3 21.9 + - + +
259E ALA* 2.9 29.5 + - - +
269E PHE* 4.5 3.8 - - - -
289E LEU* 3.6 26.2 - - + +
292E SER* 3.6 21.1 - - - +
293E LEU* 3.7 15.9 - - - +
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Residues in contact with GLU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E HIS* 2.7 25.4 + - - +
253E LEU* 3.5 7.1 - - - +
255E MET* 1.3 71.9 - - - +
257E MET* 1.3 62.3 + - - +
259E ALA* 3.5 3.6 + - - +
260E GLU* 3.2 22.7 + - - +
292E SER* 4.0 22.6 + - - +
296E GLU 4.6 11.6 - - - +
297E LYS* 5.3 1.4 - - + -
298E LEU* 4.4 10.7 + - - +
196F HIS* 2.7 44.3 + - + +
411F GAI 2.7 42.3 + - - -
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Residues in contact with MET 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E THR* 3.8 30.7 - - + +
207E MET* 3.9 19.5 - - + -
208E GLU* 3.8 17.9 - - + +
211E ILE* 3.5 22.0 - - + +
253E LEU* 2.8 43.1 + - + +
254E ALA 3.7 4.7 - - - +
256E GLU* 1.3 74.7 - - - +
258E LEU* 1.3 60.3 + - - +
260E GLU* 3.6 12.6 - - - +
261E ALA* 3.1 19.6 + - - +
196F HIS* 4.2 0.7 - - + -
200F ARG* 3.4 43.1 - - - +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ILE* 3.7 20.0 - - + -
207E MET* 3.6 23.1 - - + -
211E ILE* 3.7 18.6 - - + -
223E LEU* 4.2 13.7 - - + -
254E ALA 3.0 15.9 + - - +
255E MET* 3.3 29.8 + - + +
257E MET* 1.3 75.6 - - - +
259E ALA* 1.3 66.8 + - - +
261E ALA* 3.0 12.2 + - - +
262E GLN* 3.0 11.8 + - - -
263E ILE* 4.1 13.4 + - + +
264E ILE* 4.0 30.3 + - + +
293E LEU* 4.2 7.9 - - + -
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E MET 2.9 9.6 + - - +
256E GLU* 3.6 6.1 - - - +
258E LEU* 1.3 75.0 - - - +
260E GLU* 1.3 63.2 + - - +
262E GLN* 3.1 22.4 + - - +
292E SER 3.3 17.0 - - - +
293E LEU* 3.1 28.4 + - - +
295E GLY* 3.9 12.8 - - - +
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Residues in contact with GLU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E GLU 3.2 13.4 + - - +
257E MET* 3.6 9.7 - - - +
259E ALA* 1.3 80.1 - - - +
261E ALA* 1.3 61.8 + - - +
262E GLN* 3.2 13.5 + - - +
196F HIS* 5.0 0.5 + - - -
200F ARG* 2.7 44.7 + - - -
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Residues in contact with ALA 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E ILE* 3.4 35.7 - - + -
215E LYS* 3.2 24.8 + - - +
257E MET 3.1 11.7 + - - +
258E LEU 3.0 9.9 + - - +
260E GLU* 1.3 79.8 + - - +
262E GLN* 1.3 67.7 + - - +
263E ILE* 3.2 9.3 + - + -
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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