Contacts of the helix formed by residues 284 - 294 (chain E) in PDB entry 6CP3
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 284 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B GLN* 3.5 19.1 - - - +
286B LEU* 4.3 14.4 - - + -
269E SER* 4.6 6.2 - - - +
274E ARG* 4.1 20.6 + - - +
282E GLN* 3.1 17.1 + - - +
283E PRO* 1.3 81.4 - - + +
285E LEU* 1.3 58.0 + - - +
286E ALA 3.5 1.3 - - - -
287E THR* 3.7 13.9 - - - -
288E ASP* 2.6 50.1 + - - +
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Residues in contact with LEU 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 6.3 0.7 - - + -
281B ARG* 5.3 12.1 - - - +
262E THR* 3.8 28.3 - - + -
281E TYR* 4.6 11.7 - - + -
282E GLN* 3.3 28.5 + - - +
283E PRO 3.2 5.2 + - - +
284E THR* 1.3 75.7 - - - +
286E ALA* 1.3 59.8 + - - +
288E ASP 3.7 0.5 - - - -
289E MET* 2.9 39.8 + - + +
320E PRO* 3.8 25.6 - - + +
321E ALA* 5.5 0.4 - - - -
324E THR* 3.4 27.4 - - + +
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Residues in contact with ALA 286 (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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238B ALA* 4.2 11.2 - - + +
245B GLN* 5.5 7.0 - - - +
275B LYS* 5.7 8.7 - - + +
278B VAL* 3.7 30.0 - - + +
282B GLN* 5.4 2.1 + - - +
285E LEU* 1.3 79.6 - - - +
287E THR* 1.3 62.0 + - + +
289E MET* 3.4 2.6 + - - +
290E GLY* 2.9 25.3 + - - -
324E THR* 4.6 14.6 - - + -
328E HIS* 5.2 2.5 + - - -
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Residues in contact with THR 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA 4.2 9.7 - - - +
239B SER 5.0 1.3 - - - +
240B GLU 4.4 11.2 - - - +
241B ALA* 4.4 5.2 - - + -
242B ALA* 4.1 20.9 - - + +
245B GLN* 5.0 7.0 - - - +
282B GLN* 3.3 36.6 + - - +
284E THR* 3.3 13.6 + - - -
286E ALA* 1.3 80.3 - - + +
288E ASP* 1.3 62.8 + - - +
290E GLY* 3.1 0.7 + - - -
291E LEU* 2.9 35.8 + - - +
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Residues in contact with ASP 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E PHE* 3.5 28.4 - - + -
265E GLY* 6.3 0.4 - - - -
274E ARG* 5.5 1.9 + - - -
282E GLN* 4.4 11.8 + - - +
284E THR* 2.6 39.9 + - - +
285E LEU 3.7 1.3 - - - -
287E THR* 1.3 83.2 + - - +
289E MET* 1.3 59.0 + - - +
291E LEU* 4.3 19.3 - - - +
292E LEU 4.6 3.9 + - - -
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Residues in contact with MET 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ILE* 4.5 13.9 - - + -
261E PHE* 4.3 20.6 - - + -
262E THR* 3.5 26.7 - - + +
285E LEU* 2.9 29.7 + - + +
286E ALA 3.8 3.1 - - - +
288E ASP* 1.3 80.3 - - - +
290E GLY* 1.3 59.2 + - - +
291E LEU 3.3 0.7 - - - -
292E LEU* 3.1 7.3 + - - +
293E GLN* 2.9 43.2 + - + +
321E ALA* 5.1 1.8 - - - +
324E THR* 4.3 19.1 - - + +
325E THR* 4.1 19.1 - - - +
328E HIS* 4.3 14.4 - - + +
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Residues in contact with GLY 290 (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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238B ALA* 3.7 26.9 - - - -
239B SER* 4.3 3.7 - - - -
286E ALA 2.9 12.3 + - - -
287E THR 3.1 3.5 + - - -
289E MET* 1.3 77.9 - - - +
291E LEU* 1.3 56.5 + - - +
293E GLN* 3.0 8.2 + - - -
294E GLU* 2.8 37.6 + - - +
328E HIS* 4.8 3.6 + - - -
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B SER* 5.8 7.2 - - - -
239B SER* 3.8 24.7 - - - +
118E HIS* 6.3 0.9 - - - +
119E ALA 5.4 3.6 - - - +
121E PRO* 4.7 19.1 - - + -
234E LEU* 4.0 12.5 - - + +
287E THR* 2.9 19.7 + - - +
288E ASP* 4.3 17.9 - - - +
289E MET 3.3 0.4 - - - -
290E GLY* 1.3 75.1 - - - +
292E LEU* 1.3 56.3 + - - +
294E GLU 4.8 0.2 - - - -
295E ARG* 3.5 30.0 + - - +
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Residues in contact with LEU 292 (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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233E ALA* 3.9 28.5 - - + +
234E LEU* 4.1 11.0 - - + -
237E LEU* 3.9 21.7 - - + +
255E ILE* 4.6 11.7 - - + -
258E ILE* 3.7 24.9 - - + -
261E PHE* 3.6 38.4 - - + -
288E ASP 4.6 1.2 + - - -
289E MET* 3.1 11.3 + - - +
290E GLY 3.1 0.6 - - - -
291E LEU* 1.3 79.5 - - - +
293E GLN* 1.3 72.3 + - - +
294E GLU 3.6 0.2 - - - -
295E ARG 4.0 3.4 + - - -
296E ILE* 3.5 18.7 - - + +
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Residues in contact with GLN 293 (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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152E LYS* 3.3 37.5 + - - +
258E ILE* 5.2 0.7 - - - +
289E MET* 2.9 32.8 + - + +
290E GLY 3.0 1.5 + - - +
292E LEU* 1.3 84.9 - - - +
294E GLU* 1.3 60.8 + - - +
295E ARG 3.1 4.3 - - - -
296E ILE* 2.9 36.1 + - - +
308E GLN* 3.3 27.2 + - - +
325E THR* 6.0 2.0 - - - -
328E HIS* 3.4 52.6 - - + +
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Residues in contact with GLU 294 (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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210B GLN 4.9 0.9 - - - -
211B LYS* 3.2 33.2 - - - +
212B ARG* 2.8 41.1 + - + +
213B SER 4.4 0.7 + - - -
238B ALA* 4.6 1.1 - - - +
239B SER* 3.6 36.1 - - - +
121E PRO* 3.7 13.2 - - + +
122E PRO* 3.7 8.8 - - - +
127E GLN* 4.8 2.4 + - - -
152E LYS* 4.9 2.7 + - - +
290E GLY* 2.8 25.3 + - - +
291E LEU* 5.7 0.2 - - - -
293E GLN* 1.3 72.7 - - - +
295E ARG* 1.3 61.0 + - - +
296E ILE 3.3 1.7 + - - -
297E THR* 4.0 11.4 - - - +
328E HIS* 3.8 11.6 + - - -
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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