Contacts of the helix formed by residues 286 - 299 (chain E) in PDB entry 2POZ
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 GLY 286 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E SER* 3.1 13.4 + - - -
97E GLU* 3.3 13.0 - - - -
98E GLN* 4.9 0.2 - - - -
281E ILE* 3.4 19.1 + - - -
285E GLY* 1.3 80.2 - - - +
287E LEU* 1.3 59.1 + - - -
288E MSE 3.5 2.0 - - - -
289E GLU 4.0 1.1 - - - -
290E THR* 2.8 32.7 + - - -
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Residues in contact with LEU 287 (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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97E GLU* 2.7 13.2 + - - +
98E GLN* 4.5 17.6 - - + +
101E TRP* 4.4 9.4 - - + -
112E VAL* 4.2 17.5 - - + -
116E PHE* 3.9 15.8 - - + -
281E ILE* 3.9 23.1 - - + +
286E GLY* 1.3 68.7 - - - -
288E MSE 1.3 60.1 + - - +
290E THR* 3.4 2.6 + - - -
291E LYS* 3.0 26.0 + - - +
317E ALA* 3.5 23.1 - - + +
320E GLN* 4.5 2.2 - - + -
321E LEU* 3.9 24.4 - - + +
366E LEU* 3.6 31.4 - - + -
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Residues in contact with MSE 288 (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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115A LEU 4.8 0.7 - - - +
116A PHE* 3.8 20.9 - - - +
288A MSE 4.7 12.6 - - + +
291A LYS* 4.0 11.7 - - - -
69E GLU* 3.9 8.5 - - - +
97E GLU* 2.8 20.9 + - - +
101E TRP* 3.7 34.3 - - + +
116E PHE* 3.8 22.3 - - + -
287E LEU* 1.3 71.2 - - - +
289E GLU* 1.3 64.5 + - - +
291E LYS* 3.1 20.1 + - - +
292E LYS* 2.8 54.1 + - - +
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Residues in contact with GLU 289 (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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72E TRP* 3.6 22.6 - - + +
97E GLU* 3.9 2.8 + - - +
261E THR* 3.5 7.8 - - - -
262E ARG* 2.7 65.6 + - - +
263E PHE* 5.4 0.5 - - - -
284E ALA 3.5 22.9 - - - +
285E GLY* 3.7 26.7 - - - +
286E GLY 3.7 0.4 + - - -
287E LEU 3.4 0.4 - - - -
288E MSE 1.3 76.7 - - - +
290E THR* 1.3 58.3 + - - +
292E LYS* 3.2 12.7 + - - +
293E ILE* 2.9 32.0 + - + +
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Residues in contact with THR 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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279E PRO* 3.9 26.5 - - + +
281E ILE* 3.7 23.5 - - + +
284E ALA* 3.7 13.5 - - - +
286E GLY 2.8 23.9 + - - -
287E LEU 3.8 3.8 - - - -
289E GLU* 1.3 74.8 - - - +
291E LYS* 1.3 60.4 + - - +
293E ILE* 3.1 8.0 + - - +
294E CYS* 2.8 30.3 + - - -
321E LEU* 3.5 28.5 - - + -
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Residues in contact with LYS 291 (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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69A GLU* 2.8 27.4 + - - -
288A MSE 4.0 19.7 - - - -
292A LYS* 4.2 10.0 - - - +
116E PHE* 3.4 43.2 + - + -
287E LEU 3.0 15.2 + - - +
288E MSE 3.1 22.9 + - - +
290E THR* 1.3 74.3 - - - +
292E LYS* 1.3 59.5 + - + +
294E CYS* 3.2 5.8 + - - +
295E ALA* 2.9 26.9 + - + +
321E LEU* 3.8 13.8 - - + +
324E ASN* 2.7 25.1 + - - +
325E ILE* 4.7 8.5 - - + +
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Residues in contact with LYS 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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291A LYS* 4.2 11.6 - - + +
292A LYS* 5.8 7.0 - - + +
295A ALA* 3.8 27.3 - - + +
296A MSE 5.5 0.7 - - - +
298A GLU* 5.5 1.2 + - - -
326A THR* 5.8 0.6 + - - -
69E GLU* 2.9 33.4 + - - -
262E ARG* 3.8 40.2 - - - +
288E MSE 2.8 42.7 + - + +
289E GLU* 3.4 14.5 + - - +
291E LYS* 1.3 77.2 - - + +
293E ILE* 1.3 61.0 + - - +
295E ALA* 3.3 7.4 + - - +
296E MSE 3.0 27.4 + - - +
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Residues in contact with ILE 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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261E THR* 3.6 28.0 - - - -
262E ARG* 3.7 21.5 - - + +
265E PHE* 3.6 40.2 - - + -
269E PHE* 3.6 2.3 - - + -
277E ILE* 3.8 17.0 - - + -
279E PRO* 4.5 7.0 - - + -
284E ALA* 3.9 18.2 - - + +
289E GLU 2.9 19.7 + - - +
290E THR* 3.4 11.7 - - - +
292E LYS* 1.3 77.0 - - - +
294E CYS* 1.3 56.9 + - - +
296E MSE 3.2 8.8 + - - +
297E ALA* 2.9 25.8 + - - +
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Residues in contact with CYS 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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279E PRO* 4.7 3.6 - - - -
290E THR* 2.8 33.6 + - - +
291E LYS 3.6 4.9 - - - +
293E ILE* 1.3 75.4 - - - +
295E ALA* 1.3 64.9 + - - +
297E ALA* 3.1 14.9 + - - -
298E GLU* 3.1 3.3 + - - +
304E VAL* 3.7 31.9 - - + -
321E LEU* 4.6 1.3 - - - -
325E ILE* 3.8 25.6 - - + -
327E ASN* 3.1 35.2 + - - +
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Residues in contact with ALA 295 (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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262A ARG* 2.9 42.8 + - - +
292A LYS* 3.7 35.0 - - + +
296A MSE 6.4 0.2 - - + -
291E LYS 2.9 16.5 + - - +
292E LYS* 3.6 7.0 - - - +
294E CYS* 1.3 75.4 - - - +
296E MSE 1.3 62.8 + - - +
298E GLU* 3.3 14.4 + - - +
299E ALA 3.7 2.1 + - - -
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Residues in contact with MSE 296 (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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295A ALA* 5.3 0.4 - - + -
296A MSE 3.6 57.6 - - + +
299A ALA* 4.7 7.4 - - + -
300A TYR* 5.7 3.4 - - - -
262E ARG* 3.2 56.5 - - + +
266E ARG* 5.2 3.6 - - - -
269E PHE* 3.6 27.6 - - + -
292E LYS* 3.0 12.6 + - + +
293E ILE* 3.4 9.2 - - - +
294E CYS 3.2 0.2 - - - -
295E ALA* 1.3 78.0 - - - +
297E ALA* 1.3 61.9 + - - +
299E ALA* 3.0 21.5 + - - +
300E TYR* 3.3 10.9 - - + -
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Residues in contact with ALA 297 (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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269E PHE* 3.6 17.9 - - + -
277E ILE* 3.6 26.0 - - + -
293E ILE 2.9 13.0 + - - +
294E CYS 3.3 10.1 - - - +
296E MSE 1.3 77.6 - - - +
298E GLU* 1.3 57.0 + - - +
300E TYR* 2.9 18.0 + - - +
302E MSE 3.2 27.2 + - + +
327E ASN* 3.8 11.9 - - - +
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Residues in contact with GLU 298 (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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262A ARG* 3.0 29.5 + - - +
263A PHE* 3.8 10.2 - - + -
292A LYS* 4.9 4.5 + - - -
294E CYS 3.1 6.1 + - - +
295E ALA* 3.5 13.2 - - - +
296E MSE 3.2 0.4 - - - -
297E ALA* 1.3 71.5 - - - +
299E ALA* 1.3 62.0 + - - +
300E TYR 2.9 6.9 + - - -
301E ASN 3.1 3.1 + - - -
302E MSE 4.3 3.1 - - - -
326E THR* 2.6 32.2 + - - -
327E ASN* 3.3 31.2 - - + +
175F ARG* 2.8 39.2 + - - +
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Residues in contact with ALA 299 (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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262A ARG* 4.4 16.4 - - + +
263A PHE* 3.5 29.4 - - + +
266A ARG* 2.9 28.7 + - + -
296A MSE 4.6 7.0 - - + -
295E ALA 3.7 3.5 + - - +
296E MSE 3.0 14.9 + - - +
298E GLU* 1.3 79.4 - - - +
300E TYR* 1.3 67.5 + - + +
301E ASN 3.5 0.7 - - - -
238F ASP* 3.5 7.4 - - - +
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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