Contacts of the helix formed by residues 282 - 296 (chain E) in PDB entry 1NZX
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 282 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E ALA* 1.3 70.1 - - - +
283E MET* 1.3 59.6 + - - +
284E ASP* 3.6 8.8 + - - +
285E TRP* 3.3 31.8 + - + +
286E ALA* 2.8 31.2 + - - +
432E PHE* 5.8 1.0 - - - -
434E LYS* 3.9 23.1 + - + +
454E ASN* 5.9 0.2 + - - -
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Residues in contact with MET 283 (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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277E ILE* 6.2 0.4 - - - -
281E ALA* 3.1 9.2 + - - +
282E ASP* 1.3 71.2 + - - +
284E ASP* 1.3 68.0 + - - +
286E ALA* 3.6 4.3 - - - +
287E VAL* 2.9 42.3 + - - +
314E ILE* 3.8 46.2 - - + +
317E GLU* 3.5 39.5 - - - +
318E PHE* 4.0 20.6 - - + +
321E ARG* 3.9 12.3 - - - +
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Residues in contact with ASP 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ASP* 3.5 7.2 + - - +
283E MET* 1.3 77.0 - - - +
285E TRP* 1.3 62.3 + - - +
287E VAL* 3.3 7.2 + - - +
288E GLU* 3.1 22.9 + - - +
321E ARG* 4.1 26.2 + - - +
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Residues in contact with TRP 285 (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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282E ASP* 3.3 28.8 + - + +
284E ASP* 1.3 77.0 - - - +
286E ALA* 1.3 58.9 + - - +
288E GLU* 3.1 11.3 + - + +
289E GLN* 2.9 66.9 + - + +
432E PHE* 3.9 15.5 - + - -
454E ASN* 2.9 30.8 + - + -
455E CYS* 5.0 2.7 - - + -
150F PHE* 6.6 0.2 - + - -
494F LYS* 3.9 33.4 - - + +
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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
----------------------------------------------------------
277E ILE* 4.1 34.1 - - + +
281E ALA* 4.5 2.5 - - + -
282E ASP 2.8 23.5 + - - +
283E MET* 3.6 4.7 - - - +
285E TRP* 1.3 72.9 - - - +
287E VAL* 1.3 59.8 + - - +
289E GLN* 3.8 0.5 - - - +
290E ALA* 2.8 33.1 + - - +
318E PHE* 4.0 5.3 - - + -
432E PHE* 4.1 23.9 - - + -
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Residues in contact with VAL 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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283E MET* 2.9 41.7 + - - +
284E ASP* 3.6 6.5 - - - +
286E ALA* 1.3 77.0 - - - +
288E GLU* 1.3 64.8 + - - +
290E ALA* 3.8 1.9 - - - +
291E HIS* 3.0 22.5 + - - +
318E PHE* 3.8 20.4 - - + +
321E ARG* 3.9 46.0 - - + +
322E SER* 4.0 10.5 + - - +
325E ARG* 4.8 8.5 - - + -
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Residues in contact with GLU 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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284E ASP 3.1 10.6 + - - +
285E TRP* 3.7 13.5 - - + +
287E VAL* 1.3 81.5 - - - +
289E GLN* 1.3 65.9 + - + +
291E HIS* 3.3 7.6 + - - +
292E PHE* 3.0 32.0 + - + +
325E ARG* 2.9 48.3 + - - -
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Residues in contact with GLN 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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275E ASN* 4.7 0.9 - - - -
285E TRP* 2.9 65.7 + - + +
286E ALA 4.0 0.4 - - - +
288E GLU* 1.3 82.3 + - - +
290E ALA* 1.3 54.7 + - - +
292E PHE* 3.3 14.3 + - - +
293E ALA* 2.7 36.5 + - - +
432E PHE* 3.6 22.4 - - + -
455E CYS* 3.5 6.1 - - - +
456E TYR* 3.2 33.6 + - + +
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ASN* 3.5 25.0 + - - +
277E ILE* 4.8 1.6 - - + -
286E ALA 2.8 19.4 + - - +
287E VAL 3.8 2.2 - - - +
289E GLN* 1.3 74.3 - - - +
291E HIS* 1.3 64.5 + - - +
293E ALA* 3.5 2.4 - - - +
294E LEU* 3.2 17.2 + - - +
305E GLY 5.2 0.3 - - - +
308E THR* 4.3 3.3 + - + -
318E PHE* 3.6 27.4 - - + -
322E SER* 5.4 0.2 - - - +
405E MET* 3.3 20.7 - - + +
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Residues in contact with HIS 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E VAL 3.0 14.2 + - - +
288E GLU* 3.4 10.3 - - - +
289E GLN 3.2 0.2 - - - -
290E ALA* 1.3 77.9 - - - +
292E PHE* 1.3 59.8 + - - +
294E LEU 3.3 1.4 + - - -
295E PHE* 2.8 67.0 + + - +
322E SER* 4.8 3.7 + - - -
325E ARG* 3.2 63.4 + - + +
326E ALA* 3.7 13.1 + - - +
329E ARG* 2.8 37.7 + - - -
405E MET* 4.2 6.0 - - - +
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Residues in contact with PHE 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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116E ILE* 6.5 0.9 - - + -
288E GLU* 3.0 20.8 + - + +
289E GLN* 3.6 17.0 - - - +
291E HIS* 1.3 79.4 - - - +
293E ALA* 1.3 64.1 + - - +
295E PHE* 5.2 0.7 - - - -
296E PHE* 3.0 69.4 + + + +
329E ARG* 5.7 2.5 - - - +
456E TYR* 4.5 8.7 - - + -
457E ASP* 3.8 33.9 - - + -
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Residues in contact with ALA 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ASN* 3.9 11.2 - - - +
289E GLN 2.7 22.1 + - - +
290E ALA 3.5 7.2 - - - +
292E PHE* 1.3 73.8 - - - +
294E LEU* 1.3 56.7 + - - +
296E PHE* 5.0 1.0 + - - +
301E CYS* 5.7 0.9 - - - +
304E ALA* 3.4 9.4 - - - +
305E GLY* 2.9 21.8 + - - +
456E TYR* 3.4 46.2 - - + -
457E ASP* 4.1 5.2 - - - +
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Residues in contact with LEU 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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290E ALA 3.2 12.7 + - - +
291E HIS 4.1 0.9 - - - +
292E PHE 3.1 0.4 - - - -
293E ALA* 1.3 81.2 - - - +
295E PHE* 1.3 75.3 + - + +
296E PHE 3.5 1.7 + - - +
299E GLY* 3.3 22.2 - - - +
304E ALA* 4.3 10.3 - - + +
305E GLY 3.5 25.1 - - - +
306E SER* 3.6 21.1 - - - -
402E GLY 4.3 5.6 - - - +
404E VAL 3.6 41.1 - - - +
405E MET* 3.7 28.3 - - + +
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Residues in contact with PHE 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E HIS* 2.8 58.0 + + - +
292E PHE* 5.2 0.2 - - - -
294E LEU* 1.3 81.8 - - + +
296E PHE* 1.3 65.5 + - - +
298E GLN* 3.2 8.7 + - - -
299E GLY* 3.1 11.1 + - - +
326E ALA* 4.4 4.3 - - + -
329E ARG* 3.3 32.8 + - - +
341E GLN* 3.9 8.1 - - - +
383E PRO* 3.7 21.8 - - + -
384E THR 3.8 16.2 - - - -
385E VAL* 4.2 7.0 - - + -
403E PRO* 3.6 41.3 - - + -
405E MET* 4.1 19.3 - - + -
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Residues in contact with PHE 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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116E ILE* 3.9 27.1 - - + -
120E VAL* 4.2 22.0 - - + -
124E MET* 6.2 0.4 - - - -
170E PHE* 3.5 37.2 - + - -
292E PHE* 3.0 55.5 + + + +
293E ALA 5.2 1.1 - - - +
294E LEU 3.5 2.1 - - - +
295E PHE* 1.3 74.6 - - - +
297E ASN* 1.3 79.4 + - + +
299E GLY* 2.9 14.2 + - - -
300E GLN 3.7 1.9 + - - -
301E CYS* 4.3 14.3 - - + +
329E ARG* 4.3 4.7 - - - +
457E ASP* 3.9 22.7 - - + +
459E PHE* 6.0 3.6 - + - -
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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
------------------------------------------------------------
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