Contacts of the helix formed by residues 282 - 295 (chain E) in PDB entry 1XSK
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
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Residue Dist Surf HB Arom Phob DC
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280E ASN* 5.6 1.0 - - - +
281E TYR* 1.3 82.6 + - - +
283E GLU* 1.3 67.4 + - - +
284E ALA* 3.0 27.7 + - - +
285E THR* 3.2 10.0 + - - -
286E VAL* 3.1 21.5 + - - +
323E LEU 5.4 0.7 - - - +
324E THR* 3.2 31.0 - - + +
325E PHE* 3.3 7.9 - - - -
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Residues in contact with GLU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ASP* 1.3 75.9 - - - +
284E ALA* 1.3 55.2 + - - +
286E VAL* 3.6 3.1 + - - +
287E ASN* 2.7 36.4 + - - +
324E THR 3.3 6.7 + - - +
325E PHE* 3.2 22.1 - - + -
326E PRO* 4.4 17.7 - - + +
327E ASP* 4.2 10.1 + - - +
331E MET* 3.1 35.4 + - - +
334E ARG* 3.2 27.2 + - - +
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Residues in contact with ALA 284 (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* 3.0 16.1 + - - +
283E GLU* 1.3 74.7 - - - +
285E THR* 1.3 66.0 + - - +
286E VAL 3.0 2.1 + - - -
287E ASN* 3.1 9.6 + - - +
288E SER* 2.9 21.5 + - - -
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Residues in contact with THR 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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275E THR* 6.4 0.2 - - - -
280E ASN 4.0 17.0 + - - +
281E TYR* 3.9 9.3 - - + -
282E ASP* 3.2 27.9 + - - -
284E ALA* 1.3 77.5 - - - +
286E VAL* 1.3 62.9 + - - +
288E SER* 3.3 8.5 - - - -
289E PHE* 3.1 50.8 + - + -
545E TYR* 4.4 3.5 + - + +
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Residues in contact with VAL 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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275E THR* 4.5 7.2 - - + -
281E TYR* 5.4 1.8 - - + -
282E ASP 3.1 15.0 + - - +
283E GLU* 3.7 9.2 - - - +
284E ALA 3.0 0.6 - - - -
285E THR* 1.3 75.8 - - - +
287E ASN* 1.3 67.5 + - - +
289E PHE* 3.2 5.9 + - - +
290E ILE* 3.0 27.1 + - + +
303E PHE* 3.8 31.3 - - + -
305E PHE* 3.7 25.6 - - + -
325E PHE* 3.9 9.4 - - + -
331E MET* 5.0 4.7 - - + -
335E LEU* 4.0 24.0 - - + -
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Residues in contact with ASN 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLU* 2.7 23.2 + - - +
284E ALA* 3.1 8.5 + - - +
286E VAL* 1.3 73.5 - - - +
288E SER* 1.3 67.2 + - - +
290E ILE* 4.4 6.0 - - - +
291E ASP* 2.8 43.3 + - - +
334E ARG* 2.6 46.0 + - - +
335E LEU* 4.0 12.3 - - - +
338E LYS* 5.0 6.0 + - - +
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Residues in contact with SER 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 ALA 2.9 12.6 + - - -
285E THR* 3.3 17.9 - - - +
287E ASN* 1.3 75.9 - - - +
289E PHE* 1.3 69.1 + - - +
291E ASP* 3.8 2.8 - - - +
292E GLY* 2.8 28.1 + - - -
549E TRP* 4.8 1.8 - - - -
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Residues in contact with PHE 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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273E LEU* 4.1 17.0 - - + -
274E THR 4.6 13.2 - - - -
275E THR* 4.6 11.4 - - - -
285E THR* 3.1 27.4 + - + -
286E VAL 3.7 5.4 - - - +
288E SER* 1.3 87.8 - - - +
290E ILE* 1.3 63.8 + - - +
292E GLY* 3.2 1.4 + - - -
293E MET* 2.9 29.2 + - - +
303E PHE* 4.9 9.4 - + + -
545E TYR* 3.1 55.0 - + + -
546E ARG 6.0 0.2 - - - -
547E VAL* 3.6 30.1 - - + -
549E TRP* 3.6 12.5 - + - -
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Residues in contact with ILE 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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273E LEU* 5.6 1.3 - - + -
286E VAL* 3.0 22.8 + - + +
287E ASN* 3.9 4.7 - - - +
289E PHE* 1.3 75.0 - - - +
291E ASP* 1.3 63.5 + - - +
293E MET* 3.3 7.8 + - - +
294E ALA* 3.2 20.8 + - + +
300E LEU* 5.7 6.9 - - + +
303E PHE* 4.3 18.4 - - + -
335E LEU* 3.2 41.5 - - + -
338E LYS* 4.2 27.1 - - + +
340E LEU* 3.4 32.5 - - + -
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Residues in contact with ASP 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E ASN* 2.8 35.7 + - - +
288E SER* 4.1 2.8 - - - +
290E ILE* 1.3 70.1 - - - +
292E GLY* 1.3 60.3 + - - +
294E ALA* 3.2 6.8 + - - +
295E GLU* 2.9 47.5 + - + +
338E LYS* 2.7 32.8 + - - -
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Residues in contact with GLY 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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288E SER 2.8 17.9 + - - -
289E PHE 3.2 2.0 + - - -
291E ASP* 1.3 80.1 - - - +
293E MET* 1.3 59.5 - - - +
295E GLU* 3.5 6.4 + - - -
296E ARG* 2.9 47.3 + - - +
549E TRP* 3.6 8.9 - - - -
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Residues in contact with MET 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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271E LEU* 4.1 11.0 - - + -
273E LEU* 4.1 20.0 - - + -
289E PHE 2.9 18.6 + - - +
290E ILE* 3.6 8.1 - - - +
291E ASP 3.2 0.2 - - - -
292E GLY* 1.3 75.3 - - - +
294E ALA* 1.3 64.2 + - - +
296E ARG 3.1 5.9 + - - -
298E LEU* 2.9 64.8 + - + +
299E PRO 4.0 5.2 - - - +
300E LEU* 3.4 36.8 - - + -
539E LEU* 5.1 3.6 - - + -
547E VAL* 5.2 0.4 - - - -
548E PRO* 4.0 13.0 - - + -
549E TRP* 3.5 23.3 - - + -
559E VAL* 5.2 0.9 - - + -
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Residues in contact with ALA 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 ILE* 3.2 12.0 + - + +
291E ASP* 3.7 9.4 - - - +
293E MET* 1.3 78.1 - - - +
295E GLU* 1.3 61.8 + - + +
296E ARG 3.1 0.2 - - - -
297E ASN* 3.2 21.1 + - - +
298E LEU 4.8 3.8 - - - +
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Residues in contact with GLU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E ASP* 2.9 32.5 + - + +
292E GLY* 4.1 6.9 - - - +
293E MET 3.2 0.4 - - - -
294E ALA* 1.3 78.0 - - + +
296E ARG* 1.3 63.9 + - + +
297E ASN* 3.4 3.5 + - - -
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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