Contacts of the helix formed by residues 266 - 278 (chain E) in PDB entry 1XPU
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 SER 266 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209E ILE* 4.1 2.8 - - - +
264E LEU* 3.6 4.0 + - - +
265E ASP* 1.3 88.2 + - - +
267E ILE* 1.3 63.6 + - - +
268E THR* 3.7 2.5 - - - +
269E ARG* 3.1 28.4 - - - +
270E LEU* 3.3 16.5 + - - +
318E THR* 2.6 25.6 + - - -
320E LEU* 3.6 26.0 - - - -
5701E FPD 2.6 19.0 + - - +
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Residues in contact with ILE 267 (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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175E LEU* 4.1 25.6 - - + -
264E LEU* 3.7 29.5 - - + +
266E SER* 1.3 72.0 - - - +
268E THR* 1.3 56.3 + - + +
270E LEU* 3.3 20.6 + - + +
271E ALA* 2.8 31.9 + - - +
297E PRO* 4.0 21.3 - - + +
300E PHE* 4.1 8.5 - - + -
301E PHE* 4.3 8.7 - - + -
317E ALA* 4.0 8.6 - - + +
318E THR 3.3 12.0 + - - +
319E ALA* 4.7 3.8 - - + -
331E ILE* 5.1 1.3 - - + -
335E PHE* 3.6 31.9 - - + -
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Residues in contact with THR 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER* 3.7 9.9 - - - -
267E ILE* 1.3 79.1 - - - +
269E ARG* 1.3 60.5 + - - +
271E ALA* 3.2 3.6 + - - +
272E ARG* 2.9 30.7 + - - +
318E THR 3.9 3.1 - - - +
319E ALA* 4.2 2.9 - - - -
320E LEU* 3.2 49.1 + - + +
328E ASP* 3.2 29.8 + - - +
331E ILE* 3.6 26.4 - - - +
332E TYR* 6.3 0.7 - - - -
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Residues in contact with ARG 269 (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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298D LYS* 6.1 0.8 - - - +
333D GLU 5.4 1.4 + - - -
334D GLU* 5.3 8.1 + - - -
336D LYS 3.3 24.0 + - - -
337D GLY* 4.7 3.2 - - - -
338D THR* 5.3 6.0 - - - +
209E ILE* 3.6 16.6 - - + +
210E ASP* 3.3 32.3 + - + +
239E HIS* 5.3 1.0 - - - +
266E SER* 3.1 29.7 + - - +
267E ILE 3.4 0.2 - - - -
268E THR* 1.3 80.0 + - - +
270E LEU* 1.3 62.1 + - - +
272E ARG* 3.2 53.3 - - - +
273E ALA* 3.4 17.5 + - - +
320E LEU* 4.1 5.6 - - + +
323E THR* 5.5 0.8 - - - +
328E ASP* 5.4 1.7 + - - +
5701E FPD 2.8 43.7 + - - +
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Residues in contact with LEU 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E ILE* 3.5 21.0 - - + +
239E HIS 4.0 9.6 - - - +
240E VAL* 4.7 1.3 - - - -
243E ALA* 3.4 34.8 - - + -
264E LEU* 4.1 11.4 - - + -
266E SER 3.3 13.2 + - - +
267E ILE* 3.3 32.8 - - + +
268E THR 3.2 0.2 - - - -
269E ARG* 1.3 77.0 - - - +
271E ALA* 1.3 60.4 + - - +
273E ALA* 3.3 11.5 + - + +
274E TYR* 3.3 42.5 + - + -
297E PRO* 5.2 1.6 - - + -
300E PHE* 4.1 16.4 - - + -
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Residues in contact with ALA 271 (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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267E ILE 2.8 14.3 + - - +
268E THR 3.2 9.2 + - - +
270E LEU* 1.3 75.6 - - - +
272E ARG* 1.3 63.2 + - - +
274E TYR* 3.7 1.4 + - - +
275E ASN* 3.1 24.8 + - - +
289E VAL* 5.4 0.2 - - - +
293E ALA* 5.6 0.9 - - - +
294E LEU* 3.8 24.4 - - + +
297E PRO* 3.9 18.3 - - + +
331E ILE* 3.7 23.5 - - + +
335E PHE* 4.7 1.1 - - + -
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Residues in contact with ARG 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D GLU* 4.5 14.6 + - - +
334D GLU* 3.5 26.7 + - - +
210E ASP* 5.5 1.3 - - - +
268E THR 2.9 21.0 + - - +
269E ARG* 3.2 55.2 - - - +
270E LEU 3.3 0.2 - - - -
271E ALA* 1.3 77.6 - - - +
273E ALA* 1.3 62.3 + - - +
275E ASN* 3.4 7.8 + - - +
276E THR* 3.4 25.5 + - - +
323E THR* 5.6 0.2 - - - +
325E SER* 4.9 4.9 + - - -
327E MET* 3.4 38.9 - - + +
328E ASP* 2.9 38.9 + - - +
331E ILE* 4.1 3.6 - - - +
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Residues in contact with ALA 273 (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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236E ALA* 3.8 13.9 - - - +
239E HIS* 3.6 35.7 - - + -
240E VAL* 3.9 10.8 - - + +
269E ARG 3.4 6.7 + - - +
270E LEU* 3.3 12.2 + - + +
271E ALA 3.2 0.6 - - - -
272E ARG* 1.3 74.3 - - - +
274E TYR* 1.3 65.7 + - - +
275E ASN 3.1 1.1 - - - -
276E THR* 3.0 10.7 + - - -
277E VAL* 2.9 24.1 + - - +
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Residues in contact with TYR 274 (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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240E VAL* 3.6 23.7 + - + +
243E ALA* 4.7 3.3 - - - +
244E GLU* 3.1 28.9 - - - +
270E LEU* 3.3 47.1 + - + +
271E ALA 4.2 3.4 - - - +
273E ALA* 1.3 77.9 - - - +
275E ASN* 1.3 55.5 + - - +
277E VAL* 4.2 4.5 - - + -
278E VAL* 2.7 41.8 + - + +
293E ALA* 4.2 15.9 - - - +
296E ARG* 3.4 60.3 + - + -
297E PRO* 3.6 22.0 - - + -
300E PHE* 5.3 5.6 - - + +
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Residues in contact with ASN 275 (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 ALA 3.1 20.3 + - - +
272E ARG* 3.4 7.2 - - - +
273E ALA 3.1 0.6 - - - -
274E TYR* 1.3 78.8 - - - +
276E THR* 1.3 69.5 + - - +
278E VAL* 3.9 13.0 - - - +
288E GLY 4.0 10.2 + - - +
289E VAL* 3.4 16.4 - - + +
290E ASP* 3.1 32.2 + - - +
293E ALA* 3.9 12.2 - - + +
327E MET* 3.4 22.8 - - + +
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Residues in contact with THR 276 (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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284D VAL* 4.2 25.3 - - + +
291D ALA* 4.5 23.3 - - + -
334D GLU* 5.7 5.2 - - - +
236E ALA* 3.2 20.9 - - - +
272E ARG 3.4 12.5 + - - +
273E ALA 3.0 12.0 + - - -
275E ASN* 1.3 86.3 - - - +
277E VAL* 1.3 63.6 + - - +
278E VAL 3.6 3.0 - - - +
327E MET* 6.2 0.2 - - + -
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Residues in contact with VAL 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E ALA* 3.6 35.7 - - + +
237E SER* 3.8 11.0 - - - +
240E VAL* 3.8 20.6 - - + -
273E ALA 2.9 19.2 + - - +
274E TYR* 4.0 5.6 - - + +
276E THR* 1.3 77.6 - - - +
278E VAL* 1.3 67.5 + - - +
279E PRO* 3.5 5.9 - - - +
296E ARG* 5.7 5.8 - - - +
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Residues in contact with VAL 278 (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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284D VAL* 6.0 1.9 - - - +
274E TYR* 2.7 27.3 + - + +
275E ASN 3.9 10.4 - - - +
276E THR 4.3 2.9 - - - +
277E VAL* 1.3 76.0 - - + +
279E PRO* 1.3 85.0 - - + +
280E ALA* 3.6 2.0 + - - -
290E ASP* 5.0 6.1 - - + -
292E ASN* 4.9 9.6 - - + +
293E ALA* 3.6 36.3 - - + +
296E ARG* 4.9 19.5 - - + +
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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