Contacts of the helix formed by residues 294 - 303 (chain C) 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 LEU 294 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C ALA* 4.1 26.7 - - + +
275C ASN* 6.5 0.2 - - + -
286C THR* 6.1 1.3 - - + -
289C VAL* 4.0 29.2 - - + -
290C ASP 4.7 0.7 - - - +
291C ALA* 4.1 14.1 + - - +
292C ASN 3.3 1.6 - - - -
293C ALA* 1.3 75.5 - - - +
295C HIS* 1.3 62.4 + - - +
296C ARG 3.2 0.7 - - - -
297C PRO* 3.4 6.0 - - + +
298C LYS* 3.3 40.7 + - + +
330C VAL* 5.3 1.3 - - + +
331C ILE* 4.1 19.7 - - + -
334C GLU* 3.6 34.1 - - + -
335C PHE* 4.5 13.0 - - + -
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Residues in contact with HIS 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ALA 5.2 0.4 + - - -
292C ASN* 3.4 18.4 + - - +
293C ALA 3.1 1.0 - - - -
294C LEU* 1.3 78.3 - - - +
296C ARG* 1.3 70.0 + - + +
298C LYS* 3.8 7.6 - - - +
299C ARG* 3.2 52.9 + - - +
233D ASP 3.1 28.5 + - - +
234D GLU* 3.7 2.4 - - - -
235D PRO* 3.4 44.8 - - + +
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Residues in contact with ARG 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C VAL* 4.9 2.6 - - - +
244C GLU* 2.7 33.1 + - - -
274C TYR* 3.4 39.3 + - + +
277C VAL* 5.8 3.2 - - - +
278C VAL* 3.9 26.1 - - + +
293C ALA* 4.1 8.5 - - - +
295C HIS* 1.3 90.7 - - + +
297C PRO* 1.3 72.5 - - + +
298C LYS 3.2 0.2 - - - -
299C ARG* 3.1 37.6 + - - +
300C PHE* 3.1 12.1 + - - +
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Residues in contact with PRO 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ILE* 4.0 10.0 - - + +
270C LEU* 5.0 1.6 - - + -
271C ALA* 3.8 26.7 - - + +
274C TYR* 3.6 21.3 - - + -
293C ALA 3.4 15.7 - - - +
294C LEU* 3.4 11.7 - - + +
296C ARG* 1.3 96.3 - - + +
298C LYS* 1.3 55.3 + - - +
300C PHE* 3.3 8.8 + - + +
301C PHE* 3.0 31.2 + - - +
335C PHE* 3.6 22.9 - - + -
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Residues in contact with LYS 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LEU* 3.3 26.9 + - - +
295C HIS* 3.8 7.9 - - - +
296C ARG 3.2 0.4 - - - -
297C PRO* 1.3 78.2 - - - +
299C ARG* 1.3 57.4 + - - +
301C PHE* 4.8 0.4 - - - +
302C GLY* 2.9 22.3 + - - -
334C GLU* 2.8 57.6 + - - -
335C PHE* 4.1 20.4 - - + -
338C THR* 5.3 0.9 - - + -
210D ASP* 5.1 10.1 + - - -
232D PHE* 3.4 37.6 + - + +
233D ASP* 3.2 23.7 - - - +
239D HIS* 6.0 1.0 + - - -
269D ARG* 5.6 0.8 - - - +
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 6.1 3.6 - - - -
244C GLU* 5.3 3.0 + - - -
251C LYS* 5.3 9.8 + - - +
295C HIS* 3.2 38.7 + - - +
296C ARG* 3.1 35.8 + - - +
298C LYS* 1.3 75.8 - - - +
300C PHE* 1.3 67.6 + - - +
302C GLY 3.7 0.5 - - - -
303C ALA* 3.1 22.2 + - - +
233D ASP* 3.9 21.7 - - + +
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Residues in contact with PHE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C LEU* 3.6 26.2 - - + -
243C ALA* 3.3 30.7 - - + -
244C GLU* 6.1 0.2 - - + -
246C VAL* 4.9 0.4 - - + -
247C ILE* 3.7 32.7 - - + +
251C LYS* 6.1 0.2 - - - +
262C ILE* 4.1 13.9 - - + -
264C LEU* 3.6 26.5 - - + -
267C ILE* 4.7 1.3 - - + -
270C LEU* 3.9 18.8 - - + -
274C TYR* 5.5 5.6 - - + +
296C ARG 3.1 8.8 + - - +
297C PRO 3.5 9.4 - - - +
299C ARG* 1.3 81.3 - - - +
301C PHE* 1.3 67.2 + - - +
303C ALA* 3.3 8.8 + - - +
315C ILE* 3.2 39.9 - - + +
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Residues in contact with PHE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 2.9 53.9 - - + +
174C GLY 3.4 31.0 - - - -
175C LEU* 3.9 19.5 - - + -
267C ILE* 4.2 8.1 - - + -
297C PRO 3.0 13.2 + - - +
298C LYS* 4.4 1.6 - - - +
300C PHE* 1.3 82.9 - + - +
302C GLY* 1.3 60.6 + - - +
303C ALA 3.2 1.3 + - - -
304C ALA* 3.5 10.4 + - - +
315C ILE* 4.0 17.5 - - + -
317C ALA* 3.6 25.1 - - + -
335C PHE* 3.9 20.4 - + + -
338C THR* 3.6 26.9 - - - -
339C GLY 4.2 6.1 - - - -
232D PHE* 4.9 1.3 - + - -
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Residues in contact with GLY 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 4.0 5.6 + - - -
298C LYS 2.9 22.0 + - - -
299C ARG 3.7 2.5 - - - -
300C PHE 3.2 0.2 - - - -
301C PHE* 1.3 74.3 - - - +
303C ALA* 1.3 54.2 + - - +
304C ALA 3.2 1.7 + - - -
305C ARG* 2.7 29.0 + - - -
213D PRO* 4.0 5.7 - - - +
232D PHE* 3.6 21.5 - - - -
233D ASP* 3.7 10.6 - - - +
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 4.4 5.1 - - + +
247C ILE* 4.3 3.1 - - + -
251C LYS* 3.9 24.2 - - - +
299C ARG 3.1 11.1 + - - +
300C PHE 3.4 12.6 - - - +
301C PHE 3.2 0.8 - - - -
302C GLY* 1.3 76.8 - - - +
304C ALA* 1.3 59.8 + - - +
305C ARG* 3.0 30.7 + - - +
313C LEU* 3.4 23.2 - - + +
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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