Contacts of the helix formed by residues 238 - 249 (chain G) in PDB entry 1R4N
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 LYS 238 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235G LYS* 5.7 2.9 - - + -
236G THR 3.6 2.8 - - - +
237G TYR* 1.3 97.1 - - + +
239G GLU* 1.3 62.4 + - + +
241G GLU 4.5 0.2 - - - -
242G ASP* 2.9 35.8 + - - +
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Residues in contact with GLU 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G TRP* 4.0 23.8 - - + -
229G THR* 5.9 2.1 - - - +
232G ARG 5.4 0.9 + - - -
233G ILE* 2.9 29.6 + - + -
234G PRO* 3.3 2.3 - - - +
235G LYS* 2.8 64.6 + - + +
237G TYR 3.8 1.4 - - - +
238G LYS* 1.3 81.1 - - + +
240G LYS* 1.3 69.7 + - - +
241G GLU 3.0 1.6 - - - -
242G ASP* 2.8 17.0 + - - +
243G PHE* 2.8 11.6 + - - +
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Residues in contact with LYS 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233G ILE* 3.6 28.0 - - - +
234G PRO* 4.8 4.3 - - - -
235G LYS 3.7 4.7 + - - +
236G THR* 3.5 29.2 + - + +
237G TYR* 4.3 5.5 - - - +
239G GLU* 1.3 78.4 - - - +
241G GLU* 1.3 64.8 + - - +
243G PHE* 3.0 12.3 + - - +
244G ARG* 3.1 26.0 + - - +
272G VAL* 4.2 11.9 - - + +
273G ASN* 4.4 10.9 + - - +
274G THR 5.5 0.8 + - - -
276G LEU* 3.7 33.4 - - + +
277G ASN* 5.4 5.7 - - - +
132L GLU* 3.0 27.9 + - - +
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Residues in contact with GLU 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G TYR* 3.3 24.6 + - - +
238G LYS 4.5 0.2 - - - +
239G GLU 2.9 0.6 + - - -
240G LYS* 1.3 77.7 - - - +
242G ASP* 1.3 62.9 + - - +
244G ARG* 2.9 49.1 + - - +
245G ASP* 2.7 29.4 - - - +
248G ARG* 5.1 3.8 + - - -
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Residues in contact with ASP 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G TRP* 4.7 12.4 - - + -
238G LYS* 2.9 20.7 - - - +
239G GLU* 2.8 12.6 + - - +
241G GLU* 1.3 78.4 - - - +
243G PHE* 1.3 65.1 + - - +
245G ASP* 3.3 14.4 + - + +
246G LEU* 3.0 20.4 + - - +
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Residues in contact with PHE 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G ILE* 3.7 22.0 - - + -
221G TYR* 2.8 40.8 - - + -
222G LEU* 3.5 18.4 - - + -
225G TRP* 4.0 19.9 - + + -
233G ILE* 3.2 37.0 - - + -
239G GLU 2.8 9.9 + - - +
240G LYS 3.0 11.4 + - - +
242G ASP* 1.3 75.9 - - - +
244G ARG* 1.3 62.9 + - - +
246G LEU* 2.9 24.9 + - + +
247G ILE* 3.1 27.9 + - + +
272G VAL* 3.6 23.3 - - + -
276G LEU* 4.7 3.4 - - + -
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Residues in contact with ARG 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240G LYS* 3.6 15.7 + - - +
241G GLU* 2.9 42.4 + - - +
243G PHE* 1.3 77.4 - - - +
245G ASP* 1.3 58.3 + - - +
247G ILE* 2.5 36.4 + - - +
248G ARG* 3.1 20.0 + - - +
269G ILE* 3.2 43.3 + - + +
270G LYS* 4.3 3.6 + - - +
272G VAL* 4.2 13.5 - - + -
273G ASN* 3.3 46.7 + - - +
128L GLU* 4.4 9.7 + - - -
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Residues in contact with ASP 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G GLU* 2.7 36.6 + - - +
242G ASP* 3.5 15.0 - - - +
244G ARG* 1.3 74.3 - - - +
246G LEU* 1.3 60.4 + - - +
248G ARG* 3.3 34.3 + - - +
249G GLN* 3.3 24.0 + - - +
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Residues in contact with LEU 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G TYR* 3.2 43.2 - - + +
224G GLN* 3.6 28.5 - - - +
225G TRP* 4.2 20.2 - - + -
228G GLU* 5.1 5.2 - - - +
242G ASP 3.0 10.9 + - - +
243G PHE* 2.9 24.4 + - + +
244G ARG 2.9 0.8 - - - -
245G ASP* 1.3 78.1 - - - +
247G ILE* 1.3 60.1 + - - +
249G GLN* 3.4 25.8 + - + +
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Residues in contact with ILE 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G ILE* 4.2 15.0 - - + -
218G ILE* 4.1 13.0 - - + -
221G TYR* 3.4 26.9 - - + -
243G PHE* 3.4 28.9 - - + +
244G ARG* 2.5 18.0 + - - +
246G LEU* 1.3 70.3 - - - +
248G ARG* 1.3 61.0 + - - -
250G GLY* 3.5 8.1 + - - -
265G PHE* 3.5 33.9 - - + +
268G ALA* 4.7 0.2 - - + -
269G ILE* 4.1 21.3 - - + +
272G VAL* 3.7 29.2 - - + -
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Residues in contact with ARG 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G GLU* 5.1 3.8 + - - -
244G ARG* 3.1 17.5 + - - +
245G ASP* 3.6 34.5 + - - +
246G LEU 3.2 0.2 - - - -
247G ILE* 1.3 72.6 - - - +
249G GLN* 1.3 54.2 + - + +
250G GLY 2.6 17.0 + - - -
251G ILE* 3.0 38.3 + - + +
265G PHE* 5.5 0.2 - - - -
266G GLU* 4.0 22.7 + - - +
269G ILE* 3.9 29.4 - - + +
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Residues in contact with GLN 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G TYR* 4.4 1.3 + - - -
245G ASP* 3.3 20.1 + - - +
246G LEU* 3.6 24.4 - - + +
247G ILE 3.3 0.8 - - - -
248G ARG* 1.3 73.3 - - + +
250G GLY* 1.3 55.5 + - - +
251G ILE 3.7 0.9 - - - -
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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