Contacts of the helix formed by residues 238 - 249 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235E LYS* 5.7 4.9 - - + -
236E THR 3.7 1.3 - - - +
237E TYR* 1.3 97.2 - - + +
239E GLU* 1.3 61.6 + - + +
242E ASP* 2.9 34.9 - - - +
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Residues in contact with GLU 239 (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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225E TRP* 3.9 23.7 + - + -
229E THR* 5.9 1.6 - - - +
231E GLY* 5.7 1.9 - - - -
232E ARG 5.4 1.2 + - - -
233E ILE* 2.9 29.9 + - + -
234E PRO* 3.3 1.9 - - - +
235E LYS* 2.8 65.7 + - + +
237E TYR 3.5 1.4 - - - +
238E LYS* 1.3 81.5 - - + +
240E LYS* 1.3 70.1 + - - +
241E GLU 3.0 1.6 - - - -
242E ASP* 2.7 17.8 + - - +
243E PHE* 2.8 11.8 + - - +
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Residues in contact with LYS 240 (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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233E ILE* 3.5 31.6 - - - +
234E PRO* 4.8 3.6 - - - -
235E LYS 3.7 6.5 + - - +
236E THR* 3.5 28.1 + - + +
237E TYR* 4.3 5.7 - - - +
239E GLU* 1.3 77.1 - - - +
241E GLU* 1.3 65.0 + - - +
243E PHE* 3.0 13.9 + - - +
244E ARG* 3.1 26.1 + - - +
272E VAL* 4.2 12.7 + - + +
273E ASN* 4.4 10.7 + - - +
274E THR 5.5 1.0 + - - -
276E LEU* 3.7 29.8 - - + +
277E ASN* 5.4 5.7 - - - +
132K GLU* 3.1 26.4 + - - +
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Residues in contact with GLU 241 (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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237E TYR* 3.3 25.2 + - - +
239E GLU 3.0 0.6 - - - -
240E LYS* 1.3 77.3 - - - +
242E ASP* 1.3 61.9 + - - +
244E ARG* 2.9 48.5 + - - +
245E ASP* 2.7 30.0 - - - +
248E ARG* 5.1 3.6 + - - -
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Residues in contact with ASP 242 (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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225E TRP* 4.7 12.7 - - + -
238E LYS* 2.9 22.3 - - - +
239E GLU* 2.7 13.7 + - - +
241E GLU* 1.3 78.5 - - - +
243E PHE* 1.3 64.2 + - - +
245E ASP* 3.3 14.0 + - + +
246E LEU* 3.1 20.4 + - - +
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Residues in contact with PHE 243 (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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218E ILE* 3.7 22.4 - - + -
221E TYR* 2.8 40.2 - - + -
222E LEU* 3.5 18.8 - - + -
225E TRP* 4.0 19.7 - + + -
233E ILE* 3.2 37.2 - - + -
239E GLU 2.8 11.1 + - - +
240E LYS 3.0 10.7 + - - +
242E ASP* 1.3 76.4 - - - +
244E ARG* 1.3 62.2 + - - +
246E LEU* 2.9 25.6 + - + +
247E ILE* 3.1 27.4 + - + +
272E VAL* 3.6 23.1 - - + -
276E LEU* 4.7 3.4 - - + -
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Residues in contact with ARG 244 (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 LYS* 3.1 13.4 + - - +
241E GLU* 2.9 45.3 + - - +
243E PHE* 1.3 78.8 - - - +
245E ASP* 1.3 58.8 + - - +
247E ILE* 2.5 37.9 + - - +
248E ARG* 3.1 20.1 + - - +
269E ILE* 3.2 42.2 + - + +
270E LYS* 4.3 3.4 + - - +
272E VAL* 4.0 13.4 - - + -
273E ASN* 3.3 46.3 + - - +
128K GLU* 4.4 9.0 + - - -
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Residues in contact with ASP 245 (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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241E GLU* 2.7 37.7 + - - +
242E ASP* 3.3 13.9 + - + +
244E ARG* 1.3 73.1 - - - +
246E LEU* 1.3 60.4 + - - +
248E ARG* 3.3 35.1 + - - +
249E GLN* 3.3 24.0 + - - +
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Residues in contact with LEU 246 (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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221E TYR* 3.2 42.8 - - + +
224E GLN* 3.6 28.5 - - - +
225E TRP* 4.3 20.0 - - + -
228E GLU* 5.1 5.6 - - - +
242E ASP 3.1 10.9 + - - +
243E PHE* 2.9 25.3 + - + +
244E ARG 2.9 0.6 - - - -
245E ASP* 1.3 78.3 - - - +
247E ILE* 1.3 59.7 + - - +
249E GLN* 3.4 27.4 + - + +
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Residues in contact with ILE 247 (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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217E ILE* 4.2 15.7 - - + -
218E ILE* 4.1 13.7 - - + -
221E TYR* 3.4 25.7 - - + -
243E PHE* 3.4 30.1 - - + +
244E ARG* 2.5 17.6 + - - +
246E LEU* 1.3 70.5 - - - +
248E ARG* 1.3 61.1 + - - +
250E GLY* 3.5 6.0 + - - -
265E PHE* 3.5 35.3 - - + +
268E ALA* 4.7 0.2 - - + -
269E ILE* 4.1 20.4 - - + -
272E VAL* 3.7 28.9 - - + -
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Residues in contact with ARG 248 (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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241E GLU* 5.1 4.0 + - - -
244E ARG* 3.1 15.3 + - - +
245E ASP* 3.6 36.0 + - - +
246E LEU 3.2 0.4 - - - -
247E ILE* 1.3 72.8 - - - +
249E GLN* 1.3 54.7 + - + +
250E GLY 2.6 18.1 + - - -
251E ILE* 3.0 38.2 + - + +
266E GLU* 3.9 23.5 + - - +
269E ILE* 3.9 30.0 - - + +
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Residues in contact with GLN 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E TYR* 4.5 1.7 + - - -
245E ASP* 3.3 20.5 + - - +
246E LEU* 3.6 23.5 - - + +
247E ILE 3.3 0.8 - - - -
248E ARG* 1.3 73.6 - - + +
250E GLY* 1.3 54.6 + - - +
251E ILE 3.7 1.3 - - - -
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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