Contacts of the helix formed by residues 238 - 249 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235C LYS* 5.8 3.8 - - + -
236C THR 3.7 1.1 - - - +
237C TYR* 1.3 95.1 - - + +
239C GLU* 1.3 61.1 + - + +
242C ASP* 2.9 35.0 - - - +
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Residues in contact with GLU 239 (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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225C TRP* 4.0 22.5 + - + -
229C THR* 5.8 1.9 - - - +
231C GLY* 5.7 1.9 - - - -
232C ARG 5.4 1.2 + - - -
233C ILE* 2.9 29.7 + - + -
234C PRO* 3.3 2.6 - - - +
235C LYS* 2.8 64.9 + - + +
237C TYR 3.8 1.4 - - - +
238C LYS* 1.3 81.1 - - + +
240C LYS* 1.3 70.2 + - - +
241C GLU 3.0 1.3 - - - -
242C ASP* 2.8 17.3 + - - +
243C PHE* 2.8 11.4 + - - +
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Residues in contact with LYS 240 (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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233C ILE* 3.6 30.7 - - - +
234C PRO* 4.8 4.3 - - - -
235C LYS 3.8 5.8 + - - +
236C THR* 3.5 27.4 + - + +
237C TYR* 4.3 6.4 - - - +
239C GLU* 1.3 76.6 - - - +
241C GLU* 1.3 65.2 + - - +
243C PHE* 3.0 13.9 + - - +
244C ARG* 3.1 26.5 + - - +
272C VAL* 4.3 13.2 - - + +
273C ASN* 4.4 9.9 + - - +
274C THR 5.5 1.0 + - - -
276C LEU* 3.8 28.5 - - + +
277C ASN* 5.4 5.5 - - - +
132J GLU* 2.9 28.9 + - - +
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Residues in contact with GLU 241 (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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237C TYR 3.3 23.9 + - - +
239C GLU 3.0 0.6 - - - -
240C LYS* 1.3 77.6 - - - +
242C ASP* 1.3 67.3 + - - +
244C ARG* 3.0 43.9 + - - +
245C ASP* 2.7 30.5 - - - +
248C ARG* 5.1 3.4 + - - -
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Residues in contact with ASP 242 (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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225C TRP* 4.7 13.0 - - + -
238C LYS* 2.9 22.3 - - - +
239C GLU* 2.8 13.1 + - - +
241C GLU* 1.3 78.5 - - - +
243C PHE* 1.3 63.6 + - - +
245C ASP* 3.3 14.4 + - - +
246C LEU* 3.0 20.3 + - - +
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Residues in contact with PHE 243 (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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218C ILE* 3.7 22.7 - - + -
221C TYR* 2.8 41.1 - - + -
222C LEU* 3.5 18.8 - - + -
225C TRP* 4.0 19.7 - + + -
233C ILE* 3.2 38.1 - - + -
239C GLU 2.8 10.5 + - - +
240C LYS 3.2 10.8 - - - +
242C ASP* 1.3 76.8 - - - +
244C ARG* 1.3 63.8 + - - +
246C LEU* 2.9 25.5 + - + +
247C ILE* 3.1 27.4 + - + +
272C VAL* 3.5 23.3 - - + -
276C LEU* 4.7 3.1 - - + -
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Residues in contact with ARG 244 (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 LYS* 3.1 13.1 + - - +
241C GLU* 3.0 46.4 + - - +
243C PHE* 1.3 77.4 - - - +
245C ASP* 1.3 57.5 + - - +
247C ILE* 2.5 37.0 + - - +
248C ARG* 3.0 19.8 + - - +
269C ILE* 3.3 44.1 + - + +
270C LYS* 4.4 2.8 + - - +
272C VAL* 4.2 13.7 - - + -
273C ASN* 3.3 46.9 + - - +
128J GLU* 4.3 11.7 + - - -
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Residues in contact with ASP 245 (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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241C GLU* 2.7 36.7 + - - +
242C ASP* 3.3 15.0 + - - +
244C ARG* 1.3 73.3 - - - +
246C LEU* 1.3 60.5 + - - +
248C ARG* 3.3 33.9 + - - +
249C GLN* 3.4 23.7 + - - +
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Residues in contact with LEU 246 (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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221C TYR* 3.2 43.5 - - + +
224C GLN* 3.6 28.9 - - - +
225C TRP* 4.2 20.0 - - + -
228C GLU* 5.1 5.2 - - - +
242C ASP 3.0 10.7 + - - +
243C PHE* 2.9 24.6 + - + +
244C ARG 2.9 0.8 - - - -
245C ASP* 1.3 78.7 - - - +
247C ILE* 1.3 58.5 + - - +
249C GLN* 3.3 28.0 + - + +
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Residues in contact with ILE 247 (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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217C ILE* 4.2 16.2 - - + -
218C ILE* 4.1 13.7 - - + -
221C TYR* 3.4 24.4 - - + -
243C PHE* 3.4 29.2 - - + +
244C ARG* 2.5 17.6 + - - +
246C LEU* 1.3 70.0 - - - +
248C ARG* 1.3 61.0 + - - -
250C GLY* 3.5 8.0 + - - -
265C PHE* 3.5 33.5 - - + +
268C ALA* 4.7 0.2 - - + -
269C ILE* 4.1 20.6 - - + +
272C VAL* 3.7 30.1 - - + -
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Residues in contact with ARG 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C GLU* 5.1 4.4 + - - -
244C ARG* 3.0 18.5 + - - +
245C ASP* 3.6 35.7 + - - +
246C LEU 3.2 0.4 - - - -
247C ILE* 1.3 72.7 - - - +
249C GLN* 1.3 52.0 + - + +
250C GLY 2.6 17.7 + - - -
251C ILE* 3.0 39.1 + - + +
266C GLU* 4.0 21.9 + - - +
269C ILE* 4.0 29.2 - - + +
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Residues in contact with GLN 249 (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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221C TYR* 4.4 2.0 + - - -
245C ASP* 3.4 18.6 + - - +
246C LEU* 3.3 24.1 + - + +
247C ILE 3.3 1.0 - - - -
248C ARG* 1.3 73.8 - - + +
250C GLY* 1.3 56.0 + - - +
251C 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