Contacts of the helix formed by residues 224 - 235 (chain C) in PDB entry 4U2M
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 ASN 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C GLU* 3.9 26.7 + - - +
205C GLY* 6.2 0.4 - - - -
208C ILE* 3.3 30.0 - - + +
219C ASN 3.4 7.1 + - - -
220C LEU* 3.6 6.2 - - - +
221C ARG* 3.0 43.3 + - + +
223C GLY* 1.3 77.5 - - - +
225C ILE* 1.3 71.2 + - - +
226C MET 3.2 2.8 + - - -
227C ALA* 3.2 12.7 + - + +
228C VAL* 3.0 25.5 + - + +
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Residues in contact with ILE 225 (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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220C LEU* 4.0 7.6 - - + -
221C ARG 3.2 8.4 + - - +
222C GLU* 3.6 18.6 - - + +
223C GLY 3.7 0.8 - - - -
224C ASN* 1.3 85.9 + - - +
226C MET* 1.3 68.2 + - + +
228C VAL* 3.3 3.0 + - - +
229C MET* 2.8 27.9 + - + +
244C CYS* 3.1 44.0 - - + +
247C PHE* 3.0 42.0 - - + -
248C ILE* 3.9 20.9 - - + -
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Residues in contact with MET 226 (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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222C GLU 5.2 1.3 + - - +
223C GLY 5.4 0.4 - - - +
224C ASN 3.2 0.6 - - - -
225C ILE* 1.3 82.1 - - + +
227C ALA* 1.3 57.0 + - - +
229C MET* 3.4 21.8 + - + +
230C ALA* 3.0 30.1 + - - +
248C ILE* 3.6 31.9 - - + -
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Residues in contact with ALA 227 (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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202C ASN* 4.1 32.8 - - + +
205C GLY* 4.6 5.8 - - - +
223C GLY 5.7 0.9 - - - +
224C ASN* 3.2 14.4 + - + +
226C MET* 1.3 77.1 - - - +
228C VAL* 1.3 56.9 + - - +
230C ALA* 3.5 5.5 + - - +
231C THR* 2.5 38.4 + - - -
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Residues in contact with VAL 228 (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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205C GLY* 4.2 11.2 - - - -
208C ILE* 3.9 32.5 - - + -
209C LEU* 3.8 24.1 - - + +
218C LEU* 4.4 3.1 - - + -
220C LEU* 3.8 21.5 - - + -
224C ASN* 3.0 33.2 + - + +
225C ILE 3.7 3.4 - - - +
227C ALA* 1.3 75.9 - - - +
229C MET* 1.3 59.6 + - - +
231C THR* 3.3 6.0 + - - -
232C ALA* 2.9 27.9 + - - +
244C CYS* 3.8 9.2 - - - -
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Residues in contact with MET 229 (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 ILE* 2.8 18.6 + - + +
226C MET* 3.7 31.4 - - + +
228C VAL* 1.3 78.3 - - - +
230C ALA* 1.3 62.9 + - + +
232C ALA* 3.3 4.8 + - - +
233C MET* 3.1 22.5 + - - +
241C VAL* 3.9 19.2 - - + +
244C CYS* 3.8 28.5 - - + -
245C ARG* 4.1 26.9 - - + -
248C ILE* 4.2 11.7 - - + -
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Residues in contact with ALA 230 (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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201C ILE* 5.7 1.3 - - - +
226C MET 3.0 17.4 + - - +
227C ALA* 3.8 6.1 - - - +
229C MET* 1.3 75.3 - - + +
231C THR* 1.3 66.9 + - - +
233C MET* 3.3 7.9 + - - +
234C TYR* 3.1 22.0 + - - +
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Residues in contact with THR 231 (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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201C ILE* 4.1 27.5 - - + +
202C ASN* 4.3 5.9 + - - +
205C GLY* 4.1 9.2 - - - -
206C PHE* 4.0 22.9 - - + +
209C LEU* 3.5 21.3 - - + -
227C ALA 2.5 23.9 + - - -
228C VAL 3.3 1.1 + - - -
230C ALA* 1.3 78.7 - - - +
232C ALA* 1.3 55.1 + - - +
234C TYR* 3.4 8.6 + - + +
235C LEU* 2.9 37.6 + - + +
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Residues in contact with ALA 232 (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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209C LEU* 3.5 12.1 - - + +
228C VAL 2.9 17.1 + - - +
229C MET* 3.7 6.1 - - - +
230C ALA 3.2 0.2 - - - -
231C THR* 1.3 74.0 - - - +
233C MET* 1.3 61.1 + - - +
235C LEU 3.4 1.1 + - - +
236C GLN 3.0 6.6 + - - -
237C MET* 2.8 38.4 + - + +
240C VAL* 3.8 26.2 - - + -
241C VAL* 3.7 15.7 - - + +
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Residues in contact with MET 233 (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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229C MET 3.1 12.4 + - - +
230C ALA* 3.6 10.3 - - - +
231C THR 3.3 0.2 - - - -
232C ALA* 1.3 74.9 - - - +
234C TYR* 1.3 65.1 + - - +
236C GLN* 3.1 17.1 + - - +
237C MET 5.0 0.2 - - - +
241C VAL* 3.5 15.8 - - + +
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Residues in contact with TYR 234 (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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179C LEU* 3.6 41.8 - - + +
183C ILE* 5.8 0.2 - - - +
197C LEU* 3.8 21.2 - - + +
198C ASP* 3.7 25.9 + - + +
201C ILE* 3.7 39.9 - - + -
230C ALA 3.1 10.0 + - - +
231C THR* 3.5 9.4 - - + +
233C MET* 1.3 79.9 - - - +
235C LEU* 1.3 75.6 + - + +
236C GLN* 3.3 6.4 + - - +
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Residues in contact with LEU 235 (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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177C SER* 2.8 25.5 + - - +
178C GLY 3.5 2.1 + - - -
179C LEU* 3.4 24.0 + - + -
180C PHE* 3.9 23.6 - - + -
197C LEU* 4.7 2.2 - - + -
206C PHE* 4.0 27.1 - - + -
209C LEU* 4.0 11.4 - - + -
213C MET* 4.4 6.3 - - + -
231C THR* 2.9 20.7 + - + +
232C ALA 4.0 0.2 - - - +
233C MET 3.2 0.2 - - - -
234C TYR* 1.3 87.1 - - + +
236C GLN* 1.3 69.3 + - - +
237C MET* 2.8 39.0 - - + +
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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