Contacts of the helix formed by residues 224 - 236 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D GLU* 4.0 23.9 + - - +
205D GLY* 6.3 0.4 - - - -
208D ILE* 3.3 22.6 - - + +
219D ASN 3.3 21.0 + - - -
220D LEU* 3.6 6.1 - - - +
221D ARG* 3.0 43.1 + - - +
223D GLY* 1.3 77.5 - - - +
225D ILE* 1.3 71.1 + - - +
226D MET* 3.3 2.9 - - - -
227D ALA* 3.2 12.0 + - + +
228D VAL* 2.9 25.9 + - + +
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Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D LEU* 4.0 9.0 - - + -
221D ARG 3.2 9.1 + - - +
222D GLU* 3.7 23.1 - - - +
223D GLY 3.8 0.8 - - - -
224D ASN* 1.3 85.4 + - - +
226D MET* 1.3 66.0 + - + +
228D VAL* 4.5 3.1 - - - -
229D MET* 2.9 28.9 + - - +
244D CYS* 3.2 42.0 - - + +
247D PHE* 3.0 41.3 - - + -
248D ILE* 3.9 22.0 - - + -
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Residues in contact with MET 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 2.9 41.4 + - - +
17C GLN* 6.4 0.2 - - + -
20C LEU* 3.5 33.4 - - + -
22C LEU* 4.0 8.7 - - + -
181C TYR* 3.6 45.5 - - + +
222D GLU 5.1 1.8 + - - +
224D ASN 3.3 0.8 - - - -
225D ILE* 1.3 83.6 - - + +
227D ALA* 1.3 58.2 + - - +
229D MET* 4.6 0.2 - - - -
230D ALA* 3.0 16.6 + - - +
248D ILE* 4.3 12.3 - - - -
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ASN* 4.0 34.3 - - + +
204D GLU* 6.0 1.3 - - - +
205D GLY* 4.5 4.9 - - - -
223D GLY 5.8 0.4 - - - +
224D ASN* 3.2 14.0 + - + +
226D MET* 1.3 79.8 - - - +
228D VAL* 1.3 57.6 + - + +
230D ALA* 3.8 4.5 - - - +
231D THR* 2.6 39.0 + - - -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D GLY* 4.3 9.2 - - - -
208D ILE* 3.9 30.7 - - + -
209D LEU* 3.8 23.9 - - + +
218D LEU* 4.4 6.7 - - + -
220D LEU* 3.8 23.1 - - + -
224D ASN* 2.9 34.2 + - + +
225D ILE 3.9 3.4 - - - +
227D ALA* 1.3 72.7 - - - +
229D MET* 1.3 60.3 + - - +
231D THR* 3.3 5.0 + - - -
232D ALA* 2.9 28.1 + - - +
240D VAL* 4.6 0.9 - - + -
244D CYS* 3.9 8.1 - - - -
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Residues in contact with MET 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 3.6 31.9 - - + +
19C GLN* 3.4 27.6 - - + +
20C LEU* 4.1 20.6 - - + -
225D ILE* 2.9 19.2 + - + +
226D MET* 4.6 0.2 - - - -
228D VAL* 1.3 78.1 - - - +
230D ALA* 1.3 56.3 + - - +
232D ALA* 3.3 5.0 + - - +
233D MET* 3.0 39.8 + - - +
241D VAL* 3.9 10.0 - - + +
244D CYS* 3.7 25.9 - - + -
245D ARG* 3.6 25.6 - - + +
248D ILE* 4.2 11.9 - - - -
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C HIS* 6.2 0.7 - - + -
12C GLU* 5.3 2.4 - - - +
13C GLN* 3.7 17.5 - - - +
16C GLN* 3.6 19.2 - - + +
201D ILE* 5.3 2.8 - - + +
226D MET 3.0 18.6 + - - +
227D ALA* 3.8 6.5 - - - +
229D MET* 1.3 72.9 - - - +
231D THR* 1.3 66.7 + - - +
233D MET* 3.2 11.8 + - - +
234D TYR* 3.1 22.9 + - - +
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 4.0 23.6 - - + +
202D ASN* 4.2 9.4 + - - +
205D GLY* 4.0 10.3 - - - -
206D PHE* 3.9 23.3 - - + +
209D LEU* 3.5 20.6 - - + -
227D ALA 2.6 23.6 + - - -
228D VAL 3.7 0.2 - - - -
230D ALA* 1.3 79.0 - - - +
232D ALA* 1.3 57.1 + - - +
234D TYR* 3.3 7.3 + - + +
235D LEU* 2.9 37.9 + - + +
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LEU* 3.4 11.6 - - + +
228D VAL 2.9 16.6 + - - +
229D MET* 3.7 2.9 - - - +
230D ALA 3.2 0.2 - - - -
231D THR* 1.3 77.3 - - - +
233D MET* 1.3 57.0 + - - +
235D LEU* 3.4 3.7 + - - +
236D GLN 2.9 7.8 + - - -
237D MET* 2.9 34.8 + - + +
240D VAL* 3.8 26.9 - - + -
241D VAL* 3.6 18.8 - - + +
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Residues in contact with MET 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU* 3.8 33.7 - - + +
15C ASN* 3.9 19.3 - - - +
16C GLN* 3.9 33.2 - - - +
19C GLN* 4.1 8.3 - - - +
229D MET* 3.0 31.4 + - - +
230D ALA* 3.4 11.2 - - - +
231D THR 3.2 0.2 - - - -
232D ALA* 1.3 75.7 - - - +
234D TYR* 1.3 66.4 + - - +
236D GLN* 3.1 18.0 + - - +
238D GLU* 4.4 7.2 - - - +
241D VAL* 3.6 22.9 - - + -
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Residues in contact with TYR 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLN* 4.0 9.0 + - - -
8C GLN* 5.9 3.4 - - + -
12C GLU* 3.6 37.4 + - - +
179D LEU* 3.6 40.4 - - + +
197D LEU* 3.8 20.6 - - + +
198D ASP* 3.1 36.9 + - + +
201D ILE* 3.7 34.1 - - + -
230D ALA 3.1 9.7 + - - +
231D THR* 3.5 7.2 - - + +
233D MET* 1.3 81.6 - - - +
235D LEU* 1.3 73.8 + - + +
236D GLN* 3.3 8.3 + - - +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D SER* 2.8 24.5 + - - +
178D GLY 3.4 0.3 + - - -
179D LEU* 3.3 18.0 + - + -
180D PHE* 3.9 22.9 - - + -
197D LEU* 4.5 2.5 - - + -
206D PHE* 4.0 28.9 - - + -
209D LEU* 4.0 15.5 - - + -
213D MET* 4.3 3.4 - - + -
231D THR* 2.9 21.4 + - + +
232D ALA 3.9 3.1 - - - +
234D TYR* 1.3 91.9 - - + +
236D GLN* 1.3 71.2 + - - +
237D MET* 3.0 33.2 - - + -
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Residues in contact with GLN 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D CYS 4.8 0.5 - - - +
177D SER* 4.4 0.3 - - - -
178D GLY* 3.5 30.1 + - - +
179D LEU* 3.7 33.8 - - - +
182D SER* 5.1 3.8 + - - -
232D ALA 2.9 4.9 + - - -
233D MET 3.1 14.1 + - - +
234D TYR 3.9 3.9 + - - +
235D LEU* 1.3 79.9 - - - +
237D MET* 1.3 59.7 + - - +
238D GLU* 3.6 21.7 + - + +
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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