Contacts of the helix formed by residues 227 - 239 (chain C) in PDB entry 4DAJ
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 GLU 227 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C PHE 4.5 0.6 + - - +
225C LEU 2.8 2.6 + - - -
226C SER* 1.3 82.0 - - - +
228C PRO* 1.3 75.4 - - - +
229C THR* 3.2 24.2 + - - +
230C ILE* 2.9 31.1 - - + +
231C THR* 3.1 12.5 + - - -
163D PHE* 4.7 0.2 - - + -
166D TYR* 2.9 39.9 + - - -
167D PHE* 3.9 20.1 - - + -
170D THR* 5.3 1.4 + - - -
171D ARG* 3.4 23.1 + - - +
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Residues in contact with PRO 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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226C SER 4.2 4.3 - - - +
227C GLU* 1.3 101.3 - - + +
229C THR* 1.3 59.5 + - + +
231C THR* 3.7 5.7 + - - +
232C PHE 2.9 22.3 + - - -
510C VAL* 5.0 1.0 - - - +
513C ASN* 4.0 21.9 - - - +
514C THR* 3.2 44.6 + - - +
252D ARG* 4.6 9.6 - - - +
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLU* 3.2 21.5 + - - +
228C PRO* 1.3 75.2 - - - +
230C ILE* 1.3 68.7 + - - +
232C PHE* 3.0 10.1 + - - +
233C GLY 2.9 20.3 + - - -
514C THR* 4.5 9.9 - - + -
163D PHE* 3.5 19.7 - - - -
166D TYR* 5.5 0.2 - - - +
245D ILE* 3.8 14.1 - - + +
248D ILE* 3.9 23.3 - - + -
249D LEU* 3.9 22.9 - - + +
252D ARG* 4.6 12.1 - - - +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE* 3.1 48.0 - - + +
225C LEU* 4.3 5.6 - - + -
227C GLU* 2.9 38.6 - - + +
229C THR* 1.3 80.2 + - - +
231C THR* 1.3 67.7 + - - +
233C GLY* 3.3 0.9 + - - -
234C THR* 3.0 35.6 + - - +
163D PHE* 4.2 18.6 - - + -
241D MET* 5.3 0.7 - - - +
245D ILE* 5.0 3.8 - - - -
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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
----------------------------------------------------------
225C LEU* 3.2 35.3 + - + +
227C GLU 3.1 13.0 + - - -
228C PRO* 3.7 10.7 - - - +
230C ILE* 1.3 79.1 - - - +
232C PHE* 1.3 57.4 + - - +
234C THR* 3.4 0.6 + - - -
235C ALA* 2.9 26.7 + - - +
506C TYR* 6.0 0.4 - - - +
510C VAL* 4.0 18.2 - - + -
513C ASN* 5.6 4.9 - - - +
525C TRP* 6.1 2.0 - - + -
2000C 0HK 3.6 29.7 - - + +
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Residues in contact with PHE 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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228C PRO 2.9 7.2 + - - +
229C THR* 3.0 12.2 + - - +
231C THR* 1.3 73.2 - - - +
233C GLY* 1.3 68.4 + - - +
235C ALA* 2.6 27.7 + - + +
236C ILE* 2.9 41.8 + - + +
240C TYR* 5.0 5.8 - + - -
510C VAL* 3.7 9.4 - - + +
511C LEU* 3.3 55.0 - - + -
514C THR* 3.1 22.4 - - + +
515C PHE* 5.5 0.7 - + - -
244D THR* 4.6 8.5 - - - -
245D ILE* 4.4 9.0 - - + -
248D ILE* 4.4 24.2 - - + -
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Residues in contact with GLY 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 THR 2.9 13.9 + - - -
230C ILE 3.9 0.4 - - - -
232C PHE* 1.3 74.5 - - - +
234C THR* 1.3 56.5 + - - +
236C ILE* 3.0 21.6 + - - +
237C ALA* 3.0 13.2 + - - +
241D MET* 3.4 22.0 - - - +
245D ILE* 3.3 27.6 - - - -
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Residues in contact with THR 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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199C TRP* 3.7 23.6 - - + -
224C PHE* 5.8 2.1 - - + -
225C LEU* 5.1 5.9 - - + +
230C ILE* 3.0 25.7 + - - +
231C THR* 3.7 5.2 - - - -
233C GLY* 1.3 72.3 - - - +
235C ALA* 1.3 60.3 + - - +
237C ALA* 4.6 2.9 - - - +
238C ALA* 2.9 42.8 + - + +
2000C 0HK 3.5 20.3 - - + -
241D MET* 4.0 5.0 - - - +
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Residues in contact with ALA 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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231C THR 2.9 12.1 + - - +
232C PHE* 2.6 20.3 + - + +
234C THR* 1.3 69.6 - - - +
236C ILE* 1.3 56.0 + - - +
239C PHE* 2.7 27.4 + - - +
240C TYR* 2.9 31.2 + - + -
507C ASN* 3.5 15.3 - - - +
510C VAL* 4.0 15.7 - - + -
2000C 0HK 3.8 12.1 - - + -
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Residues in contact with ILE 236 (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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232C PHE* 2.9 52.9 + - + +
233C GLY* 3.0 7.8 + - - +
235C ALA* 1.3 79.0 - - - +
237C ALA* 1.3 61.4 + - - +
240C TYR* 3.1 17.7 + - + -
241C MET* 2.8 29.2 + - + +
236D ILE* 4.3 17.0 - - + -
241D MET* 3.4 30.5 - - + +
244D THR* 3.9 19.7 - - + +
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Residues in contact with ALA 237 (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 GLY 3.0 12.4 + - - +
234C THR* 4.7 2.7 - - - +
236C ILE* 1.3 80.6 - - - +
238C ALA* 1.3 58.5 + - - +
241C MET* 4.0 15.4 - - - +
242C PRO* 3.3 19.4 - - - +
237D ALA* 3.9 29.8 - - + +
241D MET* 4.8 7.6 - - + -
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Residues in contact with ALA 238 (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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152C ASN* 4.1 19.5 - - - +
155C VAL* 4.2 8.5 - - - +
199C TRP* 4.4 7.4 - - + -
234C THR* 2.9 31.9 + - + +
237C ALA* 1.3 77.0 - - + +
239C PHE* 1.3 58.8 + - - +
242C PRO* 4.0 10.3 - - - +
2000C 0HK 3.7 26.5 - - + -
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Residues in contact with PHE 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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235C ALA 2.7 12.5 + - - +
237C ALA 3.4 0.4 - - - -
238C ALA* 1.3 79.3 - - - +
240C TYR* 1.3 92.1 + + - +
241C MET 3.2 2.2 - - - -
242C PRO* 2.9 13.1 - - - +
243C VAL* 2.9 32.3 + - + +
499C PHE* 3.8 15.9 - + - -
500C ILE 4.7 0.4 - - - -
503C TRP* 3.4 40.6 - + + -
504C THR* 3.1 42.2 - - + -
507C ASN* 3.2 39.3 - - + +
2000C 0HK 3.0 16.8 - - - +
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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