Contacts of the helix formed by residues 225 - 242 (chain C) in PDB entry 3TDD
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 SER 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C ALA 5.4 0.4 - - - -
224C LEU* 1.3 74.3 - - - +
226C SER* 1.3 69.6 + - - +
227C GLU* 4.0 14.9 + - - +
228C GLU* 2.9 46.2 + - - +
229C ILE* 3.0 11.7 + - - +
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Residues in contact with SER 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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52C ARG* 5.6 3.8 + - - -
207C ALA* 5.2 12.3 - - - +
208C LYS* 5.5 6.5 - - - +
225C SER* 1.3 71.0 - - - +
227C GLU* 1.3 64.8 + - - +
229C ILE* 3.2 10.4 + - - +
230C ASN* 2.5 40.6 + - - +
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Residues in contact with GLU 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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225C SER* 2.9 16.5 + - - +
226C SER* 1.3 83.9 + - - +
228C GLU* 1.3 55.6 + - + +
230C ASN* 2.9 9.5 + - - +
231C GLN* 2.6 52.1 + - + +
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ALA 4.4 2.3 - - - +
224C LEU* 3.7 24.6 - - + +
225C SER* 2.9 44.8 + - - +
227C GLU* 1.3 74.3 - - + +
229C ILE* 1.3 62.2 + - - +
231C GLN* 3.3 23.8 - - - +
232C TYR* 3.1 24.8 - - + -
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Residues in contact with ILE 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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52C ARG* 5.8 1.1 - - - +
194C VAL* 4.7 7.2 - - + -
207C ALA* 4.9 5.8 - - - +
210C ILE* 3.2 43.7 - - + +
211C GLU* 3.8 3.4 - - + -
212C ILE* 3.6 28.0 - - + +
224C LEU* 3.6 33.7 - - + +
225C SER 3.0 12.9 + - - +
226C SER* 3.4 8.1 - - - +
228C GLU* 1.3 71.5 - - - +
230C ASN* 1.3 55.7 + - - +
231C GLN 2.9 4.5 - - - -
232C TYR* 2.6 35.3 + - - +
233C VAL* 3.1 19.9 + - + +
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Residues in contact with ASN 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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207C ALA* 3.3 29.2 + - + +
226C SER* 2.5 25.0 + - - +
227C GLU* 3.4 7.3 - - - +
229C ILE* 1.3 71.9 - - - +
231C GLN* 1.3 60.9 + - - +
233C VAL* 3.4 13.7 + - - +
234C THR* 2.8 36.7 + - - -
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Residues in contact with GLN 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLU* 2.6 37.7 + - + +
228C GLU* 3.3 18.9 - - - +
230C ASN* 1.3 73.0 - - - +
232C TYR* 1.3 66.5 + - + +
234C THR* 3.5 6.7 + - - -
235C GLN* 3.1 23.9 + - - +
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Residues in contact with TYR 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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186C VAL* 5.8 0.2 - - - +
187C GLU* 3.0 59.6 - - + +
190C VAL* 3.8 22.3 - - + +
191C LYS* 3.6 30.1 - - + -
194C VAL* 4.1 17.5 - - + -
224C LEU* 4.5 8.5 - - + +
228C GLU* 3.1 26.9 + - + -
229C ILE* 2.6 19.4 + - - +
231C GLN* 1.3 72.9 - - + +
233C VAL* 1.3 61.0 + - - +
235C GLN* 3.4 11.9 + - - +
236C ILE* 2.8 32.3 + - + +
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Residues in contact with VAL 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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194C VAL* 4.2 14.3 - - + +
198C LEU* 4.0 28.0 - - + -
203C THR* 6.1 3.1 - - + -
206C GLY 5.9 2.5 - - - +
207C ALA* 5.1 12.8 - - + +
210C ILE* 5.8 2.5 - - + -
229C ILE* 3.1 20.8 + - + +
230C ASN* 3.6 20.2 - - - +
232C TYR* 1.3 76.0 - - - +
234C THR* 1.3 64.7 + - - +
236C ILE* 2.8 20.7 + - - +
237C GLU* 2.9 34.0 + - - +
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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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230C ASN* 2.8 29.8 + - - -
231C GLN* 3.7 7.8 - - - -
233C VAL* 1.3 79.7 - - - +
235C GLN* 1.3 64.0 + - - +
236C ILE 3.1 0.2 + - - -
237C GLU* 3.2 17.6 + - - +
238C GLN* 3.3 30.8 + - + +
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Residues in contact with GLN 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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187C GLU* 4.7 13.2 + - - +
191C LYS* 4.5 22.9 + - - +
231C GLN 3.1 14.7 + - - +
232C TYR* 3.8 11.9 - - - +
234C THR* 1.3 79.8 - - - +
236C ILE* 1.3 58.2 + - - +
238C GLN* 3.7 14.9 - - - +
239C GLU* 2.8 42.6 + - - +
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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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191C LYS* 4.0 21.5 - - + +
194C VAL* 3.9 19.5 - - + -
195C ARG* 3.5 48.9 - - + +
198C LEU* 4.1 16.2 - - + -
232C TYR* 2.8 23.6 + - + +
233C VAL* 2.8 10.2 + - - +
235C GLN* 1.3 76.9 - - + +
237C GLU* 1.3 65.1 + - - +
238C GLN 3.0 1.8 - - - -
239C GLU* 3.1 24.9 + - + +
240C LYS* 3.5 20.0 + - + +
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Residues in contact with GLU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 5.4 3.6 - - + -
203C THR* 5.3 11.4 + - - +
233C VAL* 2.9 38.4 + - + +
234C THR* 3.9 9.6 + - - +
236C ILE* 1.3 78.5 - - + +
238C GLN* 1.3 60.7 + - + +
240C LYS* 3.5 17.8 + - + +
241C GLN* 3.1 41.3 + - - +
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Residues in contact with GLN 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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234C THR* 3.3 35.0 + - + +
235C GLN* 3.7 15.2 - - - +
236C ILE 3.0 0.6 - - - -
237C GLU* 1.3 75.7 - - - +
239C GLU* 1.3 59.2 - - - +
240C LYS 2.9 1.8 - - - -
241C GLN* 3.2 10.8 + - - +
242C GLU* 2.7 59.4 + - + +
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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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191C LYS* 3.4 29.3 + - - +
195C ARG* 6.5 0.4 - - - -
235C GLN* 2.8 35.1 - - - +
236C ILE* 3.3 16.6 - - + +
238C GLN* 1.3 79.9 - - - +
240C LYS* 1.3 63.3 + - + +
242C GLU* 3.9 27.9 + - - +
243C GLN* 4.1 10.6 + - - -
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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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198C LEU* 5.9 6.1 - - - -
199C GLU* 4.6 12.4 + - - -
236C ILE* 3.8 26.4 - - + +
237C GLU* 3.5 17.0 - - + +
238C GLN 2.9 1.0 + - - -
239C GLU* 1.3 75.1 - - + +
241C GLN* 1.3 68.0 + - + +
242C GLU 3.1 1.3 - - - -
243C GLN* 3.0 28.1 + - - +
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Residues in contact with GLN 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 GLU* 3.1 34.0 + - - +
238C GLN* 3.9 10.4 - - - +
240C LYS* 1.3 75.7 - - + +
242C GLU* 1.3 52.6 + - + +
243C GLN* 2.5 25.2 + - - +
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Residues in contact with GLU 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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238C GLN* 2.7 54.6 + - + +
239C GLU* 4.0 20.3 - - - +
240C LYS 3.1 0.4 - - - -
241C GLN* 1.3 68.8 - - + +
243C GLN* 1.3 62.2 + - - +
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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