Contacts of the helix formed by residues 211 - 225 (chain C) in PDB entry 1TYG
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 ASP 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C SER 5.3 1.0 - - - +
201C VAL* 2.9 29.3 + - + +
203C GLY* 4.8 14.2 - - - -
209C LEU 4.6 0.2 - - - -
210C PRO* 1.3 70.3 - - - +
212C PRO* 1.3 64.3 - - - +
213C VAL* 3.1 22.9 + - - +
214C GLU* 3.2 22.5 + - - +
215C THR* 2.8 35.7 + - - -
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Residues in contact with PRO 212 (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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210C PRO* 3.4 11.6 - - + +
211C ASP* 1.3 86.2 - - - +
213C VAL* 1.3 71.3 + - + +
215C THR* 4.8 3.1 - - - -
216C LEU* 3.2 25.6 + - - +
239C LEU* 4.0 38.0 - - + +
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Residues in contact with VAL 213 (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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211C ASP* 3.1 14.9 + - - +
212C PRO* 1.3 84.7 - - + +
214C GLU* 1.3 78.8 + - + +
216C LEU* 3.6 2.6 + - - +
217C LYS* 2.8 33.5 + - - +
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Residues in contact with GLU 214 (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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176C SER 4.1 8.7 - - - +
177C THR* 3.4 10.6 - - - +
178C ALA* 3.0 34.0 + - + +
179C GLU* 4.1 7.6 - - - +
201C VAL* 3.8 18.4 - - + -
211C ASP* 3.2 23.9 + - - +
213C VAL* 1.3 85.1 - - + +
215C THR* 1.3 58.6 + - - +
217C LYS* 4.2 2.9 - - - -
218C ALA* 2.6 37.4 + - - +
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Residues in contact with THR 215 (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 VAL* 3.9 24.2 - - + +
201C VAL* 3.2 26.9 + - + +
210C PRO* 4.1 3.1 - - - +
211C ASP 2.8 34.3 + - - -
212C PRO* 4.6 3.1 - - - -
214C GLU* 1.3 71.6 - - - +
216C LEU* 1.3 58.6 + - - +
219C SER* 3.2 26.5 + - - -
231C PRO* 4.1 11.2 - - + -
232C TYR 3.2 26.2 - - - +
233C THR* 5.3 2.7 - - - +
239C LEU* 6.4 0.7 - - - -
243C LEU* 3.9 7.7 - - + +
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Residues in contact with LEU 216 (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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212C PRO 3.2 17.4 + - - +
213C VAL* 3.9 2.7 - - - +
214C GLU 3.2 0.4 - - - -
215C THR* 1.3 75.9 - - - +
217C LYS* 1.3 68.1 + - - +
219C SER* 2.9 14.7 + - - -
220C GLU* 3.2 12.4 + - + +
239C LEU* 4.0 19.7 - - + -
242C LYS* 3.9 31.6 - - + -
243C LEU* 3.6 21.7 - - + +
246C LEU* 3.9 27.7 - - + +
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Residues in contact with LYS 217 (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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178C ALA* 4.7 11.1 - - + +
179C GLU* 5.6 4.0 + - - +
213C VAL* 2.8 23.7 + - + +
214C GLU* 3.8 5.8 - - - +
216C LEU* 1.3 73.6 - - - +
218C ALA* 1.3 63.7 + - - +
220C GLU* 3.1 35.7 + - - +
221C GLN* 3.4 33.4 + - - +
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Residues in contact with ALA 218 (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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178C ALA* 3.3 30.8 - - + +
181C ALA* 4.8 7.2 - - + -
182C VAL* 4.9 5.0 - - + +
199C VAL* 4.5 13.0 - - + -
201C VAL* 5.0 1.1 - - + -
214C GLU 2.6 24.1 + - - +
215C THR* 4.3 2.5 - - - +
217C LYS* 1.3 73.7 - - - +
219C SER* 1.3 59.9 + - - +
221C GLN* 3.6 2.9 + - - +
222C LEU* 3.2 34.9 + - + +
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Residues in contact with SER 219 (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 VAL* 3.6 11.8 - - - +
215C THR 3.2 20.7 + - - -
216C LEU 2.9 7.2 + - - -
218C ALA* 1.3 76.9 - - - +
220C GLU* 1.3 61.9 + - - +
222C LEU* 4.3 1.8 - - - +
223C LEU* 3.3 30.3 + - - +
229C VAL* 3.4 26.6 - - - +
231C PRO* 3.8 11.6 - - - +
243C LEU* 3.8 13.0 - - - +
246C LEU* 4.6 3.4 - - - -
248C VAL* 4.7 6.1 - - - -
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Residues in contact with GLU 220 (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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216C LEU* 3.2 9.6 + - + +
217C LYS* 3.1 20.4 + - - +
219C SER* 1.3 77.7 - - - +
221C GLN* 1.3 87.8 + - - +
223C LEU* 3.2 20.0 + - - +
224C GLU* 3.3 25.5 + - - +
246C LEU* 4.3 16.8 - - + +
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Residues in contact with GLN 221 (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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182C VAL* 4.8 12.6 - - + -
217C LYS* 3.4 34.5 + - - +
218C ALA* 3.6 3.3 + - - +
220C GLU* 1.3 98.1 - - - +
222C LEU* 1.3 62.2 + - - +
224C GLU* 3.9 21.6 + - - +
225C GLU* 2.2 36.4 - - - +
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Residues in contact with LEU 222 (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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172C THR* 5.4 3.8 - - + +
181C ALA* 5.0 2.0 - - + +
182C VAL* 3.7 28.9 - - + +
185C ALA* 3.6 34.5 - - + -
186C ARG* 5.0 0.4 - - + -
197C ILE* 4.3 18.8 - - + -
199C VAL* 4.6 11.2 - - + -
218C ALA* 3.2 23.9 + - + +
219C SER* 4.3 0.7 - - - +
221C GLN* 1.3 77.4 - - - +
223C LEU* 1.4 60.9 + - - +
224C GLU 3.2 0.7 - - - -
225C GLU* 2.9 26.5 - - - +
227C PHE* 2.9 42.1 - - + +
229C VAL* 4.0 15.0 - - + -
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Residues in contact with LEU 223 (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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219C SER 3.3 21.6 + - - +
220C GLU* 3.2 9.0 + - - +
222C LEU* 1.4 79.2 - - - +
224C GLU* 1.3 63.6 + - - +
225C GLU 4.5 0.4 - - - -
226C GLY* 4.1 6.8 + - - -
227C PHE 4.1 8.9 + - - +
229C VAL* 3.8 11.4 - - + -
246C LEU* 3.2 26.5 - - + +
247C GLY* 3.4 19.5 - - - +
248C VAL* 3.4 25.6 - - + -
249C HIS* 3.5 23.1 - - + +
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Residues in contact with GLU 224 (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 GLU* 3.3 34.4 + - - +
221C GLN* 4.1 23.3 - - - +
222C LEU 3.2 0.8 - - - -
223C LEU* 1.3 78.5 - - - +
225C GLU* 1.3 57.7 + - - +
226C GLY* 2.7 15.9 + - - -
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Residues in contact with GLU 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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182C VAL* 4.9 4.5 - - - +
186C ARG* 3.5 29.8 - - + +
221C GLN* 2.2 30.3 - - - +
222C LEU* 2.9 22.9 - - - +
224C GLU* 1.3 80.2 - - - +
226C GLY* 1.3 51.0 + - - +
227C PHE* 2.5 41.0 + - + -
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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