Contacts of the helix formed by residues 238 - 250 (chain C) in PDB entry 1TAD
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 ARG 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLY 3.9 8.2 + - - -
39C GLU* 2.9 42.2 + - - +
143C GLN* 3.0 27.1 + - - -
225C ALA* 3.5 24.6 - - + +
228C MET* 2.7 45.2 + - - +
229C VAL 3.1 26.6 + - - -
230C LEU* 3.8 21.9 - - + +
231C VAL* 3.6 18.8 - - - +
236C VAL 3.5 0.4 + - - -
237C ASN* 1.3 71.9 + - - +
239C MET* 1.3 55.6 + - - +
241C GLU* 3.4 4.3 + - - +
242C SER* 3.1 25.6 + - - -
266C LYS* 5.7 2.4 - - - +
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Residues in contact with MET 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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221C ALA* 6.0 0.2 - - + -
222C ALA 3.5 25.6 - - - +
223C LEU* 3.5 19.7 - - - +
225C ALA* 3.6 3.2 + - - -
226C TYR* 3.9 21.1 - - - +
237C ASN* 2.9 14.2 + - - +
238C ARG* 1.3 72.6 - - - +
240C HIS* 1.3 65.1 + - - +
241C GLU 3.1 0.2 - - - -
242C SER* 2.9 12.1 + - - +
243C LEU* 2.9 37.1 + - + +
264C LEU* 6.0 0.2 - - + -
282C CYS* 3.6 10.5 - - - -
283C PHE* 3.8 25.1 - - + -
299C ILE* 3.9 28.5 - - + -
303C PHE* 4.4 10.3 - - + -
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Residues in contact with HIS 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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236C VAL* 5.3 3.4 - - + -
237C ASN* 3.1 33.6 + - + +
239C MET* 1.3 76.1 - - - +
241C GLU* 1.3 63.0 + - - +
243C LEU* 3.3 16.5 + - + +
244C HIS* 3.0 45.6 + + + +
281C ILE 5.1 3.1 - - - -
282C CYS* 2.7 43.3 + - - -
283C PHE* 4.8 4.1 - + - -
284C PRO* 5.9 0.9 - - + -
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Residues in contact with GLU 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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37C ALA* 4.7 4.7 - - + -
201C ARG* 2.9 35.4 + - - +
204C ARG* 2.8 42.0 + - - +
230C LEU* 3.4 30.7 - - + +
236C VAL* 4.0 4.8 - - + +
237C ASN 3.0 12.3 + - - +
238C ARG 3.4 9.4 - - - +
240C HIS* 1.3 76.7 - - - +
242C SER* 1.3 58.0 + - - +
244C HIS* 3.2 17.1 + - - +
245C LEU* 2.9 26.2 + - + +
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Residues in contact with SER 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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37C ALA* 4.6 15.9 - - - +
219C PHE* 3.7 8.0 - - - -
221C ALA* 4.4 13.7 - - - +
222C ALA 5.6 1.7 + - - -
225C ALA* 5.8 0.9 - - - +
238C ARG 3.1 9.4 + - - -
239C MET* 2.9 24.6 + - - +
241C GLU* 1.3 76.8 - - - +
243C LEU* 1.3 52.1 + - - +
245C LEU* 3.3 7.3 + - - +
246C PHE* 2.8 35.9 + - - +
303C PHE* 3.4 21.9 - - - -
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Residues in contact with LEU 243 (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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239C MET* 2.9 26.9 + - + +
240C HIS* 3.5 17.3 - - + +
242C SER* 1.3 76.5 + - - +
244C HIS* 1.3 60.6 + - + +
246C PHE* 3.3 0.5 + - - +
247C ASN* 3.0 25.2 + - - +
283C PHE* 3.7 33.0 - - + -
302C GLN* 4.0 24.2 - - + +
303C PHE* 3.7 40.8 - - + -
306C LEU* 3.1 19.3 - - + +
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Residues in contact with HIS 244 (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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236C VAL* 5.8 3.1 - - + +
240C HIS* 3.0 39.5 + + + +
241C GLU* 3.2 17.9 + - - +
243C LEU* 1.3 81.0 - - + +
245C LEU* 1.3 62.3 + - - +
247C ASN* 3.3 9.2 + - - +
248C SER* 3.1 24.9 + - - -
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Residues in contact with LEU 245 (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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36C GLY 3.8 7.2 - - - -
37C ALA* 3.6 31.6 - - + +
204C ARG* 3.9 37.7 - - + +
207C TRP* 3.8 29.2 - - + -
219C PHE* 3.8 12.3 - - + -
241C GLU 2.9 16.1 + - - +
242C SER* 3.7 4.7 - - - +
244C HIS* 1.3 77.6 - - - +
246C PHE* 1.3 57.3 + - - +
248C SER* 3.2 10.9 + - - -
249C ILE* 2.9 38.1 + - + +
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Residues in contact with PHE 246 (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 PHE* 3.5 46.1 - + + -
242C SER 2.8 21.6 + - - +
243C LEU 3.7 4.0 - - - +
245C LEU* 1.3 69.5 - - - +
247C ASN* 1.3 61.5 + - - +
249C ILE* 3.1 1.7 + - + -
250C CYS* 2.7 67.6 + - + -
260C ILE* 4.4 8.5 - - + -
262C LEU* 4.3 13.7 - - + -
303C PHE* 3.3 52.0 - + + -
304C LEU* 4.5 2.0 - - + -
306C LEU* 4.3 3.6 - - + -
307C ASN 5.3 0.4 - - - -
315C ILE* 3.9 25.6 - - + -
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Residues in contact with ASN 247 (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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243C LEU 3.0 14.3 + - - +
244C HIS* 3.3 13.3 - - - +
246C PHE* 1.3 78.0 - - - +
248C SER* 1.3 62.8 + - - +
250C CYS* 4.3 4.5 - - - -
251C ASN* 3.1 42.9 + - - +
306C LEU* 3.7 31.2 + - + +
308C MET* 5.5 2.0 - - - +
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Residues in contact with SER 248 (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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244C HIS 3.1 14.4 + - - -
245C LEU* 3.4 13.9 - - - +
247C ASN* 1.3 79.8 + - - +
249C ILE* 1.3 66.8 + - - +
251C ASN* 4.0 1.5 - - - -
252C HIS* 3.3 27.8 + - - +
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Residues in contact with ILE 249 (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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35C LEU* 4.0 24.9 - - + -
207C TRP* 4.0 24.9 - - + -
211C PHE* 4.1 16.4 - - + -
217C ILE* 4.2 18.6 - - + -
219C PHE* 4.2 19.5 - - + -
245C LEU* 2.9 33.8 + - + +
246C PHE* 3.7 8.5 - - + +
248C SER* 1.3 75.5 - - - +
250C CYS* 1.3 68.0 + - + +
251C ASN 3.1 1.6 - - - -
252C HIS* 3.1 22.7 + - - +
255C PHE* 3.4 10.3 - - + -
260C ILE* 5.8 1.3 - - + -
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Residues in contact with CYS 250 (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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246C PHE* 2.7 64.4 + - + +
247C ASN* 4.0 1.3 - - - -
249C ILE* 1.3 73.7 - - - +
251C ASN* 1.3 74.9 + - - +
252C HIS 3.4 1.6 + - - +
255C PHE* 5.3 0.7 - - - +
260C ILE* 3.8 24.7 - - + +
306C LEU 4.0 3.8 - - - -
307C ASN* 3.9 25.8 - - - +
309C ARG* 4.8 3.1 - - - +
313C LYS* 4.5 7.6 + - - -
315C ILE* 3.9 12.8 - - + -
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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