Contacts of the helix formed by residues 238 - 250 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLY 4.2 7.1 + - - -
39B GLU* 2.9 46.2 + - - +
143B GLN* 2.8 35.2 - - - +
225B ALA* 3.6 24.1 - - + +
228B MET* 2.7 40.1 + - - +
229B VAL 2.8 29.4 + - - -
230B LEU* 3.6 22.9 - - + +
231B VAL* 4.2 12.8 - - - +
236B VAL 3.4 1.2 + - - -
237B ASN* 1.3 70.8 - - - +
239B MET* 1.3 60.3 + - - +
241B GLU* 3.5 3.1 + - - +
242B SER* 3.1 22.3 + - - -
266B LYS* 5.9 1.0 - - - +
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Residues in contact with MET 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ALA* 5.9 0.9 - - + -
222B ALA 3.3 17.9 - - - +
223B LEU* 3.3 30.7 - - - +
225B ALA* 3.6 5.9 + - - -
226B TYR* 3.8 24.7 - - - +
237B ASN* 2.9 14.7 + - - +
238B ARG* 1.3 72.1 - - - +
240B HIS* 1.3 61.0 + - - +
242B SER* 3.3 6.6 + - - -
243B LEU* 2.8 29.1 + - + +
264B LEU* 5.9 0.7 - - + -
282B CYS* 3.7 10.3 - - - -
283B PHE* 4.0 18.6 - - + -
299B ILE* 3.8 35.9 - - + -
303B PHE* 4.4 16.4 - - + -
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Residues in contact with HIS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B VAL* 5.0 3.4 - - + -
237B ASN* 3.0 34.8 + - + +
239B MET* 1.3 73.9 - - - +
241B GLU* 1.3 59.3 + - - +
243B LEU* 3.2 16.0 + - + +
244B HIS* 2.9 53.2 + + + -
281B ILE 5.4 1.3 - - - -
282B CYS* 2.8 44.7 + - - -
283B PHE* 4.7 3.1 - + - -
284B PRO* 5.8 0.7 - - + -
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.8 6.5 - - + -
201B ARG* 2.8 34.3 + - - +
204B ARG* 2.7 35.4 + - - +
230B LEU* 3.4 38.9 - - + +
232B GLU* 5.0 0.4 - - - +
236B VAL* 4.2 6.3 - - + +
237B ASN 3.1 8.2 + - - +
238B ARG 3.6 8.3 - - - +
239B MET 3.3 0.2 - - - -
240B HIS* 1.3 77.2 - - - +
242B SER* 1.3 56.9 + - - +
244B HIS* 3.3 13.6 + - - +
245B LEU* 2.9 30.1 + - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.8 14.7 - - - +
219B PHE* 3.7 8.6 - - - -
220B ILE 4.8 0.5 + - - -
221B ALA* 3.4 18.2 - - - +
222B ALA 5.7 1.6 - - - -
225B ALA* 6.3 1.1 - - - -
238B ARG 3.1 11.5 + - - -
239B MET* 3.5 11.0 - - - -
240B HIS 3.3 0.2 - - - -
241B GLU* 1.3 80.6 - - - +
243B LEU* 1.3 56.4 + - - +
245B LEU* 3.4 6.7 + - - +
246B PHE* 2.9 30.0 + - - +
303B PHE* 3.4 20.3 - - - -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B MET* 2.8 21.4 + - + +
240B HIS* 3.4 18.4 - - + +
242B SER* 1.3 75.2 - - - +
244B HIS* 1.3 64.5 + - + +
246B PHE* 3.2 1.4 + - - +
247B ASN 2.9 23.9 + - - -
283B PHE* 3.7 32.5 - - + -
302B GLN* 3.9 24.2 - - + +
303B PHE* 3.7 41.5 - - + -
306B LEU* 3.2 19.1 - - + +
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B VAL* 5.9 3.3 - - + +
240B HIS* 2.9 38.9 + + + +
241B GLU* 3.6 14.7 + - - +
243B LEU* 1.3 82.1 - - + +
245B LEU* 1.3 62.8 + - - +
247B ASN* 3.1 19.1 + - + +
248B SER* 3.1 17.2 + - - -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY 4.0 4.7 - - - -
37B ALA* 3.8 31.0 - - + +
204B ARG* 3.6 50.3 - - - +
207B TRP* 4.0 15.7 - - + -
219B PHE* 3.9 13.2 - - + -
241B GLU 2.9 18.3 + - - +
242B SER 3.6 4.3 - - - +
244B HIS* 1.3 75.5 - - - +
246B PHE* 1.3 58.3 + - - +
248B SER* 3.2 11.2 + - - -
249B ILE* 2.9 38.9 + - + +
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B PHE* 3.6 46.9 - + + -
242B SER 2.9 18.7 + - - +
243B LEU 3.5 3.6 - - - +
245B LEU* 1.3 73.0 - - - +
247B ASN* 1.3 59.1 + - - +
249B ILE* 4.5 1.8 - - + +
250B CYS* 2.7 57.6 + - + +
260B ILE* 4.3 12.6 - - + -
262B LEU* 4.2 13.5 - - + -
303B PHE* 3.2 52.3 - + + -
304B LEU* 4.3 0.9 - - + -
306B LEU* 3.9 9.0 - - + -
315B ILE* 3.7 31.9 - - + -
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LEU 2.9 14.2 + - - +
244B HIS* 3.1 13.3 + - - +
246B PHE* 1.3 76.3 - - - +
248B SER* 1.3 63.1 + - - +
250B CYS* 4.6 0.2 - - - -
251B ASN* 2.8 59.3 + - - +
306B LEU* 3.7 33.5 - - + +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B HIS 3.1 13.0 + - - -
245B LEU* 3.2 13.6 + - - +
247B ASN* 1.3 82.2 + - - +
249B ILE* 1.3 65.7 + - - +
251B ASN* 3.8 1.4 - - - -
252B HIS* 3.3 27.1 + - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.9 23.8 - - + -
207B TRP* 4.1 10.8 - - + -
211B PHE* 3.8 32.1 - - + -
217B ILE* 4.2 10.8 - - + -
219B PHE* 4.3 18.4 - - + -
245B LEU* 2.9 31.9 + - + +
246B PHE* 3.9 7.6 - - + +
248B SER* 1.3 78.0 - - - +
250B CYS* 1.3 67.6 + - - +
252B HIS* 3.0 9.2 + - - +
255B PHE* 3.0 37.4 - - + -
260B ILE* 5.3 2.5 - - + -
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Residues in contact with CYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B PHE* 2.7 43.7 + - + +
247B ASN* 4.1 3.1 - - - +
249B ILE* 1.3 74.7 - - - +
251B ASN* 1.3 59.6 + - - +
252B HIS 3.4 3.3 + - - +
255B PHE* 4.7 0.2 - - - +
260B ILE* 3.9 10.7 - - - +
306B LEU 5.1 0.4 - - - +
307B ASN* 3.7 27.8 - - - -
309B ARG* 4.7 1.7 + - - -
313B LYS* 2.9 29.6 + - - -
315B ILE* 3.1 36.1 - - - -
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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