Contacts of the helix formed by residues 292 - 304 (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 TYR 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B LYS* 3.2 51.7 - - + +
270B PHE* 3.4 35.5 - + - -
271B SER* 3.8 21.5 - - - +
274B ILE* 3.8 13.2 - - + +
291B THR* 1.3 71.1 - - - +
293B GLU* 1.3 65.7 + - + +
296B GLY* 2.9 27.9 + - - -
319B MET* 3.8 22.8 - - + +
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Residues in contact with GLU 293 (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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291B THR* 3.8 5.3 + - - +
292B TYR* 1.3 89.5 - - + +
294B ASP* 1.3 79.2 + - - +
296B GLY* 5.1 0.2 - - - -
297B ASN* 2.9 31.4 + - - +
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Residues in contact with ASP 294 (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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286B TYR* 3.5 19.4 + - - +
289B PRO* 3.3 28.3 - - + +
291B THR* 2.8 23.5 + - - +
293B GLU* 1.3 94.1 - - - +
295B ALA* 1.3 65.1 + - - +
297B ASN* 3.3 5.1 + - - +
298B TYR* 3.1 21.1 + - - +
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Residues in contact with ALA 295 (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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270B PHE* 3.7 9.0 - - + -
274B ILE* 3.7 28.5 - - + -
279B LEU* 3.6 25.0 - - + +
286B TYR* 3.6 5.3 + - - +
289B PRO 3.9 3.1 + - - +
290B ASN* 4.6 0.7 - - - -
291B THR 2.7 26.8 + - - +
294B ASP* 1.3 73.4 - - - +
296B GLY* 1.3 59.1 + - - +
298B TYR 3.4 0.7 + - - -
299B ILE* 3.1 28.4 + - - +
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Residues in contact with GLY 296 (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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223B LEU* 4.6 1.7 - - - +
264B LEU* 4.6 1.7 - - - +
270B PHE* 3.6 14.9 - - - -
292B TYR 2.9 21.7 + - - -
293B GLU 4.0 0.2 - - - -
295B ALA* 1.3 78.3 - - - +
297B ASN* 1.3 55.6 + - - +
299B ILE* 3.4 7.0 + - - +
300B LYS* 2.9 27.7 + - - +
319B MET* 4.0 19.2 - - - +
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Residues in contact with ASN 297 (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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293B GLU 2.9 20.9 + - - +
294B ASP* 3.7 5.5 - - - +
295B ALA 3.3 0.2 - - - -
296B GLY* 1.3 73.9 - - - +
298B TYR* 1.3 62.3 + - - +
300B LYS* 3.1 21.6 + - - +
301B VAL* 2.8 48.6 + - - +
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Residues in contact with TYR 298 (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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279B LEU* 3.9 3.1 - - + -
283B PHE* 3.7 37.7 - + + -
285B ASP* 2.6 26.8 + - - +
286B TYR* 3.5 40.2 - + + -
294B ASP 3.1 16.5 + - - +
295B ALA 3.7 4.7 - - - +
297B ASN* 1.3 79.6 + - - +
299B ILE* 1.3 62.4 + - - +
301B VAL* 3.1 10.4 + - + +
302B GLN* 2.9 55.4 + - + +
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Residues in contact with ILE 299 (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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223B LEU* 4.0 26.9 - - + +
226B TYR* 4.9 0.4 - - + -
239B MET* 3.8 36.3 - - + -
264B LEU* 4.2 3.4 - - + -
270B PHE* 4.0 16.6 - - + -
279B LEU* 3.7 29.8 - - + -
283B PHE* 4.0 8.1 - - + -
295B ALA 3.1 15.7 + - - +
296B GLY 3.6 6.5 - - - +
298B TYR* 1.3 75.7 - - - +
300B LYS* 1.3 63.2 + - - +
302B GLN* 3.0 19.9 + - - +
303B PHE* 3.2 26.7 + - + -
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Residues in contact with LYS 300 (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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262B LEU* 4.9 0.4 - - - +
264B LEU* 3.5 23.3 - - + +
296B GLY 2.9 12.7 + - - +
297B ASN* 3.2 24.7 - - - +
299B ILE* 1.3 77.8 - - - +
301B VAL* 1.3 62.7 + - + +
303B PHE* 3.3 3.5 + - - +
304B LEU* 3.2 38.1 + - + +
317B SER* 3.2 39.8 + - - +
318B HIS* 4.2 6.1 - - - +
319B MET* 3.6 24.8 - - - +
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Residues in contact with VAL 301 (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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297B ASN* 2.8 38.9 + - - +
298B TYR* 3.1 13.2 + - + +
300B LYS* 1.3 76.5 - - + +
302B GLN* 1.3 68.6 + - - +
304B LEU* 4.3 4.4 - - - +
305B GLU* 2.9 45.5 + - + +
310B ARG* 5.2 6.6 + - - +
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Residues in contact with GLN 302 (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* 3.9 19.0 - - + +
283B PHE* 3.8 32.2 - - + -
285B ASP* 5.2 1.0 + - - -
298B TYR* 2.9 61.8 + - + +
299B ILE 3.0 7.4 + - - +
301B VAL* 1.3 86.0 - - - +
303B PHE* 1.3 63.7 + - + +
305B GLU* 3.7 30.8 + - - +
306B LEU* 3.8 12.1 - - - +
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Residues in contact with PHE 303 (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* 4.3 2.2 - + - -
221B ALA* 3.5 19.5 - - + -
239B MET* 4.4 11.7 - - + -
242B SER* 3.4 44.4 - - - -
243B LEU* 3.7 24.9 - - + -
246B PHE* 3.2 42.1 - + + -
262B LEU* 3.4 27.8 - - + -
264B LEU* 4.2 7.4 - - + -
283B PHE* 6.0 0.2 - + - -
299B ILE* 3.2 35.4 + - + -
300B LYS 3.8 2.9 - - - +
302B GLN* 1.3 75.3 - - + +
304B LEU* 1.3 59.6 + - - +
305B GLU 3.1 1.3 - - - -
306B LEU* 2.9 23.6 + - - +
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Residues in contact with LEU 304 (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* 4.6 3.6 - - + -
262B LEU* 4.0 17.9 - - + -
300B LYS* 3.2 27.0 + - + +
301B VAL* 4.3 3.1 - - - +
303B PHE* 1.3 78.3 - - - +
305B GLU* 1.3 60.4 + - - +
306B LEU 3.1 1.7 + - - -
307B ASN* 3.2 19.7 + - - +
310B ARG* 3.3 29.6 + - - +
315B ILE* 3.6 47.3 - - + +
317B SER* 4.4 17.0 - - - +
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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