Contacts of the helix formed by residues 292 - 304 (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 TYR 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267C LYS* 3.4 51.3 - - + +
270C PHE* 3.6 31.5 - + - -
271C SER* 3.8 22.0 - - - +
274C ILE* 3.9 12.4 - - + +
291C THR* 1.3 72.9 - - - +
293C GLU* 1.3 65.2 + - + +
296C GLY* 2.9 28.2 + - - -
319C MET* 3.6 22.5 - - + +
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Residues in contact with GLU 293 (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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291C THR* 3.4 3.8 + - - +
292C TYR* 1.3 88.8 - - + +
294C ASP* 1.3 72.3 + - - +
296C GLY* 3.9 0.2 - - - -
297C ASN* 3.0 28.8 + - + +
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Residues in contact with ASP 294 (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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286C TYR* 3.3 18.2 + - + +
289C PRO* 3.1 26.3 - - + +
291C THR* 2.7 24.5 + - - +
293C GLU* 1.3 84.5 - - - +
295C ALA* 1.3 64.1 + - - +
297C ASN* 3.2 7.3 + - - +
298C TYR* 2.9 23.0 + - - +
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Residues in contact with ALA 295 (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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270C PHE* 3.7 9.0 - - + -
274C ILE* 3.6 28.7 - - + -
279C LEU* 3.7 18.8 - - + +
286C TYR* 3.4 11.6 + - + +
289C PRO 4.6 0.4 - - - +
291C THR 2.8 24.7 + - - +
294C ASP* 1.3 73.6 - - - +
296C GLY* 1.3 61.0 + - - +
298C TYR* 3.3 2.5 + - - +
299C ILE* 3.0 28.1 + - - +
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Residues in contact with GLY 296 (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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223C LEU* 4.6 5.1 - - - +
264C LEU* 4.6 4.2 - - - +
270C PHE* 3.9 13.8 - - - -
292C TYR 2.9 21.9 + - - -
293C GLU 3.9 0.2 - - - -
295C ALA* 1.3 77.7 - - - +
297C ASN* 1.3 56.0 + - - +
299C ILE* 3.4 4.2 + - - +
300C LYS* 3.0 27.4 + - - +
319C MET* 4.1 18.1 - - - +
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Residues in contact with ASN 297 (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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293C GLU* 3.0 21.5 + - + +
294C ASP* 3.7 4.9 - - - +
296C GLY* 1.3 72.5 - - - +
298C TYR* 1.3 62.0 + - - +
300C LYS* 3.2 31.3 + - - +
301C VAL* 2.9 45.1 + - - +
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Residues in contact with TYR 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 3.9 10.1 - - + -
283C PHE* 3.7 31.5 - + + +
285C ASP* 4.3 9.7 - - - +
286C TYR* 3.4 53.5 + + + -
294C ASP 2.9 17.2 + - - +
295C ALA 3.6 4.3 - - - +
297C ASN* 1.3 81.6 + - - +
299C ILE* 1.3 64.1 + - - +
301C VAL* 3.2 5.1 + - + -
302C GLN* 3.0 62.5 + - + -
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Residues in contact with ILE 299 (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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223C LEU* 3.9 24.7 - - + +
226C TYR* 4.9 0.2 - - + -
239C MET* 3.9 36.3 - - + -
264C LEU* 4.2 4.5 - - + -
270C PHE* 3.8 26.9 - - + -
279C LEU* 4.0 25.1 - - + -
283C PHE* 4.1 4.7 - - + -
295C ALA 3.0 21.0 + - - +
296C GLY 3.6 3.8 - - - +
298C TYR* 1.3 74.1 - - - +
300C LYS* 1.3 64.8 + - - +
302C GLN* 3.0 21.3 + - - +
303C PHE* 3.2 27.4 + - + -
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Residues in contact with LYS 300 (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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262C LEU* 5.4 0.2 - - + -
264C LEU* 3.6 22.2 - - + -
296C GLY 3.0 14.1 + - - +
297C ASN* 3.3 33.4 - - - +
299C ILE* 1.3 77.5 - - - +
301C VAL* 1.3 63.5 + - - +
303C PHE* 3.4 5.1 + - - +
304C LEU* 3.0 37.9 + - + +
317C SER* 3.2 28.7 - - - +
319C MET* 5.6 3.8 - - + -
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Residues in contact with VAL 301 (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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297C ASN* 2.9 36.4 + - - +
298C TYR* 3.5 10.3 - - + +
300C LYS* 1.3 77.4 - - - +
302C GLN* 1.3 69.4 + - - +
304C LEU* 4.6 4.9 - - - +
305C GLU* 2.9 60.2 + - + +
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Residues in contact with GLN 302 (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* 4.0 17.2 - - + +
283C PHE* 3.7 33.0 - - + -
298C TYR* 3.0 59.8 + - + +
299C ILE 3.0 8.7 + - - +
301C VAL* 1.3 90.2 - - - +
303C PHE* 1.3 61.7 - - - +
305C GLU* 3.9 8.3 + - - +
306C LEU* 3.5 18.7 + - - +
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Residues in contact with PHE 303 (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* 4.2 1.8 - + - -
221C ALA* 3.5 24.5 - - + -
239C MET* 4.4 11.7 - - + -
242C SER* 3.4 39.5 - - - -
243C LEU* 3.7 24.7 - - + -
246C PHE* 3.3 37.1 - + + -
262C LEU* 3.5 26.5 - - + -
264C LEU* 4.1 11.2 - - + -
283C PHE* 6.0 0.2 - + - -
299C ILE* 3.2 39.3 + - + -
300C LYS 3.8 2.9 - - - +
301C VAL 3.2 0.2 - - - -
302C GLN* 1.3 77.3 - - - +
304C LEU* 1.3 65.7 + - - +
306C LEU* 3.0 22.7 + - - +
307C ASN 4.2 0.2 + - - -
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Residues in contact with LEU 304 (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* 4.8 4.0 - - + -
262C LEU* 4.0 17.9 - - + -
300C LYS* 3.0 41.7 + - + +
301C VAL* 4.2 4.3 - - - +
303C PHE* 1.3 79.2 - - - +
305C GLU* 1.3 61.4 + - + +
306C LEU 3.1 1.1 + - - -
307C ASN* 3.2 16.5 + - - +
310C ARG* 3.4 16.5 + - - -
315C ILE* 3.9 45.3 - - + +
317C SER* 3.9 11.4 - - - +
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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