Contacts of the helix formed by residues 269 - 287 (chain A) in PDB entry 1TYY
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 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A TRP* 1.3 81.5 - - - +
270A HIS* 1.3 55.1 + - - +
271A ALA* 2.9 35.9 + - - +
272A LEU* 3.1 7.2 + - - +
273A LEU* 2.7 36.6 + - - +
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Residues in contact with HIS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 4.1 17.1 - - + +
230A THR* 5.3 11.3 + - + +
232A GLU* 4.6 26.5 - - + +
235A PHE* 3.3 45.0 - + + -
237A PHE* 4.5 5.6 - + - -
269A ASP* 1.3 75.6 - - - +
271A ALA* 1.3 72.3 - - - +
273A LEU* 3.3 8.3 - - - +
274A ALA* 2.7 34.2 + - + +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASP* 2.9 24.4 + - - +
270A HIS* 1.3 89.0 - - - +
272A LEU* 1.3 55.8 + - - +
274A ALA* 2.7 20.9 + - - +
275A GLU* 3.2 10.0 + - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A THR* 3.3 39.9 - - + +
262A LEU* 3.7 16.4 - - + +
264A ARG* 5.5 3.6 - - + -
265A ALA* 4.3 25.6 - - + +
267A CYS 4.9 0.4 - - - +
268A TRP* 4.4 9.6 - - + -
269A ASP* 3.1 18.4 + - - +
271A ALA* 1.3 79.3 - - + +
273A LEU* 1.3 58.0 + - - +
275A GLU* 3.7 7.4 - - + +
276A ALA* 2.7 34.2 + - + +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ILE* 3.9 6.7 - - + -
216A THR* 4.7 4.3 - - + -
218A ILE* 3.7 28.7 - - + -
228A LEU* 3.9 19.5 - - + -
230A THR* 5.3 2.7 - - + -
237A PHE* 5.4 0.2 - - - -
258A LEU* 5.2 0.2 - - + -
262A LEU* 3.7 20.9 - - + -
268A TRP* 3.4 37.2 - - + -
269A ASP 2.7 19.1 + - - +
270A HIS* 3.3 13.0 - - - +
272A LEU* 1.3 73.9 - - - +
274A ALA* 1.3 56.9 + - - +
276A ALA* 4.0 4.9 - - + -
277A ILE* 3.0 46.3 + - + +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 3.8 30.9 - - + -
270A HIS* 2.7 25.9 + - + +
271A ALA* 2.7 13.2 + - - +
273A LEU* 1.3 70.1 - - - +
275A GLU* 1.3 61.8 + - - +
276A ALA 3.1 1.3 - - - -
277A ILE 4.0 0.3 - - - -
278A SER* 2.9 29.5 + - - -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A THR* 3.9 10.1 - - + -
271A ALA 3.2 9.4 + - - +
272A LEU* 3.2 11.9 + - + +
274A ALA* 1.3 76.7 - - - +
276A ALA* 1.3 63.7 + - - +
278A SER* 3.6 7.7 + - - -
279A ASN* 3.2 29.7 + - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 3.5 30.6 - - + +
261A THR* 3.5 24.0 - - + +
262A LEU* 4.3 10.1 - - + -
272A LEU 2.7 18.3 + - - +
273A LEU* 3.6 9.2 - - + +
275A GLU* 1.3 79.0 - - - +
277A ILE* 1.3 63.2 + - - +
279A ASN* 3.1 7.8 + - - +
280A ALA 3.0 15.8 + - - -
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 3.9 19.5 - - + -
226A ALA* 3.8 21.8 - - + -
227A LEU 5.1 0.2 - - - -
228A LEU* 3.5 33.7 - - + +
237A PHE* 3.8 30.7 - - + -
254A PHE* 4.5 4.9 - - + -
258A LEU* 4.1 8.3 - - + -
273A LEU* 3.0 32.3 + - + +
274A ALA 3.6 3.1 + - - +
275A GLU 3.5 0.2 - - - -
276A ALA* 1.3 73.4 - - - +
278A SER* 1.3 58.4 - - - +
280A ALA* 3.3 5.8 - - - +
281A ASN* 3.0 29.2 + - - +
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 4.3 13.6 - - - -
274A ALA 2.9 21.4 + - - -
275A GLU* 3.7 8.6 - - - -
276A ALA 3.2 0.2 - - - -
277A ILE* 1.3 77.5 - - - +
279A ASN* 1.3 62.9 + - - +
281A ASN* 3.7 5.3 + - - +
282A ALA* 3.1 23.9 + - - +
307A LEU* 5.3 4.7 - - - +
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Residues in contact with ASN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 5.4 1.2 - - - +
257A GLY* 3.7 13.7 - - - +
260A PHE* 4.9 11.6 - - - -
261A THR* 2.8 28.4 + - - +
275A GLU* 3.2 14.6 + - - +
276A ALA 3.1 9.3 + - - +
278A SER* 1.3 78.8 - - - +
280A ALA* 1.3 55.3 + - - +
282A ALA* 3.4 4.8 - - - +
283A CYS* 2.8 40.6 + - - +
303A LEU* 3.5 27.9 - - - +
307A LEU* 5.4 4.3 - - - +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A PHE* 3.1 61.0 - - + +
257A GLY 4.8 0.4 - - - -
258A LEU* 4.4 6.1 - - + +
276A ALA 3.0 11.5 + - - +
277A ILE* 3.3 10.8 - - - +
279A ASN* 1.3 74.9 - - - +
281A ASN* 1.3 56.6 + - - +
282A ALA 3.0 0.5 + - - -
283A CYS* 3.5 1.1 - - - -
284A GLY* 2.6 35.9 + - - -
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLY 5.3 1.0 + - - -
225A GLY* 3.5 27.7 + - - -
226A ALA* 3.7 2.4 + - - +
237A PHE* 3.2 39.5 - - - +
238A PRO 3.6 14.0 - - - +
239A ALA* 4.3 7.5 - - - +
240A PRO* 3.7 5.9 - - + +
254A PHE* 3.2 24.4 - - - -
277A ILE* 3.0 12.1 + - - +
278A SER* 4.0 4.7 - - - +
280A ALA* 1.3 78.4 - - - +
282A ALA* 1.3 62.1 - - - +
284A GLY* 3.3 1.8 + - - -
285A ALA* 3.0 23.6 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PRO* 4.4 8.0 - - + +
278A SER 3.1 18.5 + - - +
279A ASN* 3.4 7.9 - - - +
280A ALA 3.1 0.6 - - - -
281A ASN* 1.3 72.4 - - - +
283A CYS* 1.3 59.8 + - - +
284A GLY 2.9 3.6 - - - -
285A ALA* 2.8 21.7 + - - +
286A MSE 3.2 15.0 + - - +
303A LEU* 4.3 12.3 - - + -
306A PHE* 4.0 15.2 - - + -
307A LEU* 4.2 22.9 - - + -
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Residues in contact with CYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 4.7 4.9 - - - -
43A LEU* 4.1 24.2 - - - -
253A ALA* 3.1 41.8 - - + +
257A GLY* 4.3 4.7 - - - -
279A ASN* 2.8 23.3 + - - +
280A ALA 3.9 0.7 - - - +
282A ALA* 1.3 73.2 - - - +
284A GLY* 1.3 58.9 + - - +
285A ALA 3.3 0.2 - - - -
286A MSE 4.2 7.1 - - - +
287A ALA* 3.6 13.9 + - - +
298A PRO* 3.7 29.3 - - + +
303A LEU* 4.3 12.6 - - - -
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA* 4.0 27.4 - - - +
254A PHE* 4.4 7.2 - - - -
280A ALA 2.6 20.8 + - - -
281A ASN* 3.6 4.7 - - - -
282A ALA 2.9 0.2 + - - -
283A CYS* 1.3 77.5 - - - +
285A ALA* 1.3 59.5 + - - +
287A ALA* 4.6 0.2 - - - +
288A VAL* 3.3 21.1 + - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ALA* 5.4 2.0 - - + -
240A PRO* 3.9 24.0 - - + +
241A ARG 5.5 2.5 - - - +
242A VAL* 5.5 10.2 - - + +
243A ASP* 5.7 0.3 - - - +
281A ASN 3.0 11.6 + - - +
282A ALA 2.8 9.5 + - - +
284A GLY* 1.3 76.3 - - - +
286A MSE 1.3 65.3 + - - +
288A VAL* 3.2 21.2 + - - +
289A THR* 3.9 6.3 - - - +
306A PHE* 3.9 16.6 - - + -
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Residues in contact with MSE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ALA 3.2 6.6 + - - +
283A CYS* 4.5 3.6 - - - +
285A ALA* 1.3 77.0 - - - +
287A ALA* 1.3 53.4 + - - +
289A THR* 2.5 49.7 + - + +
296A ALA* 4.2 12.8 - - + +
298A PRO* 3.7 33.4 - - + -
302A GLN* 3.6 26.5 - - + +
303A LEU* 4.3 9.6 - - - -
306A PHE* 3.4 51.8 - - + -
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A THR 5.3 0.9 - - - +
249A GLY 4.3 11.2 - - - +
250A ALA* 4.9 0.4 - - - -
253A ALA* 3.7 18.4 - - + -
283A CYS 3.6 17.2 + - - +
284A GLY 4.6 3.1 - - - +
285A ALA 3.4 0.6 - - - -
286A MSE 1.3 78.2 - - - +
288A VAL* 1.3 58.4 + - - +
289A THR 3.1 1.4 + - - -
290A ALA 3.7 7.6 + - - -
292A GLY 4.2 4.2 - - - +
293A ALA 4.7 6.1 - - - +
296A ALA* 4.0 18.1 + - - +
297A LEU* 4.4 12.3 - - + -
298A PRO* 5.4 0.6 - - + +
404A K 3.2 19.4 - - - -
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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