Contacts of the helix formed by residues 273 - 290 (chain A) in PDB entry 1YRT
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 THR 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A SER 5.1 3.1 - - - -
252A ALA 5.0 3.3 + - - +
253A VAL 3.6 11.7 - - - +
254A GLY* 3.5 33.2 - - - +
257A ALA* 3.9 6.7 - - - -
258A ARG* 3.9 7.9 - - + -
262A ARG* 5.8 0.4 - - - -
272A ILE* 1.3 77.7 - - - +
274A ASP* 1.3 66.1 + - - +
275A PHE* 3.6 7.4 + - - +
276A GLU* 3.0 44.0 + - - +
277A LEU* 3.0 20.8 + - - +
345A TYR* 3.8 12.6 - - + +
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Residues in contact with ASP 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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254A GLY* 5.6 0.6 - - - -
257A ALA* 3.7 18.5 - - - +
262A ARG* 3.8 19.8 + - - +
272A ILE 5.0 0.2 - - - +
273A THR* 1.3 71.2 - - - +
275A PHE* 1.3 63.7 + - - +
277A LEU* 3.1 9.5 + - - +
278A GLU* 3.0 31.0 + - - +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.7 40.4 - - + -
36A ALA* 4.0 13.0 - - + -
194A ILE* 4.0 10.5 - - + -
196A PRO* 3.5 21.3 - - + -
200A ASN* 3.5 34.1 - - + -
201A PHE* 3.9 31.6 - + + -
251A SER 5.6 0.8 + - - +
252A ALA 5.7 0.9 - - - +
273A THR* 3.2 7.0 + - - +
274A ASP* 1.3 79.3 - - - +
276A GLU* 1.3 59.9 + - + +
278A GLU* 3.2 20.5 + - - +
279A VAL* 3.0 41.2 + - + +
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Residues in contact with GLU 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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191A MET* 5.8 0.2 - - - +
194A ILE* 4.1 42.2 + - + +
196A PRO* 6.4 0.4 - - + -
272A ILE* 3.4 29.1 - - + +
273A THR* 3.0 40.2 + - - +
275A PHE* 1.3 78.9 - - + +
277A LEU* 1.3 56.3 + - - +
279A VAL* 3.4 2.8 + - - +
280A ARG* 3.0 22.0 + - - +
300A THR* 4.5 19.7 + - - +
303A ASN* 4.1 4.2 + - - -
345A TYR* 2.7 36.2 + - - -
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Residues in contact with LEU 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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262A ARG* 3.6 43.3 - - + +
269A ILE* 5.3 4.0 - - + -
272A ILE* 3.6 17.4 - - + +
273A THR 3.0 10.1 + - - +
274A ASP* 3.3 11.4 - - - +
276A GLU* 1.3 75.0 - - - +
278A GLU* 1.3 68.8 + - + +
279A VAL 3.2 0.2 - - - -
280A ARG* 3.2 22.9 + - - +
281A ASN* 2.8 46.8 + - - +
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Residues in contact with GLU 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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34A LYS* 2.8 30.5 + - - +
274A ASP* 3.0 22.8 + - - +
275A PHE* 3.3 22.4 - - - +
277A LEU* 1.3 78.0 - - + +
279A VAL* 1.3 52.0 + - - +
281A ASN* 3.1 10.4 + - - +
282A ALA* 2.7 36.0 + - - +
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Residues in contact with VAL 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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30A VAL* 4.6 3.4 - - + -
34A LYS* 3.9 19.5 - - + -
38A LEU* 4.1 17.9 - - + -
191A MET* 4.5 0.7 - - + -
194A ILE* 3.8 27.4 - - + -
275A PHE* 3.0 42.1 + - + +
276A GLU 3.6 7.2 - - - +
277A LEU 3.2 0.2 - - - -
278A GLU* 1.3 72.7 - - - +
280A ARG* 1.3 67.0 + - - +
282A ALA* 3.7 1.2 - - - +
283A LEU* 2.9 46.8 + - + +
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Residues in contact with ARG 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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191A MET* 5.5 1.3 - - - -
264A ASP* 3.0 35.6 + - - +
267A MET* 4.9 0.6 - - - -
269A ILE* 3.6 32.8 - - - +
272A ILE* 4.6 4.5 - - + -
276A GLU 3.0 15.1 + - - +
277A LEU* 3.2 22.2 + - - +
279A VAL* 1.3 78.3 - - - +
281A ASN* 1.3 74.2 + - - +
283A LEU* 3.2 5.2 + - - +
284A ASN* 2.9 39.7 + - - +
294A ASP* 4.2 2.8 + - - -
296A VAL* 2.8 45.5 + - + +
297A GLN* 3.1 31.3 - - - +
298A HIS 4.3 3.6 - - - +
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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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264A ASP* 5.4 0.2 - - - +
277A LEU* 2.8 38.7 + - - +
278A GLU* 3.6 6.2 - - - +
280A ARG* 1.3 98.7 + - - +
282A ALA* 1.3 63.2 + - - +
284A ASN* 3.5 6.3 + - - +
285A ARG* 3.0 24.1 + - - +
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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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30A VAL* 3.8 26.9 - - + -
33A GLU* 5.9 0.9 - - - +
34A LYS* 4.2 11.0 - - + -
278A GLU 2.7 19.9 + - - +
279A VAL 3.8 0.9 - - - +
281A ASN* 1.3 75.2 - - - +
283A LEU* 1.3 56.4 + - - +
285A ARG* 3.1 10.8 + - - +
286A ARG* 3.1 30.5 + - - +
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Residues in contact with LEU 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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26A GLY 4.7 0.4 - - - -
27A ILE* 3.5 42.2 - - + +
30A VAL* 3.7 20.0 - - + -
38A LEU* 4.3 6.1 - - + -
40A PHE* 4.5 8.5 - - + -
191A MET* 4.1 15.7 - - + -
279A VAL* 2.9 38.7 + - + +
280A ARG* 3.6 2.9 - - - +
282A ALA* 1.3 72.6 - - - +
284A ASN* 1.3 66.9 + - - +
285A ARG 3.0 1.8 - - - -
286A ARG* 3.1 5.2 + - - +
287A ALA* 2.9 22.2 + - - +
295A VAL* 4.7 4.8 - - + +
296A VAL* 4.1 26.7 - - + -
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Residues in contact with ASN 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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280A ARG* 2.9 35.0 + - - +
281A ASN* 3.9 7.0 + - - +
283A LEU* 1.3 78.0 - - - +
285A ARG* 1.3 63.8 + - - +
287A ALA* 3.2 5.6 + - - +
288A HIS* 3.0 31.9 + - - +
294A ASP* 3.4 34.7 - - - +
295A VAL* 2.8 25.3 + - - +
296A VAL* 3.1 30.7 + - - +
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Residues in contact with ARG 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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33A GLU* 5.6 2.2 + - - -
281A ASN 3.0 14.1 + - - +
282A ALA* 3.1 15.9 + - - +
284A ASN* 1.3 78.0 - - - +
286A ARG* 1.3 86.8 + - - +
288A HIS* 3.2 22.4 + - + +
289A ALA* 3.2 13.6 + - - +
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Residues in contact with ARG 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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22A ALA 5.4 1.2 - - - +
23A VAL* 5.6 1.8 - - - +
25A ASP 4.9 1.6 + - - -
26A GLY* 3.7 26.4 - - - +
29A ALA* 3.4 24.6 - - - +
30A VAL* 3.7 19.3 - - + -
33A GLU* 3.1 30.2 + - - -
282A ALA 3.1 17.7 + - - +
283A LEU* 3.1 5.6 + - - +
285A ARG* 1.3 98.9 - - - +
287A ALA* 1.3 61.7 + - - +
289A ALA* 3.2 22.5 + - - +
290A VAL* 3.4 12.0 + - - +
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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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23A VAL* 4.5 10.3 - - + +
283A LEU 2.9 13.1 + - - +
284A ASN 3.4 9.6 - - - +
285A ARG 3.1 0.2 - - - -
286A ARG* 1.3 75.1 - - - +
288A HIS* 1.3 66.0 + - - +
290A VAL* 3.0 13.7 + - - +
292A ALA* 2.9 32.1 + - + +
293A GLN 3.7 19.5 - - - +
295A VAL* 4.0 17.7 - - + -
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Residues in contact with HIS 288 (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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284A ASN* 3.0 22.2 + - - +
285A ARG* 3.2 12.8 + - + +
287A ALA* 1.3 76.5 - - - +
289A ALA* 1.3 55.2 + - - +
290A VAL 2.4 21.3 - - - +
291A GLY* 4.2 0.7 - - - -
292A ALA 3.1 17.3 + - - +
293A GLN* 3.8 4.1 - - - -
294A ASP* 2.8 44.5 + - - -
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Residues in contact with ALA 289 (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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285A ARG* 3.2 13.8 + - - +
286A ARG* 3.3 19.3 - - - +
287A ALA 3.1 0.6 - - - -
288A HIS* 1.3 81.0 - - - +
290A VAL* 1.3 62.7 + - + +
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Residues in contact with VAL 290 (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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22A ALA* 3.4 43.1 - - + +
23A VAL* 4.0 22.7 - - + +
52A ALA* 5.9 1.8 - - - +
286A ARG 3.7 9.6 - - - +
287A ALA 3.0 9.2 + - - +
288A HIS 2.4 26.0 - - - +
289A ALA* 1.3 84.2 - - + +
291A GLY* 1.3 66.2 + - - +
292A ALA* 3.2 2.7 - - + +
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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
------------------------------------------------------------
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