Contacts of the helix formed by residues 250 - 260 (chain B) in PDB entry 1Y8Q
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 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B THR* 3.5 20.5 + - - +
248B GLY 3.4 0.6 - - - -
249B TYR* 1.3 74.2 - - - +
251B PRO* 1.3 74.9 - - - +
252B VAL* 3.3 13.7 - - - +
253B LYS* 2.8 50.8 + - + +
254B LEU* 2.8 24.7 + - - +
330B ARG* 4.2 3.7 + - - +
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Residues in contact with PRO 251 (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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249B TYR 3.1 11.6 - - - +
250B ASP* 1.3 87.5 - - - +
252B VAL* 1.3 57.2 + - + +
254B LEU* 3.7 1.3 - - + +
255B PHE* 2.7 37.0 + - - +
284B TRP* 5.3 2.7 - - + -
322B PHE* 3.9 4.2 - - + -
323B SER* 3.3 51.8 - - - +
326B ILE* 4.1 21.1 - - + -
327B GLU* 4.4 9.0 - - + +
330B ARG* 4.0 9.6 - - - +
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Residues in contact with VAL 252 (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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250B ASP* 3.2 14.0 + - - +
251B PRO* 1.3 75.0 - - + +
253B LYS* 1.3 73.8 + - + +
255B PHE* 3.5 5.8 - - - +
256B THR* 2.8 38.0 + - - +
284B TRP* 4.0 47.3 - - + +
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Residues in contact with LYS 253 (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 TRP* 3.5 21.6 - - + +
247B THR* 4.3 19.5 - - + +
250B ASP* 2.8 43.1 + - + +
252B VAL* 1.3 82.0 - - + +
254B LEU* 1.3 65.6 + - - +
256B THR* 3.4 5.2 + - - -
257B LYS* 3.1 18.5 + - - +
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Residues in contact with LEU 254 (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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196B LEU* 4.1 20.2 - - + -
197B PHE* 5.7 0.4 - - + -
243B TRP* 3.5 28.9 - - + -
244B ALA* 3.8 22.4 - - + -
247B THR* 4.9 1.3 - - - +
249B TYR* 4.1 32.3 - - + -
250B ASP 2.8 18.0 + - - +
251B PRO* 3.7 4.0 - - + +
253B LYS* 1.3 76.6 - - - +
255B PHE* 1.3 62.7 + - - +
257B LYS* 3.8 0.5 - - - +
258B LEU* 3.1 35.1 + - + +
322B PHE* 4.4 10.1 - - + -
326B ILE* 3.9 23.6 - - + -
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Residues in contact with PHE 255 (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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251B PRO 2.7 22.1 + - - +
252B VAL 3.5 4.5 - - - +
254B LEU* 1.3 73.5 - - - +
256B THR* 1.3 69.7 + - - +
258B LEU 3.1 2.3 + - - -
259B PHE* 2.8 51.0 + + + -
282B LEU* 3.8 31.9 - - + -
283B ASP 4.0 1.1 - - - -
284B TRP* 3.5 55.2 - + + -
287B VAL* 4.5 11.7 - - + -
319B ALA* 4.0 16.6 - - + -
322B PHE* 3.9 15.2 - + + -
361B LEU* 3.6 23.3 - - + -
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Residues in contact with THR 256 (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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252B VAL* 2.8 24.5 + - - +
253B LYS* 3.7 5.7 - - - -
255B PHE* 1.3 81.9 - - - +
257B LYS* 1.3 57.8 + - - +
260B LYS* 2.8 41.1 + - + +
261B ASP* 2.8 38.6 + - - +
283B ASP* 5.6 1.4 + - - +
284B TRP* 4.7 9.0 + - - +
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Residues in contact with LYS 257 (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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207B SER* 4.3 14.5 + - - -
240B THR* 4.8 9.8 + - - +
243B TRP* 3.1 58.8 - - + +
253B LYS 3.1 3.3 + - - +
256B THR* 1.3 80.4 - - - +
258B LEU* 1.3 66.7 + - + +
261B ASP* 3.8 17.5 + - + +
262B ASP* 2.9 65.7 + - - +
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Residues in contact with LEU 258 (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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188B TRP* 4.3 13.5 - - + -
192B LEU* 3.5 44.9 - - + -
196B LEU* 5.1 4.7 - - + -
206B VAL* 4.1 19.7 - - + -
240B THR* 5.8 2.2 - - + -
243B TRP* 5.1 4.0 - - + -
254B LEU* 3.1 24.6 + - + +
255B PHE 3.1 2.2 + - - -
257B LYS* 1.3 94.3 - - + +
259B PHE* 1.3 75.9 + - + +
262B ASP* 4.0 11.9 - - - +
263B ILE* 2.8 20.2 - - - +
322B PHE* 4.3 13.9 - - + -
362B ARG* 5.3 0.3 + - - -
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Residues in contact with PHE 259 (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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188B TRP* 3.8 31.2 - + - -
255B PHE* 2.8 58.2 + + + +
258B LEU* 1.3 82.9 - - + +
260B LYS* 1.3 55.9 + - - +
263B ILE* 3.6 10.6 - - - +
281B PRO* 3.4 6.8 - - - +
282B LEU* 2.7 33.7 + - + -
322B PHE* 3.8 31.0 - + - -
358B ALA* 4.0 7.6 - - + -
361B LEU* 3.4 40.6 - - + -
362B ARG* 4.2 4.0 - - + -
365B ILE* 3.6 27.4 - - + +
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Residues in contact with LYS 260 (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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256B THR* 2.8 33.9 + - + +
258B LEU 3.7 0.6 - - - -
259B PHE* 1.3 78.7 - - - +
261B ASP* 1.3 72.0 - - - +
262B ASP 3.5 0.7 - - - -
263B ILE 3.6 1.3 + - - -
264B ARG* 2.9 51.6 + - - +
281B PRO* 3.9 15.1 - - + +
282B LEU 3.2 18.6 - - - +
283B ASP* 2.7 36.3 + - - +
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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