Contacts of the helix formed by residues 238 - 253 (chain A) 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 SER 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A THR 3.5 3.4 + - - -
237A THR* 1.3 72.7 + - - +
239A ASP* 1.3 69.9 + - - +
240A TYR 3.1 0.4 - - - -
241A PHE* 3.0 25.7 + - - +
242A LEU 3.0 9.2 + - - -
286A LEU* 4.0 23.8 - - - -
287A LEU* 3.7 24.1 - - - +
288A PRO* 5.6 2.1 - - - +
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Residues in contact with ASP 239 (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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162A HIS* 3.1 39.3 + - - +
163A GLY 4.9 0.7 - - - +
237A THR* 2.9 15.4 + - - +
238A SER* 1.3 84.5 + - - +
240A TYR* 1.3 57.0 + - - +
242A LEU* 3.5 12.1 - - + +
243A LEU* 2.9 28.2 + - - +
330A PHE* 3.7 31.8 - - + +
331A PHE 3.7 13.2 - - - +
332A ASP* 4.1 8.1 + - - +
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Residues in contact with TYR 240 (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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219A ALA 2.6 29.1 + - - -
220A LEU* 3.6 9.4 - - + -
222A VAL* 4.0 11.7 + - + +
224A TRP* 3.6 25.8 - + - -
236A THR* 4.2 9.6 - - + -
237A THR* 3.2 13.4 + - - +
238A SER 3.1 0.4 - - - -
239A ASP* 1.3 77.6 - - - +
241A PHE* 1.3 83.1 + + + +
243A LEU* 3.2 8.3 - - + +
244A GLN* 3.2 49.7 + - + +
280A LEU* 5.7 1.1 - - + -
328A PHE* 4.0 12.3 - + - -
330A PHE* 3.7 25.4 - + + -
343A LEU* 3.4 26.0 - - + -
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Residues in contact with PHE 241 (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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224A TRP* 3.8 22.7 - + - -
233A LEU* 3.4 34.5 - - + -
236A THR* 4.6 8.5 - - + -
237A THR 4.3 7.9 - - - -
238A SER* 3.0 17.8 + - - +
240A TYR* 1.3 90.9 - + - +
242A LEU* 1.3 64.5 + - - +
243A LEU 3.1 1.3 - - - -
244A GLN* 3.3 9.3 + - + +
245A VAL* 3.1 27.7 + - - +
276A VAL* 5.4 0.6 - - + +
277A LEU* 3.6 31.6 - - + -
280A LEU* 4.0 12.1 - - + -
282A ILE* 3.4 18.8 - - + -
286A LEU* 3.6 21.8 - - + -
287A LEU* 4.6 6.7 - - + -
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Residues in contact with LEU 242 (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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162A HIS* 3.6 48.7 - - + +
238A SER 3.0 12.1 + - - +
239A ASP* 3.2 15.2 + - + +
241A PHE* 1.3 78.0 - - - +
243A LEU* 1.3 62.8 + - - +
245A VAL* 3.4 3.0 + - + +
246A LEU* 3.0 42.5 + - + +
287A LEU* 4.1 15.7 - - + +
291A PHE* 3.4 42.4 - - + +
295A CYS* 4.5 7.4 - - + -
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Residues in contact with LEU 243 (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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159A PHE* 4.9 8.3 - - + -
164A TYR* 3.6 39.0 - - + -
220A LEU* 4.5 11.0 - - + -
239A ASP 2.9 12.8 + - - +
240A TYR* 3.2 12.3 - - + +
241A PHE 3.1 0.2 - - - -
242A LEU* 1.3 76.7 - - - +
244A GLN* 1.3 59.6 + - - +
246A LEU* 3.3 5.9 + - + -
247A LEU* 2.8 52.1 + - + +
328A PHE* 3.8 30.7 - - + -
330A PHE* 4.0 15.7 - - + -
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Residues in contact with GLN 244 (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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136A ARG* 5.9 3.8 - - - +
220A LEU* 3.0 36.6 + - - +
240A TYR* 3.2 40.5 + - + +
241A PHE* 3.5 17.5 - - + +
242A LEU 3.3 0.4 - - - -
243A LEU* 1.3 79.0 - - - +
245A VAL* 1.3 62.3 + - - +
247A LEU* 3.4 16.2 + - - +
248A LYS* 3.0 25.1 + - - +
276A VAL* 3.8 23.7 - - + +
280A LEU* 5.1 5.4 - - + +
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Residues in contact with VAL 245 (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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241A PHE 3.1 13.3 + - - +
242A LEU* 3.6 9.4 - - - +
243A LEU 3.3 0.2 - - - -
244A GLN* 1.3 76.5 - - - +
246A LEU* 1.3 58.6 + - + +
248A LYS* 3.3 4.4 + - - +
249A PHE* 3.0 24.9 + - - +
269A LEU* 3.9 36.6 - - + +
272A ILE* 3.7 16.8 - - + +
273A ARG* 3.6 28.9 - - + +
276A VAL* 4.5 8.7 - - + -
277A LEU* 5.5 2.9 - - + -
287A LEU* 4.3 10.1 - - + -
291A PHE* 4.3 11.7 - - + -
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Residues in contact with LEU 246 (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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159A PHE* 3.3 59.3 - - + -
162A HIS* 6.0 0.4 - - + -
242A LEU* 3.0 43.9 + - + +
243A LEU* 3.9 5.6 - - + +
245A VAL* 1.3 73.3 - - + +
247A LEU* 1.3 66.7 + - - +
249A PHE* 3.2 5.5 + - - +
250A ARG* 2.9 23.6 + - - +
256A ASP* 4.7 2.6 - - - +
257A PRO* 4.2 24.4 - - + +
269A LEU* 4.2 11.9 - - + -
291A PHE* 5.8 0.2 - - + -
295A CYS* 4.3 18.2 - - + +
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Residues in contact with LEU 247 (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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134A CYS 4.7 5.2 - - - +
136A ARG* 4.5 27.7 + - + +
139A ILE* 4.3 23.6 - - + -
157A ASP* 5.5 1.3 - - - +
159A PHE* 5.6 2.7 - - + -
164A TYR* 5.1 3.6 - - + +
220A LEU* 3.9 35.0 - - + -
243A LEU* 2.8 40.9 + - + +
244A GLN* 3.7 12.1 - - - +
246A LEU* 1.3 75.8 - - - +
248A LYS* 1.3 63.5 + - - +
250A ARG* 3.1 26.5 + - - +
251A THR* 3.1 17.3 + - - -
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Residues in contact with LYS 248 (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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244A GLN 3.0 18.6 + - - +
245A VAL 3.6 4.3 - - - +
247A LEU* 1.3 75.0 - - - +
249A PHE* 1.3 64.0 + - - +
251A THR* 3.2 9.2 + - + -
252A ASP* 2.7 63.6 + - - +
272A ILE* 3.6 26.3 - - + +
275A ASP* 5.4 10.3 + - - +
276A VAL* 4.3 11.7 - - + -
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Residues in contact with PHE 249 (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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245A VAL 3.0 14.1 + - - +
246A LEU* 3.2 9.8 + - - +
248A LYS* 1.3 77.1 - - - +
250A ARG* 1.3 56.6 + - - +
251A THR 3.1 0.4 - - - -
252A ASP* 4.7 1.1 - - - +
253A LYS* 3.0 33.1 + - + +
255A ARG* 3.1 31.2 - - - -
256A ASP* 3.4 2.7 - - - -
257A PRO* 3.3 38.1 - - + -
265A ASP* 3.6 34.1 - - + -
268A LEU* 3.4 32.3 - - + -
269A LEU* 3.5 24.5 - - + -
272A ILE* 3.6 14.1 - - + +
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A CYS* 3.4 11.7 + - - +
134A CYS 2.7 52.4 + - - +
135A SER* 3.8 15.4 - - - +
157A ASP* 3.0 32.9 + - - +
158A VAL 5.6 1.0 + - - -
159A PHE* 3.3 24.8 - - - -
246A LEU 2.9 12.2 + - - +
247A LEU* 3.1 20.1 + - - +
249A PHE* 1.3 74.8 - - - +
251A THR* 1.3 54.6 + - - +
253A LYS 2.4 25.8 - - - +
254A GLY* 3.9 7.0 - - - +
255A ARG 3.7 10.3 - - - +
256A ASP* 2.7 41.3 + - - +
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A SER* 4.8 4.9 - - - -
136A ARG* 4.4 20.4 + - - +
137A ASP* 5.4 9.7 + - - +
247A LEU 3.1 12.4 + - - -
248A LYS* 3.6 15.2 - - + -
249A PHE 3.1 1.0 - - - -
250A ARG* 1.3 77.8 - - - +
252A ASP* 1.3 71.5 - - - +
253A LYS 3.1 4.7 + - - +
254A GLY* 5.3 0.3 - - - -
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Residues in contact with ASP 252 (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 LYS* 2.7 53.4 + - - +
249A PHE* 4.3 4.3 - - - +
251A THR* 1.3 81.6 - - - +
253A LYS* 1.3 66.6 + - + +
254A GLY 4.4 0.2 - - - -
268A LEU* 5.4 7.3 - - + +
272A ILE* 4.5 10.1 - - + +
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Residues in contact with LYS 253 (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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249A PHE* 3.0 18.3 + - + +
250A ARG* 2.4 31.8 - - - +
251A THR 4.2 2.0 - - - -
252A ASP* 1.3 83.0 - - + +
254A GLY* 1.3 54.3 + - - +
255A ARG* 2.7 53.6 + - + +
265A ASP* 5.3 0.8 + - - -
268A LEU* 3.9 30.7 - - + -
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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
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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