Contacts of the helix formed by residues 227 - 240 (chain A) in PDB entry 1Y2C
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ASN* 4.3 1.8 - - - +
225A ASP 4.2 1.0 + - - -
226A SER* 1.3 72.1 - - - +
228A VAL* 1.3 64.6 + - - +
229A LEU 3.4 2.2 - - - -
230A GLU* 3.5 14.4 - - - -
231A ASN* 2.9 31.8 + - - -
269A LEU* 4.0 12.1 - - - -
272A ASP* 2.8 24.1 + - - -
275A LYS* 2.8 33.8 + - - -
504A EDO 4.7 4.4 + - - -
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Residues in contact with VAL 228 (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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209A ASN* 3.4 14.8 + - + +
212A LEU* 4.2 12.8 - - + -
213A ILE* 4.5 7.9 - - + -
219A LEU* 3.5 41.7 - - + +
220A ALA* 3.6 16.6 - - + +
223A TYR* 3.5 17.4 - - + -
225A ASP* 3.6 36.3 - - - +
226A SER 3.8 2.9 - - - +
227A SER* 1.3 77.9 - - - +
229A LEU* 1.3 65.7 + - - +
232A HIS* 3.3 16.5 + - - +
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Residues in contact with LEU 229 (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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203A ASP 5.6 0.2 - - - +
204A HIS* 3.9 14.8 - - + +
205A PRO* 3.5 31.6 - - + -
207A VAL 3.5 18.8 - - - +
208A SER* 4.0 1.8 - - - -
209A ASN* 2.8 42.8 + - - +
212A LEU* 3.6 18.8 - - + -
219A LEU* 4.7 6.3 - - + -
228A VAL* 1.3 73.1 - - - +
230A GLU* 1.3 67.4 + - - +
232A HIS* 3.1 8.9 + - + +
233A HIS* 2.8 51.3 + - + +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASN* 3.0 28.0 + - - -
227A SER* 3.4 22.0 + - - +
229A LEU* 1.3 81.5 - - - +
231A ASN* 1.3 64.9 + - - +
233A HIS* 3.4 13.7 + - + +
234A LEU* 3.2 27.5 + - - +
268A VAL* 3.8 13.6 - - + +
269A LEU* 4.2 8.7 - - + -
271A THR* 3.6 23.1 - - - +
272A ASP* 3.5 28.9 + - - +
273A MET 4.7 0.9 + - - -
1002A MG 4.0 11.6 - - - -
1003A 3DE 6.1 0.5 - - - -
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Residues in contact with ASN 231 (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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223A TYR* 3.5 34.9 + - + +
226A SER* 3.2 16.6 + - - -
227A SER* 2.9 33.9 + - - +
230A GLU* 1.3 76.5 - - - +
232A HIS* 1.3 58.2 + - - +
234A LEU 3.4 0.7 + - - -
235A ALA* 3.0 25.6 + - - +
269A LEU* 4.0 15.1 - - - +
223B TYR* 4.3 6.1 - - - +
224B ASN* 3.0 35.9 + - - +
226B SER* 5.8 1.6 - - - -
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Residues in contact with HIS 232 (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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202A VAL 4.4 2.2 - - - -
203A ASP* 2.7 46.6 + - + -
219A LEU* 3.7 32.4 - - + +
222A MET* 5.8 0.6 - - - -
223A TYR* 3.8 11.4 + - + -
228A VAL 3.3 11.0 + - - +
229A LEU* 3.1 12.4 + - + +
231A ASN* 1.3 77.3 - - - +
233A HIS* 1.3 68.7 + + - +
235A ALA* 3.2 1.7 + - - +
236A VAL* 3.0 40.2 + - + +
524A EDO 3.8 26.3 + - - -
533A EDO 4.2 9.5 - - - -
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Residues in contact with HIS 233 (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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199A ILE* 3.6 14.0 - - - +
200A HIS* 2.8 30.3 - - - +
201A ASP* 3.3 28.9 + - - -
202A VAL* 2.8 35.9 + - - +
203A ASP 4.6 0.9 - - - -
204A HIS* 3.9 24.0 - + + -
229A LEU* 2.8 50.0 + - + +
230A GLU* 3.7 11.4 - - + +
231A ASN 3.4 0.2 - - - -
232A HIS* 1.3 74.2 - + - +
234A LEU* 1.3 57.5 + - - +
237A GLY* 2.9 26.2 + - - -
268A VAL* 4.5 1.6 - - + -
1002A MG 4.2 4.3 - - - -
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Residues in contact with LEU 234 (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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199A ILE* 4.1 5.4 - - + -
230A GLU 3.2 15.5 + - - +
231A ASN 3.6 3.8 - - - +
233A HIS* 1.3 79.3 - - - +
235A ALA* 1.3 63.7 + - - +
237A GLY 3.2 0.9 + - - -
238A PHE* 3.0 47.5 + - + -
264A VAL* 3.7 7.9 - - + +
265A ILE* 3.7 27.8 - - + -
268A VAL* 3.6 31.4 - - + -
269A LEU* 3.9 30.1 - - + -
224B ASN* 3.2 25.6 - - - +
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Residues in contact with ALA 235 (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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223A TYR* 3.7 15.9 - - - +
231A ASN 3.0 17.8 + - - +
232A HIS* 3.2 5.1 + - - +
234A LEU* 1.3 75.4 - - - +
236A VAL* 1.3 57.5 + - - +
238A PHE* 3.9 2.2 - - - +
239A LYS* 2.9 36.1 + - - +
524A EDO 3.7 14.8 - - - +
221B LEU* 3.4 26.8 - - - +
222B MET* 3.9 4.7 - - - +
224B ASN* 3.8 1.3 + - - +
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Residues in contact with VAL 236 (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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152A HIS* 4.5 11.7 - - + -
202A VAL* 3.7 26.2 - - + -
203A ASP* 4.2 10.8 - - + +
232A HIS* 3.0 48.6 + - + +
235A ALA* 1.3 73.6 - - - +
237A GLY* 1.3 66.7 + - - +
239A LYS* 3.2 4.5 + - - +
240A LEU* 3.1 44.8 + - + +
524A EDO 4.2 12.8 - - - +
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Residues in contact with GLY 237 (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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145A TYR* 2.8 35.8 + - - -
149A LEU* 4.5 4.3 - - - -
195A PHE* 4.1 1.6 - - - -
199A ILE* 4.0 22.4 - - - -
202A VAL* 3.9 4.2 - - - +
233A HIS 2.9 16.7 + - - -
234A LEU 3.7 1.3 - - - -
236A VAL* 1.3 77.5 - - - +
238A PHE* 1.3 61.7 + - - +
240A LEU* 3.8 1.1 + - - +
241A LEU* 3.9 2.8 - - - +
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Residues in contact with PHE 238 (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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195A PHE* 4.1 13.2 - + - -
199A ILE* 4.6 2.5 - - + -
234A LEU* 3.0 52.5 + - + +
235A ALA* 4.1 1.1 - - - +
237A GLY* 1.3 73.7 - - - +
239A LYS* 1.3 67.1 + - - +
240A LEU 3.2 0.4 - - - -
241A LEU* 3.2 33.5 + - + +
242A GLN* 4.2 4.7 + - - +
260A LEU* 4.7 1.8 - - + -
261A ARG* 3.4 37.2 - - + -
264A VAL* 3.6 27.4 - - + -
265A ILE* 4.1 7.4 - - + -
520A EDO 3.6 30.5 - - - -
221B LEU* 3.8 21.7 - - + +
224B ASN* 4.6 2.2 - - - -
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Residues in contact with LYS 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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235A ALA* 2.9 21.2 + - - +
236A VAL* 3.2 5.1 + - - +
238A PHE* 1.3 76.2 - - - +
240A LEU* 1.3 60.1 + - + +
242A GLN* 3.1 34.3 + - - +
243A GLU* 4.2 6.0 + - - +
524A EDO 2.8 46.0 + - - +
218B GLU* 3.7 24.9 + - - +
221B LEU* 4.2 32.3 - - + -
222B MET* 4.6 21.9 - - - +
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Residues in contact with LEU 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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145A TYR* 3.8 17.4 - - + -
148A THR* 3.9 13.2 - - + +
149A LEU* 4.0 28.0 - - + +
152A HIS* 3.5 50.5 - - + +
236A VAL* 3.1 30.9 + - + +
237A GLY 4.0 1.1 - - - +
238A PHE 3.2 0.4 - - - -
239A LYS* 1.3 73.9 - - + +
241A LEU* 1.3 59.7 + - - +
242A GLN 3.1 6.1 + - - -
243A GLU* 3.2 29.3 + - + +
246A CYS* 3.3 14.7 - - - +
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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