Contacts of the helix formed by residues 210 - 221 (chain X) in PDB entry 1Y1F
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 210 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148X GLU* 2.5 33.4 + - - -
208X HIS 4.0 1.0 + - - -
209X VAL* 1.3 76.5 - - - +
211X TRP* 1.3 59.1 + - - +
212X ASN 3.3 0.2 + - - -
213X ASP* 2.8 31.3 + - - -
214X ALA* 2.9 28.6 + - - +
301X TRP* 3.3 3.8 + - - +
354X PRO 3.4 4.3 - - - -
355X ASP 4.0 7.0 - - - -
356X SER 3.1 20.8 + - - -
357X SER* 4.2 2.4 - - - -
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Residues in contact with TRP 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X SER* 1.3 75.7 - - - +
212X ASN* 1.3 82.8 + - - +
214X ALA* 3.3 3.3 + - - +
215X VAL* 2.9 58.5 + - + +
225X LEU* 3.5 11.6 - - + +
301X TRP* 3.4 37.3 - + + +
302X THR 2.8 28.1 + - - -
303X SER* 3.8 15.3 - - - -
327X ARG* 3.5 52.1 - - + +
354X PRO* 3.0 31.5 + - + +
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Residues in contact with ASN 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X TYR* 4.0 6.2 + - - +
148X GLU* 3.0 34.3 + - - +
210X SER* 3.2 0.8 + - - -
211X TRP* 1.3 95.8 - - - +
213X ASP* 1.3 58.4 - - - +
215X VAL* 3.3 5.3 + - - +
216X ALA* 3.0 29.3 + - - +
354X PRO* 3.6 21.4 + - - +
355X ASP* 4.2 2.8 - - - +
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Residues in contact with ASP 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X PHE* 4.5 6.3 - - + -
139X PHE* 4.6 0.9 - - - -
145X TYR* 2.5 37.4 + - + -
147X THR* 3.4 24.3 - - + -
148X GLU* 3.1 20.9 + - - +
149X ALA 4.8 0.5 + - - -
208X HIS 4.0 1.9 - - - +
209X VAL* 3.4 17.9 - - + -
210X SER* 2.8 36.4 + - - +
212X ASN* 1.3 76.1 - - - +
214X ALA* 1.3 62.2 + - - +
216X ALA* 3.3 3.5 + - - +
217X TYR* 3.0 23.3 + - - +
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Residues in contact with ALA 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X SER 2.9 16.2 + - - +
211X TRP* 3.5 5.4 - - - +
213X ASP* 1.3 77.1 - - - +
215X VAL* 1.3 56.3 + - - +
217X TYR* 3.4 1.4 + - - +
218X CYS* 3.0 35.3 + - - -
225X LEU* 4.0 14.4 - - + -
301X TRP* 4.1 8.3 - - + -
363X PHE* 3.6 42.4 - - + -
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Residues in contact with VAL 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X TRP* 2.9 51.0 + - + +
212X ASN* 3.3 6.5 + - - +
214X ALA* 1.3 75.0 - - - +
216X ALA* 1.3 53.0 + - - +
218X CYS* 4.0 3.5 - - - -
219X THR* 2.8 55.7 + - + +
225X LEU* 3.7 24.2 - - + +
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Residues in contact with ALA 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X PHE* 3.7 19.8 - - + -
145X TYR* 4.2 19.1 - - + -
212X ASN 3.0 14.2 + - - +
213X ASP 3.4 8.7 - - - +
215X VAL* 1.3 76.7 - - - +
217X TYR* 1.3 57.6 + - - +
219X THR* 3.1 6.8 + - - -
220X TRP* 2.9 30.8 + - - +
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Residues in contact with TYR 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X SER* 3.6 20.1 + - - -
127X ASP* 5.3 0.9 - - - -
131X VAL* 3.7 23.4 - - + +
135X GLU* 3.6 36.4 + - - +
136X PHE* 3.8 15.5 - + + -
139X PHE* 3.4 34.7 - + + -
213X ASP 3.0 10.5 + - - +
214X ALA 3.7 1.3 - - - +
216X ALA* 1.3 75.7 - - - +
218X CYS* 1.3 66.4 + - - +
220X TRP* 3.1 13.8 + + - +
221X ALA* 2.9 34.6 + - + +
223X LYS* 5.6 2.6 + - + -
363X PHE* 3.6 32.8 - + + -
365X CYS* 3.7 11.2 - - - -
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Residues in contact with CYS 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X ALA 3.0 20.9 + - - +
215X VAL* 4.1 2.9 - - - +
217X TYR* 1.3 74.7 - - - +
219X THR* 1.3 60.9 + - - +
221X ALA* 3.0 7.2 + - - -
222X GLY 3.3 0.2 + - - -
223X LYS* 2.8 28.1 + - - +
224X ARG* 3.6 26.2 - - - +
225X LEU* 4.0 8.1 - - - +
363X PHE* 3.6 13.5 - - - -
365X CYS* 2.1 55.0 - - - -
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Residues in contact with THR 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215X VAL* 2.8 40.4 + - + +
216X ALA* 3.1 12.6 + - - -
218X CYS* 1.3 74.8 - - + +
220X TRP* 1.3 64.2 + - - +
222X GLY* 3.0 14.2 + - - -
223X LYS 3.5 13.0 - - - +
224X ARG* 5.1 4.5 - - + -
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Residues in contact with TRP 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X GLU 4.8 1.6 - - - -
138X LYS* 4.0 10.8 - - + -
139X PHE* 3.6 47.6 - + + -
142X SER* 3.1 37.9 + - - -
143X THR* 3.4 20.2 - - + +
216X ALA 2.9 19.8 + - - +
217X TYR* 3.3 19.5 - + - +
219X THR* 1.3 77.5 + - - +
221X ALA* 1.4 78.3 + - + +
222X GLY 3.3 3.5 + - - -
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Residues in contact with ALA 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217X TYR* 2.9 32.9 + - + +
218X CYS 3.0 6.2 + - - +
220X TRP* 1.4 91.9 - - + +
222X GLY* 1.3 61.7 + - - +
223X LYS* 3.5 24.5 - - + +
371X PRO* 3.7 13.0 - - - +
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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