Contacts of the helix formed by residues 221 - 231 (chain C) in PDB entry 1YA8
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 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C GLY* 4.7 3.4 - - - -
220C GLU* 1.3 78.8 - - - +
222C ALA* 1.3 58.4 + - - +
224C GLY* 2.7 4.2 + - - +
225C GLU* 2.7 31.8 + - - +
246C GLU 2.9 13.5 + - - -
247C SER 2.9 16.3 + - - -
248C GLY* 3.8 7.4 - - - -
255C LEU* 5.2 2.1 - - - +
426C PHE* 4.7 4.2 - - - -
468C HIS* 3.1 23.2 + - - -
4003C SMB 2.6 32.3 + - - +
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C HIS 4.5 0.4 - - - -
141C GLY* 4.0 1.1 - - - -
142C GLY 3.8 6.5 - - - +
143C GLY* 3.5 30.5 - - - +
144C LEU* 3.6 22.1 - - + +
170C TYR* 4.8 2.7 - - - +
220C GLU 3.0 0.4 + - - -
221C SER* 1.3 81.3 + - - +
223C GLY* 1.3 58.4 + - - +
225C GLU* 3.0 5.2 + - - +
226C SER* 2.9 31.8 + - - -
255C LEU* 3.9 20.4 - - + +
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Residues in contact with GLY 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ILE* 3.2 32.6 - - - +
140C HIS 3.4 8.5 - - - -
141C GLY* 3.6 3.0 - - - -
170C TYR* 4.8 0.2 - - - -
219C GLY* 3.5 7.7 - - - -
220C GLU 2.6 12.8 + - - -
222C ALA* 1.3 74.9 - - - +
224C GLY* 1.3 61.6 + - - +
226C SER* 3.7 2.1 - - - -
227C VAL* 3.2 28.2 + - - +
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Residues in contact with GLY 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLY* 3.5 17.0 - - - -
220C GLU 3.2 7.9 - - - -
221C SER 2.7 10.7 + - - -
223C GLY* 1.3 77.2 - - - +
225C GLU* 1.3 63.4 + - - +
227C VAL* 3.3 1.5 + - - -
228C SER* 3.0 9.2 + - - -
245C SER* 3.0 25.1 + - - -
246C GLU 4.4 3.6 - - - -
248C GLY 3.1 15.0 - - - +
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 4.5 5.0 - - - +
191C HIS* 3.6 12.8 - - - -
221C SER 2.7 10.5 + - - +
222C ALA 3.0 9.1 + - - +
224C GLY* 1.3 78.7 - - - +
226C SER* 1.3 60.2 + - - +
228C SER* 3.3 3.3 + - - -
229C VAL* 2.9 38.5 + - - +
248C GLY* 3.5 6.4 + - - -
249C VAL 3.5 26.7 - - - +
250C ALA* 4.2 3.6 - - - -
252C THR* 5.2 2.5 - - - +
255C LEU* 3.8 29.8 - - + +
256C VAL* 3.3 20.2 - - + +
321C THR* 2.7 28.3 + - - -
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Residues in contact with SER 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ILE* 4.0 8.3 - - - +
144C LEU* 4.4 5.7 - - - +
170C TYR* 4.9 0.3 + - - -
191C HIS* 3.7 12.4 - - - -
194C GLN* 3.0 39.0 + - - +
222C ALA 2.9 18.4 + - - -
223C GLY* 3.7 6.5 - - - -
224C GLY 3.2 0.2 - - - -
225C GLU* 1.3 78.8 + - - +
227C VAL* 1.3 65.8 + - - +
229C VAL* 3.0 6.9 + - - +
230C LEU* 2.9 29.6 + - - +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ILE* 4.3 11.7 - - + -
217C ILE* 3.7 16.3 - - + +
218C PHE* 3.7 10.5 - - - +
219C GLY* 3.4 22.7 - - - +
223C GLY 3.2 16.0 + - - +
224C GLY 3.3 7.2 + - - +
226C SER* 1.3 76.8 - - - +
228C SER* 1.3 63.0 + - - +
230C LEU* 3.2 4.1 + - - +
231C VAL* 3.0 26.7 + - - +
243C ALA* 3.7 27.1 - - + -
244C ILE 3.6 14.8 - - - +
245C SER* 3.8 8.5 - - - +
346C TYR* 4.4 2.0 - - + -
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLY 3.0 7.8 + - - -
225C GLU 3.4 5.6 - - - -
226C SER 3.2 0.2 - - - -
227C VAL* 1.3 79.5 - - - +
229C VAL* 1.3 59.5 + - - +
231C VAL* 3.3 16.6 - - - +
232C LEU* 3.5 14.4 - - - +
245C SER* 3.7 0.2 + - - -
249C VAL* 3.6 14.4 - - - +
250C ALA* 2.7 37.0 + - - +
346C TYR* 3.4 22.1 + - - -
433C VAL* 4.8 6.9 - - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C HIS* 4.5 9.9 - - + +
225C GLU* 2.9 47.1 + - - +
226C SER* 3.0 9.1 + - - +
228C SER* 1.3 72.9 - - - +
230C LEU* 1.3 66.4 + - + +
231C VAL 3.1 1.6 - - - -
232C LEU* 3.1 7.2 + - - +
233C SER* 3.0 19.4 + - - -
250C ALA* 4.3 14.1 - - + -
256C VAL* 5.3 1.1 - - + -
321C THR* 4.4 8.3 - - + -
327C LEU* 3.9 23.3 - - + -
328C LEU* 3.8 28.6 - - + +
332C PRO* 5.8 0.4 - - + -
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ILE* 3.8 23.3 - - + -
191C HIS* 4.6 7.2 - - + +
194C GLN* 4.7 12.1 - - + +
195C VAL* 3.8 29.2 - - + -
198C LEU* 4.1 16.8 - - + -
217C ILE* 3.8 26.5 - - + -
226C SER 2.9 20.1 + - - +
227C VAL 3.6 4.7 - - - +
229C VAL* 1.3 77.9 - - + +
231C VAL* 1.3 63.5 + - - +
233C SER* 3.2 20.9 + - - +
236C ALA* 3.8 15.6 - - + +
240C PHE* 3.5 13.7 - - + -
327C LEU* 4.9 8.5 - - + -
341C PHE* 4.9 0.7 - - - -
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C VAL 3.0 20.7 + - - +
228C SER* 3.3 11.9 - - - +
229C VAL 3.1 0.2 - - - -
230C LEU* 1.3 79.0 - - - +
232C LEU* 1.3 66.4 + - + +
240C PHE* 4.0 15.4 - - + -
243C ALA* 3.9 26.5 - - + -
341C PHE* 3.4 21.5 - - - -
342C HIS 4.5 4.2 - - - +
344C VAL* 5.4 4.9 - - + -
346C TYR* 4.2 27.8 - - + -
437C HIS* 4.9 12.6 - - + +
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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