Contacts of the helix formed by residues 229 - 238 (chain A) in PDB entry 1YI8
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ASP* 1.3 76.0 - - - +
230A ALA* 1.3 54.0 + - - +
231A ASP* 3.7 6.9 + - - +
232A GLU* 2.7 43.4 + - - +
233A VAL* 2.6 42.1 + - - +
307A ARG* 4.6 3.1 - - - +
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Residues in contact with ALA 230 (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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229A SER* 1.3 71.0 - - - +
231A ASP* 1.3 57.8 + - - +
233A VAL* 3.1 2.3 + - - +
234A ALA* 2.9 29.1 + - - +
300A ASN* 3.1 38.1 - - - +
307A ARG* 3.9 24.4 - - - +
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Residues in contact with ASP 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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229A SER* 3.1 6.7 + - - +
230A ALA* 1.3 81.9 - - - +
232A GLU* 1.3 60.8 + - - +
233A VAL 3.1 0.7 + - - -
234A ALA* 4.2 5.1 - - - +
235A ARG* 3.4 35.5 + - - +
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Residues in contact with GLU 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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228A ASP* 4.8 6.2 - - + +
229A SER* 2.7 38.1 + - - +
231A ASP* 1.3 74.5 - - - +
233A VAL* 1.3 58.5 - - - +
235A ARG* 4.2 6.2 - - - +
236A LYS* 3.0 36.0 + - - +
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Residues in contact with VAL 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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224A ILE* 3.7 27.1 - - + -
228A ASP* 4.3 16.2 - - + +
229A SER 2.6 31.6 + - - +
230A ALA* 3.5 6.7 - - - +
232A GLU* 1.3 73.2 - - - +
234A ALA* 1.3 61.8 + - - +
235A ARG 3.2 1.3 - - - -
236A LYS* 2.7 24.3 + - + +
237A VAL* 2.8 14.9 + - + +
296A ILE 5.3 0.7 - - - +
299A LEU* 4.1 20.0 - - + -
300A ASN* 4.4 6.1 - - - +
303A LEU* 3.6 29.2 - - + -
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Residues in contact with ALA 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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230A ALA 2.9 15.4 + - - +
231A ASP* 4.2 7.2 - - - +
233A VAL* 1.3 76.6 - - - +
235A ARG* 1.3 69.3 + - - +
238A MET* 3.0 32.7 + - - +
296A ILE* 3.1 39.8 - - + +
300A ASN* 4.5 4.8 + - - +
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Residues in contact with ARG 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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231A ASP* 3.4 25.7 + - - +
232A GLU* 4.2 8.7 - - - +
233A VAL 3.2 0.2 - - - -
234A ALA* 1.3 83.6 - - - +
236A LYS* 1.3 62.0 + - - +
237A VAL 3.4 0.2 - - - -
238A MET* 4.0 27.9 - - + +
239A GLY* 3.9 10.7 + - - -
293A LYS* 5.5 7.3 - - - +
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Residues in contact with LYS 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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210A LEU* 3.9 24.0 - - + +
221A GLY 4.5 9.4 - - - -
223A ALA 2.4 31.1 + - - -
224A ILE* 3.4 23.1 - - + +
228A ASP* 3.9 11.3 + - - +
232A GLU* 3.0 24.7 + - + +
233A VAL* 2.7 20.9 + - + +
235A ARG* 1.3 76.3 - - - +
237A VAL* 1.3 67.1 + - + +
239A GLY* 3.5 8.7 + - - -
240A MET* 3.7 10.7 + - - +
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Residues in contact with VAL 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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210A LEU* 5.4 0.7 - - + -
224A ILE* 5.9 0.2 - - + -
233A VAL* 2.8 17.6 + - + +
236A LYS* 1.3 73.3 - - + +
238A MET* 1.3 54.9 + - - +
239A GLY 2.6 2.3 + - - -
240A MET* 2.3 51.1 + - + +
292A LYS* 3.9 17.1 + - + +
295A LEU* 3.5 35.4 - - + +
296A ILE* 3.3 27.8 - - + -
299A LEU* 3.6 30.5 - - + -
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Residues in contact with MET 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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234A ALA 3.0 24.8 + - - +
235A ARG* 4.0 30.3 - - + +
237A VAL* 1.3 77.6 - - - +
239A GLY* 1.3 57.9 + - - +
289A VAL* 4.0 11.4 - - - +
292A LYS* 3.1 44.7 + - + +
293A LYS* 3.3 53.2 - - + +
296A ILE* 4.3 7.6 - - + -
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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