Contacts of the helix formed by residues 227 - 235 (chain A) in PDB entry 1D0L
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 MET 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 4.8 0.2 - - + -
191A TYR* 3.7 24.0 - - + +
192A PHE* 3.9 16.8 - - + -
195A GLU* 3.6 22.9 - - + +
218A ALA* 3.2 31.2 - - + +
219A GLY 4.2 0.4 - - - -
220A ALA* 4.0 19.5 - - - -
221A MET* 4.2 0.4 - - - -
225A GLN 3.8 0.2 + - - -
226A PHE* 1.3 76.2 - - - +
228A PRO* 1.3 76.8 - - + +
229A SER* 4.3 3.4 - - - +
230A SER* 3.0 15.0 + - - +
231A TYR* 3.0 10.7 + - - +
401A BLG 3.0 49.8 + - - +
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Residues in contact with PRO 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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174A ILE* 5.0 0.2 - - + -
178A LEU* 3.9 17.5 - - + -
195A GLU* 3.1 39.0 - - + +
198A THR* 3.4 14.1 - - + +
199A PHE* 3.9 15.5 - - + +
202A MET* 4.0 6.1 - - + -
219A GLY 3.6 15.0 - - - +
221A MET* 3.7 20.6 - - + -
227A MET* 1.3 88.3 - - + +
229A SER* 1.3 57.2 + - - +
231A TYR* 3.1 5.4 + - + +
232A LYS 2.9 23.2 + - - -
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Residues in contact with SER 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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191A TYR* 4.5 3.3 + - - -
194A GLY 5.9 0.9 - - - -
195A GLU* 2.6 38.6 + - - -
198A THR* 4.2 8.2 - - - +
227A MET* 4.3 4.3 - - - +
228A PRO* 1.3 73.3 - - - +
230A SER* 1.3 61.0 + - - +
232A LYS* 3.6 14.7 - - - +
233A GLN* 3.0 48.7 + - - +
401A BLG 5.3 4.0 + - - -
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Residues in contact with SER 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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226A PHE* 3.7 15.8 - - - -
227A MET* 3.0 9.5 + - - +
229A SER* 1.3 78.4 + - - +
231A TYR* 1.3 59.0 + - - +
233A GLN* 4.8 0.6 + - - +
234A TYR* 2.7 41.4 + - - +
235A ALA 3.3 5.0 + - - -
259A TYR* 3.6 16.3 - - - -
401A BLG 2.8 41.0 + - - -
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Residues in contact with TYR 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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198A THR* 5.4 0.9 - - + -
202A MET* 3.5 46.1 - - + +
206A GLU* 3.3 32.8 + - + +
226A PHE* 3.7 4.1 - - - -
227A MET 3.0 10.3 + - - +
228A PRO* 3.3 7.9 - - + +
230A SER* 1.3 76.7 - - - +
232A LYS* 1.3 72.0 + - + +
235A ALA* 3.1 38.9 + - + +
244A ILE* 3.5 41.6 + - + +
246A LEU* 3.7 33.2 - - + -
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Residues in contact with LYS 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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198A THR* 3.8 26.7 + - + +
228A PRO 2.9 13.6 + - - +
229A SER* 3.6 14.5 - - - +
231A TYR* 1.3 88.6 - - + +
233A GLN* 1.3 84.2 + - - +
235A ALA 5.5 0.5 - - - +
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Residues in contact with GLN 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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229A SER* 3.0 36.9 + - - +
230A SER* 5.6 0.2 + - - -
232A LYS* 1.3 97.1 - - - +
234A TYR* 1.3 102.8 + - + +
235A ALA 5.3 0.7 - - - -
258A ASN* 4.5 3.1 + - - -
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Residues in contact with TYR 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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226A PHE* 4.2 3.8 - - + -
230A SER* 2.7 26.1 + - - +
233A GLN* 1.3 117.3 + - + +
235A ALA* 1.3 64.8 + - - +
236A VAL 3.6 1.4 + - - -
255A SER 3.9 3.5 - - - +
258A ASN* 2.9 34.9 + - - +
259A TYR* 3.5 43.3 - + + -
262A ALA* 3.7 32.3 - - + -
263A HIS* 3.5 25.4 + + - -
401A BLG 6.0 0.2 - - - -
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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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226A PHE* 4.0 3.1 - - + -
230A SER 3.3 3.0 + - - -
231A TYR* 3.1 37.7 + - + +
232A LYS 5.5 0.5 - - - +
233A GLN 5.3 0.7 - - - -
234A TYR* 1.3 79.1 + - - +
236A VAL* 1.3 62.7 + - - +
244A ILE* 3.4 33.5 - - + +
246A LEU* 4.2 7.9 - - + -
255A SER* 3.3 14.1 - - - +
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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