Contacts of the helix formed by residues 225 - 232 (chain A) in PDB entry 1LDJ
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 LEU 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.9 29.2 - - + -
223A PRO* 2.5 47.8 + - + +
224A THR* 1.2 69.6 + - - +
226A THR* 1.3 61.8 + - - +
227A VAL 3.6 1.1 - - - +
228A TYR* 4.0 24.2 - - + +
229A LYS* 3.7 35.4 + - - +
280A HIS* 5.3 5.4 - - + -
281A GLU* 4.2 17.0 - - - +
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Residues in contact with THR 226 (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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213A LEU* 4.6 8.8 + - + +
224A THR 2.5 17.7 + - - -
225A LEU* 1.3 71.3 - - - +
227A VAL* 1.3 62.9 + - + +
229A LYS* 3.6 3.8 + - - +
230A GLU* 2.7 51.2 + - + +
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Residues in contact with VAL 227 (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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168A ARG* 6.1 0.4 - - + -
171A LEU* 4.2 21.1 - - + -
208A TYR* 3.4 36.3 - - + +
211A LEU* 3.2 27.1 - - + +
212A GLY* 4.1 6.3 - - - +
213A LEU* 4.8 6.7 - - + -
226A THR* 1.3 78.3 - - + +
228A TYR* 1.3 56.7 + - - +
230A GLU* 3.6 14.4 - - - +
231A SER* 2.6 51.3 + - - +
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Residues in contact with TYR 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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205A VAL* 3.4 24.0 - - + -
208A TYR* 4.0 11.8 + - + -
209A VAL* 3.8 30.7 - - + -
225A LEU* 4.0 22.2 + - + +
226A THR 3.3 0.4 - - - -
227A VAL* 1.3 77.3 - - - +
229A LYS* 1.3 56.6 + - + +
232A PHE* 2.7 69.4 + + + +
233A GLU* 2.7 39.1 + - + -
236A PHE* 5.5 0.2 - - - -
278A TYR 4.1 2.4 + - - -
279A LEU* 2.7 23.8 + - - -
280A HIS* 3.7 15.0 + + + -
283A THR* 3.6 16.3 + - - +
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Residues in contact with LYS 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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225A LEU* 3.7 26.8 + - - +
226A THR* 3.6 4.3 + - - +
227A VAL 3.4 0.2 - - - -
228A TYR* 1.3 83.0 - - + +
230A GLU* 1.3 63.1 + - - +
232A PHE 3.2 0.9 + - - -
233A GLU* 2.9 55.3 + - + +
234A SER* 2.6 29.1 + - - +
282A SER* 3.7 12.7 + - - -
286A GLU* 3.6 15.4 + - - -
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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
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172A PHE* 6.0 1.9 - - - -
176A ASN* 5.7 0.8 + - - -
226A THR* 2.7 42.6 + - + +
227A VAL* 3.6 13.0 - - - +
229A LYS* 1.3 79.7 - - + +
231A SER* 1.3 64.3 + - - +
234A SER* 4.5 6.1 - - - -
235A GLN* 2.9 18.5 + - - +
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Residues in contact with SER 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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171A LEU* 5.0 0.2 - - - +
176A ASN* 3.5 35.0 + - - +
180A THR* 3.1 24.4 + - - +
208A TYR* 3.6 20.9 - - - -
227A VAL* 2.6 39.6 + - - +
230A GLU* 1.3 80.8 + - - +
232A PHE* 1.3 55.8 + - - +
235A GLN* 2.6 14.5 - - - +
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Residues in contact with PHE 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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180A THR* 3.8 20.9 - - + +
183A VAL* 3.6 27.8 - - + -
184A LEU* 3.9 17.5 - - + -
187A ILE* 3.7 22.4 - - + -
201A ILE* 5.1 0.7 - - + -
205A VAL* 4.2 15.9 - - + -
208A TYR* 4.6 14.1 - + + -
228A TYR* 2.7 52.1 + + + +
231A SER* 1.3 82.0 - - - +
233A GLU* 1.3 63.4 + - - +
234A SER 3.1 1.6 - - - -
235A GLN* 2.7 6.3 + - - -
236A PHE* 2.6 51.4 + + + +
278A TYR 4.7 5.2 - - - -
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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