Contacts of the helix formed by residues 232 - 244 (chain E) in PDB entry 3LSG
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 ASP 232 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E PHE* 4.4 6.4 - - - +
231E GLU* 1.3 77.6 - - + +
233E VAL* 1.3 68.6 + - - +
234E ASN* 2.9 30.6 + - - +
235E TYR* 3.5 25.4 + - + +
236E PHE* 3.1 20.3 + - - +
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Residues in contact with VAL 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ASN* 4.1 5.8 - - + +
222E TYR* 3.8 36.8 - - + +
225E ALA* 4.2 9.4 - - + -
231E GLU 3.5 5.4 + - - +
232E ASP* 1.3 77.6 + - - +
234E ASN* 1.3 72.9 + - - +
236E PHE* 3.1 6.5 + - - +
237E ILE* 2.8 53.3 + - + +
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Residues in contact with ASN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E ASP* 2.9 18.3 + - - +
233E VAL* 1.3 88.3 - - - +
235E TYR* 1.3 64.7 - - - +
237E ILE* 3.5 7.3 + - - +
238E THR* 3.1 26.4 + - - +
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Residues in contact with TYR 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E PHE* 3.6 33.7 - + - -
232E ASP* 3.4 25.2 + - + +
233E VAL 3.3 0.2 - - - -
234E ASN* 1.3 77.1 - - - +
236E PHE* 1.3 58.6 + - - +
238E THR* 2.9 28.6 - - + +
239E LYS* 3.0 52.5 + - + +
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Residues in contact with PHE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASN* 6.0 1.8 - - - -
207E MSE 3.9 14.4 - - + -
210E ALA* 3.9 22.9 - - + -
214E LEU* 6.2 3.1 - - + -
221E ASN* 3.8 22.4 - - + -
224E ILE* 3.8 21.8 - - + -
225E ALA* 3.7 23.1 - - + -
228E VAL* 4.3 6.5 - - + -
230E PHE* 4.0 29.4 - + + -
232E ASP 3.1 14.0 + - - +
233E VAL* 3.1 9.1 + - + +
235E TYR* 1.3 75.5 - - - +
237E ILE* 1.3 77.5 + - + +
239E LYS* 3.1 4.0 + - - +
240E PHE* 2.6 49.0 + + + +
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Residues in contact with ILE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASN* 5.1 11.4 - - - +
221E ASN* 3.6 35.4 - - + +
233E VAL* 2.8 30.9 + - + +
234E ASN* 3.9 7.2 - - - +
236E PHE* 1.3 94.1 - - + +
238E THR* 1.3 58.6 + - - +
240E PHE* 3.3 5.0 + - + +
241E LYS* 2.9 44.4 + - + +
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Residues in contact with THR 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ASN 3.1 13.7 + - - +
235E TYR* 2.9 41.1 - - + +
237E ILE* 1.3 78.8 - - - +
239E LYS* 1.3 58.9 + - + +
241E LYS* 3.4 6.2 + - - +
242E LYS* 2.8 32.8 + - - +
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Residues in contact with LYS 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E LEU* 3.5 33.6 - - + +
207E MSE 4.0 9.6 - - - +
230E PHE* 4.8 9.4 - - + -
235E TYR* 3.0 63.3 + - + +
236E PHE* 3.6 4.5 - - - +
238E THR* 1.3 77.7 - - + +
240E PHE* 1.3 60.3 + - - +
242E LYS* 3.9 19.1 - - + +
243E TYR* 2.8 34.1 + - + +
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Residues in contact with PHE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASN* 4.6 17.9 - - - +
156D LEU* 4.1 20.6 - - + -
207E MSE 3.7 19.6 - - - -
210E ALA* 3.8 31.4 - - + -
211E LYS* 3.8 10.1 - - - -
214E LEU* 3.5 30.5 - - + -
236E PHE* 2.6 35.0 + + + +
237E ILE* 3.8 5.8 - - - +
239E LYS* 1.3 74.4 - - - +
241E LYS* 1.3 66.7 + - + +
244E TYR* 3.2 55.4 + + + +
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Residues in contact with LYS 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASN* 5.1 12.8 + - - +
155D GLU* 4.3 17.3 + - - +
237E ILE* 2.9 32.8 + - + +
238E THR* 3.5 6.5 - - - +
240E PHE* 1.3 82.0 - - + +
242E LYS* 1.3 64.1 + - - +
244E TYR* 3.7 0.9 - - - -
245E GLN* 2.9 55.1 + - - +
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Residues in contact with LYS 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E THR* 2.8 22.7 + - - +
239E LYS* 3.9 20.9 - - + +
241E LYS* 1.3 74.3 - - - +
243E TYR* 1.3 64.9 + - - +
245E GLN* 3.5 19.7 + - - +
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Residues in contact with TYR 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ASP 5.6 0.9 - - - -
203E LEU* 4.2 19.5 - - + -
204E GLN* 3.2 41.9 - - + +
207E MSE 3.6 27.4 - - + -
208E GLU* 4.7 2.1 + - + -
239E LYS* 2.8 20.4 + - + +
240E PHE 3.8 3.4 - - - +
241E LYS 3.2 0.2 - - - -
242E LYS* 1.3 82.8 - - - +
244E TYR* 1.3 98.1 + + - +
245E GLN 3.3 2.0 + - - +
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Residues in contact with TYR 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 4.9 11.6 - - + +
159D ASN* 4.3 8.1 - - - +
207E MSE 3.3 27.1 + - + -
208E GLU* 3.4 19.1 + - - +
211E LYS* 3.7 34.3 + - + +
240E PHE* 3.2 56.5 + + + +
241E LYS* 3.7 2.0 - - - -
243E TYR* 1.3 104.3 - + + +
245E GLN* 1.3 64.5 + - - +
246E ILE* 3.2 5.0 + - - +
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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