Contacts of the helix formed by residues 232 - 245 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C LEU* 3.3 9.2 - - + +
183C SER 4.3 3.4 - - - +
184C GLY* 4.4 7.6 - - - -
187C SER* 2.5 39.8 + - - +
199C GLN* 2.9 30.5 + - - +
225D ALA* 4.5 5.6 - - - -
230D PHE* 3.4 3.8 - - - +
231D GLU* 1.3 78.9 - - - +
233D VAL* 1.3 62.1 + - - +
234D ASN* 3.3 4.7 + - - +
235D TYR* 2.9 26.8 + - - +
236D PHE* 3.1 18.9 + - - +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLY* 5.7 3.7 - - - -
221D ASN* 3.6 18.2 - - + +
222D TYR* 3.5 45.3 - - + +
225D ALA* 3.8 11.1 - - + +
232D ASP* 1.3 74.1 - - - +
234D ASN* 1.3 76.1 + - - +
236D PHE* 3.2 1.6 + - + +
237D ILE* 2.8 39.0 + - + +
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Residues in contact with ASN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLY* 4.3 1.2 - - - +
187C SER* 3.2 19.2 + - - +
188C ILE* 3.4 29.3 + - - +
191C LYS* 5.4 13.4 - - + +
197C PRO* 6.1 2.5 - - + -
232D ASP* 3.2 6.8 - - - +
233D VAL* 1.3 92.5 - - - +
235D TYR* 1.3 61.1 + - - +
237D ILE* 3.3 12.9 + - - +
238D THR* 2.9 30.8 + - + +
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Residues in contact with TYR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C PRO* 4.1 12.1 - - + +
199C GLN* 3.4 50.7 - - + +
200C ASP* 3.9 22.1 + - - -
230D PHE* 4.0 16.8 - + + -
231D GLU 6.2 0.9 - - - -
232D ASP* 2.9 28.1 + - - +
234D ASN* 1.3 73.8 - - - +
236D PHE* 1.3 66.6 + - - +
238D THR* 3.2 12.5 + - - -
239D LYS* 2.9 63.1 + - + +
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Residues in contact with PHE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D MSE 3.9 19.1 - - + -
210D ALA* 3.5 26.7 - - + -
214D LEU* 6.4 1.6 - - + -
221D ASN* 4.2 23.6 - - + -
224D ILE* 3.7 22.4 - - + -
225D ALA* 3.8 21.3 - - + -
228D VAL* 4.0 16.8 - - + -
230D PHE* 3.4 19.6 - + + -
232D ASP 3.1 14.7 + - - +
233D VAL* 3.4 9.0 - - + +
235D TYR* 1.3 77.4 - - - +
237D ILE* 1.3 67.6 + - + +
239D LYS* 3.4 1.2 + - - +
240D PHE* 2.9 45.8 + + + +
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Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ASN* 3.7 28.7 - - + +
233D VAL* 2.8 30.3 + - + +
234D ASN* 3.5 14.4 - - - +
236D PHE* 1.3 87.6 - - + +
238D THR* 1.3 69.2 + - + +
240D PHE* 3.8 3.6 - - - +
241D LYS* 3.1 43.3 + - + +
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 5.8 6.5 - - + -
197C PRO* 4.8 13.4 - - + +
200C ASP* 4.8 4.9 + - - -
234D ASN* 2.9 22.0 - - + +
235D TYR* 3.2 19.4 + - - -
237D ILE* 1.3 81.4 - - + +
239D LYS* 1.3 68.1 + - - +
241D LYS* 3.5 5.0 + - - +
242D LYS* 3.0 25.4 + - - +
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASP* 5.4 3.0 + - - -
239C LYS* 5.1 10.3 - - - +
242C LYS* 5.3 6.8 - - - +
203D LEU* 3.9 33.8 - - + +
207D MSE 4.1 6.3 - - - -
230D PHE* 4.0 15.5 - - + -
235D TYR* 2.9 63.9 + - + +
236D PHE 4.0 2.7 - - - +
238D THR* 1.3 78.4 + - - +
240D PHE* 1.3 52.9 + - - +
242D LYS* 3.3 17.9 + - - +
243D TYR* 2.7 38.2 + - - +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D MSE 3.7 14.5 - - - -
210D ALA* 4.0 8.3 - - + -
211D LYS* 3.7 32.5 - - + -
214D LEU* 4.3 25.6 - - + -
236D PHE* 2.9 44.4 + + + +
237D ILE* 3.8 4.0 - - - +
239D LYS* 1.3 77.8 - - - +
241D LYS* 1.3 71.2 + - + +
243D TYR 3.3 0.3 + - - -
244D TYR* 3.0 62.1 + + + +
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Residues in contact with LYS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ILE* 3.1 30.1 + - + +
238D THR* 4.0 4.9 - - - +
240D PHE* 1.3 84.4 - - + +
242D LYS* 1.3 58.6 + - - +
244D TYR* 5.4 0.7 - - - -
245D GLN 2.8 42.6 + - - -
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Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASP* 6.0 0.2 + - - -
242C LYS* 5.4 13.3 - - - +
238D THR* 3.0 19.1 + - - +
239D LYS* 3.6 20.8 - - - +
241D LYS* 1.3 75.3 - - - +
243D TYR* 1.3 67.7 + - - +
244D TYR 3.2 0.7 + - - -
245D GLN* 3.2 11.0 + - - +
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Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 4.6 16.6 - - + -
204D GLN* 3.0 37.3 - - + +
207D MSE 3.5 37.7 - - + -
208D GLU* 4.8 2.7 + - + +
239D LYS* 2.7 22.5 + - - +
240D PHE 3.7 4.0 - - - +
242D LYS* 1.3 73.4 - - - +
244D TYR* 1.3 92.0 + + + +
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D MSE 2.9 30.1 + - + +
208D GLU* 3.5 12.0 + - - +
211D LYS* 3.6 31.8 - - + +
240D PHE* 3.0 62.5 + + + +
241D LYS* 4.7 0.7 - - - +
243D TYR* 1.3 104.7 - + + +
245D GLN* 1.3 73.7 + - - +
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Residues in contact with GLN 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LYS* 2.8 30.5 + - - -
242D LYS* 3.2 10.2 + - - +
243D TYR 3.5 0.2 - - - -
244D TYR* 1.3 86.3 + - - +
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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