Contacts of the helix formed by residues 230 - 243 (chain O) in PDB entry 5LN3
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 ARG 230 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197O ALA* 3.3 40.1 + - + +
200O LEU* 3.6 20.8 - - - +
201O GLY* 3.3 23.0 - - - +
216O LEU* 3.7 19.9 - - - +
221O VAL* 3.8 37.7 - - - +
222O LEU* 4.9 7.2 - - + +
225O LEU* 3.6 33.5 - - + +
226O ARG* 4.3 4.2 - - - -
228O THR 3.2 5.1 + - - -
229O ASP* 1.3 76.7 + - - +
231O GLN* 1.3 63.6 + - - +
232O TRP 3.1 1.1 - - - -
233O LEU* 3.1 50.6 + - + +
234O ILE* 3.6 7.8 - - - +
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Residues in contact with GLN 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O ARG* 3.2 25.8 + - - +
227O ASN 3.3 17.9 + - - +
228O THR* 3.5 13.0 + - - -
229O ASP 3.9 0.4 - - - +
230O ARG* 1.3 74.8 - - - +
232O TRP* 1.3 75.8 + - + +
234O ILE* 3.1 26.5 - - - +
235O ASP* 2.7 31.8 - - - +
252O LYS* 3.5 12.6 + - - +
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Residues in contact with TRP 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198O PHE* 3.8 25.6 - + - -
202O LEU* 5.0 9.4 - - + -
228O THR* 3.0 18.9 + - - -
229O ASP* 3.1 49.8 - - - +
231O GLN* 1.3 95.0 - - + +
233O LEU* 1.4 61.5 + - - +
235O ASP* 3.3 14.5 + - - +
236O THR* 3.1 24.4 + - - -
248O PHE* 4.2 3.6 - - + -
252O LYS* 3.2 32.6 - - + +
254O ALA* 3.9 20.4 - - + -
255O TRP* 3.4 42.6 - + + +
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Residues in contact with LEU 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O GLY* 6.2 0.9 - - - -
213O PHE* 4.0 20.0 - - + +
216O LEU* 3.6 45.3 - - + -
217O LEU* 4.6 16.6 - - + -
221O VAL* 5.9 0.2 - - + -
222O LEU* 5.7 3.4 - - + -
229O ASP 4.1 1.6 + - - -
230O ARG* 3.1 55.4 + - + +
232O TRP* 1.4 73.4 - - - +
234O ILE* 1.3 74.1 + - + +
236O THR* 3.1 22.4 + - + -
237O LEU* 3.6 6.8 + - + +
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Residues in contact with ILE 234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217O LEU* 5.5 6.3 - - + -
222O LEU* 4.1 26.0 - - + -
226O ARG* 5.7 4.5 - - + -
230O ARG* 3.6 12.1 - - + +
231O GLN* 3.1 17.0 - - - +
233O LEU* 1.3 87.8 - - + +
235O ASP* 1.4 63.8 + - - +
237O LEU* 3.2 30.0 + - + +
238O TYR* 3.4 38.1 + - + +
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Residues in contact with ASP 235 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231O GLN* 2.7 35.9 - - - +
232O TRP* 3.3 17.8 - - - +
233O LEU 3.2 0.4 - - - -
234O ILE* 1.4 84.4 - - - +
236O THR* 1.5 58.2 + - - +
238O TYR* 3.5 15.2 + - - +
239O ALA 3.2 16.3 + - - -
247O ARG* 3.3 13.9 + - - +
248O PHE* 3.3 19.4 - - + -
251O LEU* 3.5 27.2 - - + +
252O LYS* 5.8 0.3 + - - -
255O TRP* 3.8 12.5 - - - -
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Residues in contact with THR 236 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205O LEU* 4.1 16.2 - - + +
212O ASN 6.0 0.2 - - - -
213O PHE* 4.9 10.5 - - + +
232O TRP 3.1 15.3 + - - -
233O LEU* 3.1 14.1 + - + +
235O ASP* 1.5 59.7 - - - +
237O LEU* 1.3 57.6 + - - +
239O ALA* 3.2 3.4 + - - +
240O PHE* 3.1 66.1 + - + -
248O PHE* 3.7 16.6 - - + -
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Residues in contact with LEU 237 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213O PHE* 3.7 48.5 - - + -
217O LEU* 4.4 20.9 - - + -
233O LEU* 3.6 6.4 + - + +
234O ILE* 3.2 21.5 + - + +
236O THR* 1.3 75.6 - - - +
238O TYR* 1.3 79.9 + - + +
240O PHE* 3.7 0.5 + - - +
241O ASN* 3.3 42.6 + - - +
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Residues in contact with TYR 238 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234O ILE* 3.4 40.9 + - + +
235O ASP* 3.8 14.8 - - - +
236O THR 3.3 0.2 - - - -
237O LEU* 1.3 91.7 - - + +
239O ALA* 1.3 61.6 + - - +
241O ASN* 4.2 3.1 - - - +
242O SER* 3.3 26.1 + - - -
247O ARG* 3.7 31.0 - - - +
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Residues in contact with ALA 239 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235O ASP 3.2 11.3 + - - +
236O THR* 3.2 10.0 + - - +
238O TYR* 1.3 80.5 - - - +
240O PHE* 1.4 59.1 + - + +
242O SER* 4.7 0.2 - - - -
243O GLY 3.4 20.3 + - - -
244O ASN 3.7 18.2 + - - +
245O VAL* 5.5 1.3 - - - -
247O ARG* 3.6 6.5 - - - +
248O PHE* 3.6 32.3 - - + -
265O GLU* 5.3 4.0 - - - +
269O LEU* 3.8 11.1 - - + +
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Residues in contact with PHE 240 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205O LEU* 4.3 12.3 - - + -
212O ASN* 3.3 37.9 - - + -
213O PHE* 3.8 17.7 - + + -
236O THR* 3.1 47.1 + - + +
237O LEU 3.8 2.9 - - - +
238O TYR 3.5 0.2 - - - -
239O ALA* 1.4 73.6 - - + +
241O ASN* 1.3 75.5 + - - +
242O SER 3.3 1.3 - - - -
243O GLY* 3.9 5.5 + - - -
265O GLU* 5.2 7.0 - - + -
268O LEU* 3.8 34.8 - - + -
269O LEU* 3.7 34.2 - - + +
272O ILE* 3.9 24.0 - - + +
273O GLN* 4.8 1.4 + - - +
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Residues in contact with ASN 241 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213O PHE* 3.3 32.8 - - - -
237O LEU* 3.3 27.5 + - - +
238O TYR* 4.2 2.7 - - - +
239O ALA 3.6 0.4 - - - -
240O PHE* 1.3 78.0 - - - +
242O SER* 1.4 62.6 - - - +
272O ILE* 3.7 22.6 - - + +
273O GLN* 5.1 6.6 - - - +
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Residues in contact with SER 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238O TYR 3.3 18.4 + - - -
239O ALA* 4.0 2.9 - - - -
241O ASN* 1.4 81.6 - - - +
243O GLY* 1.3 59.3 - - - +
244O ASN* 3.4 21.0 + - - +
247O ARG* 5.2 5.1 - - - +
273O GLN* 5.3 0.8 + - - -
299O SER* 4.5 7.3 - - - +
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Residues in contact with GLY 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239O ALA 3.4 4.4 + - - -
240O PHE 3.9 0.8 + - - -
241O ASN 3.4 2.0 - - - -
242O SER* 1.3 78.7 - - - +
244O ASN* 1.3 57.7 + - - +
245O VAL 3.7 0.2 + - - -
269O LEU* 3.3 30.5 - - - +
273O GLN* 3.9 11.0 - - - -
299O SER 3.8 14.4 - - - +
300O ALA 4.3 0.7 - - - +
301O LYS* 3.0 23.6 - - - +
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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