Contacts of the helix formed by residues 249 - 266 (chain L) 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 ALA 249 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L SER* 1.3 77.7 - - - +
250L ASP* 1.3 59.7 + - - +
251L ARG* 3.2 6.7 - - - -
252L GLU* 2.9 33.5 + - - +
253L ILE* 3.9 3.9 + - + +
261M ILE* 4.7 20.6 - - + -
304M ARG* 4.1 16.0 + - - +
305M GLU* 3.7 26.2 - - + +
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Residues in contact with ASP 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L ARG* 3.8 12.3 - - - +
244L SER* 5.0 3.9 + - - -
246L GLY* 3.3 35.6 + - - +
248L SER* 3.2 21.0 + - - -
249L ALA* 1.3 79.0 - - - +
251L ARG* 1.4 61.5 + - - +
252L GLU 3.3 0.7 - - - -
253L ILE* 3.2 31.9 - - + +
254L GLN* 3.4 23.7 + - - +
301M ALA* 3.7 13.9 - - - +
302M GLY* 4.2 11.8 - - - +
305M GLU* 5.7 0.2 - - - +
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Residues in contact with ARG 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236K VAL* 4.6 21.8 - - + +
237K GLN 4.3 6.0 + - - -
238K LYS* 3.4 60.9 + - + +
239K TYR* 4.2 13.9 + - - -
269K ALA* 6.5 0.2 - - - -
281K ALA* 3.4 30.5 - - - +
284K GLU* 4.2 5.7 + - - +
247L THR* 3.6 33.5 + - + +
248L SER 3.4 24.2 + - - +
249L ALA 4.2 1.6 - - - +
250L ASP* 1.4 76.2 - - - +
252L GLU* 1.4 68.6 + - + +
254L GLN* 3.3 8.7 + - - +
255L ARG* 3.0 27.6 + - - +
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Residues in contact with GLU 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238K LYS* 4.0 17.4 + - + +
204L VAL* 4.0 20.5 - - + +
205L ASP 3.1 27.5 + - - +
211L SER* 4.8 1.7 + - - +
249L ALA* 2.9 15.1 + - - +
251L ARG* 1.4 87.0 - - + +
253L ILE* 1.3 55.0 + - - +
255L ARG* 3.1 44.9 + - - +
256L THR* 3.1 20.8 + - - +
261M ILE* 3.4 32.1 - - - +
304M ARG* 4.6 5.2 + - - +
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Residues in contact with ILE 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237L ALA 4.6 9.5 - - - +
238L ILE* 6.0 1.0 - - - -
239L GLY 5.0 2.0 - - - +
240L GLY* 3.2 34.3 - - - +
242L ARG* 4.7 10.5 - - + -
249L ALA* 4.3 3.1 - - + +
250L ASP* 3.2 42.8 - - + +
251L ARG 3.2 0.2 - - - -
252L GLU* 1.3 75.1 - - - +
254L GLN* 1.4 60.1 + - - +
256L THR* 3.0 18.6 + - - -
257L LEU* 3.1 20.1 + - + +
301M ALA* 4.0 19.1 - - + +
304M ARG* 3.4 34.5 - - - +
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Residues in contact with GLN 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K SER* 5.0 3.7 + - - +
236K VAL* 5.8 0.4 - - + -
266K GLU* 3.3 24.4 + - - +
268K ASP* 4.3 6.6 + - - +
269K ALA* 4.8 17.0 - - + -
313K ARG* 4.0 11.9 + - - +
241L ARG 4.3 2.4 - - - +
242L ARG* 3.0 58.2 + - - +
250L ASP 3.4 6.2 + - - +
251L ARG* 3.3 10.7 + - - +
253L ILE* 1.4 80.4 - - - +
255L ARG* 1.3 63.1 + - - +
257L LEU* 3.9 21.5 - - - +
258L MET* 3.1 26.6 + - - +
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Residues in contact with ARG 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K MET* 5.0 3.1 - - - -
233K SER 4.3 5.6 - - - +
234K GLU* 3.1 44.7 - - - +
236K VAL* 5.2 14.8 + - + +
237K GLN* 4.9 5.4 + - - +
238K LYS* 4.2 17.8 - - - +
205L ASP* 4.9 3.0 + - - +
207L TYR 3.3 22.4 + - - -
208L ILE* 4.3 1.0 - - - +
209L GLY* 3.4 22.6 - - - +
210L GLU* 5.2 0.2 - - - +
211L SER* 3.5 39.1 + - - +
212L ALA* 4.0 13.5 - - + +
251L ARG* 3.0 14.1 + - - +
252L GLU* 3.1 31.1 + - - +
254L GLN* 1.3 77.2 - - - +
256L THR* 1.4 60.1 + - - +
259L GLU* 3.3 15.2 + - - +
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Residues in contact with THR 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ILE* 4.7 11.0 - - + -
204L VAL* 5.2 8.1 - - + -
211L SER* 3.5 34.5 - - - +
215L ILE* 5.4 5.4 - - + +
237L ALA* 3.5 17.0 + - + +
238L ILE* 3.9 21.9 - - + +
252L GLU 3.1 11.0 + - - +
253L ILE* 3.0 16.3 + - - -
255L ARG* 1.4 74.4 - - - +
257L LEU* 1.4 62.6 + - - +
259L GLU* 3.1 17.6 + - - +
260L LEU* 3.3 12.1 + - - +
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Residues in contact with LEU 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266K GLU* 5.6 1.6 - - - +
313K ARG* 5.4 3.8 - - - +
238L ILE* 4.6 21.1 - - + -
240L GLY 4.3 16.2 - - - +
241L ARG* 4.9 11.0 - - + -
253L ILE* 3.1 15.8 + - + +
254L GLN* 3.9 28.0 - - - +
255L ARG 3.5 0.2 - - - -
256L THR* 1.4 72.7 + - - +
258L MET* 1.3 65.9 + - - +
260L LEU* 3.3 19.3 + - + +
261L LEU* 3.3 32.2 + - + +
284L THR 6.1 0.9 - - - +
286L ASP* 3.9 28.5 - - + +
289L LEU* 6.4 0.2 - - + -
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Residues in contact with MET 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K VAL* 3.8 18.2 - - + -
233K SER* 3.8 25.4 - - - +
234K GLU* 3.3 17.9 - - + +
265K ASP* 3.6 25.8 - - + +
266K GLU* 3.5 35.9 + - - +
254L GLN 3.1 17.7 + - - +
255L ARG 3.5 3.8 - - - +
257L LEU* 1.3 79.3 - - - +
259L GLU* 1.4 54.1 + - - +
261L LEU* 3.4 5.7 + - - +
262L ASN* 2.9 65.4 + - - +
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Residues in contact with GLU 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K ILE 4.2 2.1 - - - +
152K MET* 4.0 11.8 - - - +
153K MET* 5.0 1.6 - - - +
234K GLU* 3.5 27.0 - - - +
211L SER 6.2 0.2 - - - -
212L ALA* 3.8 19.6 - - - +
215L ILE* 4.1 19.3 - - + -
216L ARG* 3.8 22.1 - - - +
255L ARG 3.3 7.8 + - - +
256L THR* 3.1 13.8 + - - +
258L MET* 1.4 75.2 - - - +
260L LEU* 1.4 64.1 - - - +
262L ASN* 3.1 23.5 + - - +
263L GLN* 3.0 46.6 + - - +
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Residues in contact with LEU 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L ILE* 5.7 1.8 - - - +
232L MET* 5.4 7.0 - - + -
238L ILE* 4.7 19.7 - - + -
256L THR 3.3 8.2 + - - +
257L LEU* 3.3 15.0 + - + +
259L GLU* 1.4 80.6 - - - +
261L LEU* 1.3 77.4 + - + +
263L GLN* 3.5 14.5 + - - +
264L MET* 3.2 45.2 + - + +
275L MET* 5.5 2.2 - - + -
277L MET* 4.4 25.1 - - + -
289L LEU* 4.5 16.2 - - + -
294L ARG* 5.0 4.5 - - + -
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Residues in contact with LEU 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K PRO* 5.2 8.1 - - + -
266K GLU* 4.3 17.3 - - - +
312K ASN* 6.1 3.1 - - + -
257L LEU* 3.3 31.0 - - + +
258L MET* 3.6 6.5 - - - +
260L LEU* 1.3 85.0 - - + +
262L ASN* 1.3 61.0 + - - +
264L MET* 3.2 5.6 + - - +
265L ASP* 2.7 45.3 + - - +
286L ASP* 3.7 38.4 - - + +
288L ALA* 4.1 16.4 - - + -
289L LEU* 4.5 5.2 - - + -
294L ARG* 5.1 4.9 - - - +
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Residues in contact with ASN 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K MET 4.4 1.4 + - - -
153K MET* 4.1 19.2 - - + +
229K ARG* 6.0 0.2 - - - -
231K VAL* 3.7 18.2 - - - +
234K GLU* 4.2 1.2 - - - +
265K ASP* 5.0 5.7 - - - +
258L MET* 2.9 62.8 + - - +
259L GLU* 3.1 26.2 + - - +
261L LEU* 1.3 78.6 - - - +
263L GLN* 1.4 64.4 + - - +
265L ASP* 3.8 10.1 - - - +
266L GLY* 3.2 21.1 + - - -
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Residues in contact with GLN 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153K MET* 3.9 11.6 - - + +
215L ILE* 3.7 25.2 - - - +
216L ARG* 3.7 13.9 - - - -
219L PHE* 3.3 52.1 - - + +
259L GLU* 3.0 54.1 + - - +
260L LEU* 3.7 12.9 - - + +
261L LEU 3.3 0.2 - - - -
262L ASN* 1.4 75.1 - - - +
264L MET* 1.4 74.0 + - + +
266L GLY* 3.5 10.2 + - - -
268L ASP* 4.1 18.5 - - - +
270L LEU* 5.8 1.6 - - - +
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Residues in contact with MET 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L LYS* 4.8 9.6 + - - +
219L PHE* 5.9 0.9 - - + -
260L LEU* 3.2 41.7 - - + +
261L LEU* 3.4 9.4 - - - +
263L GLN* 1.4 84.4 - - + +
265L ASP* 1.3 62.7 + - - +
266L GLY 3.4 5.7 + - - +
268L ASP 4.8 3.3 - - - +
270L LEU* 4.1 25.6 - - + -
275L MET* 4.0 20.6 - - + -
293L GLY 3.6 12.2 - - - +
294L ARG* 3.6 52.6 + - + +
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Residues in contact with ASP 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K PRO* 3.5 40.4 - - - +
213K THR* 4.4 15.2 + - + +
217K LYS* 3.5 23.8 - - - -
229K ARG* 5.5 0.7 - - - -
265K ASP* 5.4 9.5 - - - +
261L LEU* 2.7 37.7 + - - +
262L ASN* 3.3 11.2 + - - +
264L MET* 1.3 79.4 - - - +
266L GLY* 1.3 60.9 + - - +
294L ARG* 4.4 7.5 + - - +
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Residues in contact with GLY 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K MET* 4.9 5.2 - - - -
217K LYS* 5.0 0.5 - - - -
229K ARG* 3.8 20.6 - - - -
262L ASN 3.2 14.6 + - - -
263L GLN 3.9 5.2 - - - -
264L MET 3.2 6.6 - - - +
265L ASP* 1.3 78.9 - - - +
267L PHE* 1.3 66.1 + - - -
268L ASP* 3.2 11.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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