Contacts of the helix formed by residues 266 - 281 (chain J) 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 ASP 266 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J GLY* 3.7 13.2 + - - -
217J SER* 3.7 14.6 + - - -
248J MET* 3.8 11.5 - - - +
250J GLU* 2.9 32.0 - - - +
251J ILE* 4.2 9.9 - - + -
259J LEU* 3.7 10.7 - - - +
261J GLY 3.5 2.4 - - - +
262J GLY* 3.5 30.6 - - - +
263J SER 4.3 1.4 + - - -
264J GLY 4.3 0.8 - - - +
265J GLY* 1.3 82.2 - - - +
267J SER* 1.4 60.1 + - - +
268J GLU 3.4 0.4 - - - -
269J VAL* 3.5 12.6 - - - +
270J GLN* 3.2 20.8 - - - +
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Residues in contact with SER 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J ILE* 3.6 10.6 - - - +
262J GLY 3.4 14.2 + - - -
263J SER* 3.7 20.0 - - - -
264J GLY 4.0 2.2 - - - -
265J GLY 3.9 0.6 - - - +
266J ASP* 1.4 76.7 - - - +
268J GLU* 1.3 60.3 + - - +
270J GLN* 3.1 11.5 + - - +
271J ARG* 2.7 31.9 + - - +
300J ILE* 3.9 12.1 + - - +
302J ASP* 6.1 2.0 - - - -
305J LEU* 4.0 21.4 - - - +
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Residues in contact with GLU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I SER* 4.8 15.8 - - - +
254I GLU* 3.9 17.7 - - - +
256I ILE* 5.9 2.3 - - - +
264J GLY* 3.0 38.1 - - - +
265J GLY* 3.4 7.7 - - - +
266J ASP 3.4 0.2 - - - -
267J SER* 1.3 82.6 - - - +
269J VAL* 1.3 63.9 + - - +
271J ARG* 3.4 21.2 + - - +
272J THR* 3.2 21.3 + - - -
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Residues in contact with VAL 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I GLU* 4.8 4.0 - - - +
216J GLY* 4.1 14.6 - - - +
219J LEU* 4.3 17.9 - - + -
220J VAL* 6.4 1.8 - - + -
231J VAL* 4.2 26.2 - - + +
248J MET* 4.0 16.6 - - + -
265J GLY* 3.5 25.1 - - - +
266J ASP* 3.5 15.5 - - - +
268J GLU* 1.3 83.0 - - - +
270J GLN* 1.4 62.3 - - - +
272J THR* 3.4 22.1 + - - -
273J MET* 3.6 5.7 + - - +
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Residues in contact with GLN 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248J MET* 3.9 25.5 - - + +
251J ILE* 3.6 21.1 - - - +
266J ASP 3.2 14.8 - - - +
267J SER* 3.1 8.6 + - - +
269J VAL* 1.4 76.8 - - - +
271J ARG* 1.4 55.7 + - - +
272J THR 3.3 0.4 - - - -
273J MET* 3.1 23.0 + - - +
274J LEU* 3.3 19.7 + - + +
291J VAL* 5.2 7.1 - - + +
293J MET* 3.4 38.7 - - + +
305J LEU* 3.8 35.6 - - - +
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Residues in contact with ARG 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I VAL* 3.5 25.3 - - - +
253I SER* 3.6 26.4 + - - -
254I GLU* 4.2 3.6 + - - +
285I ASP* 5.7 1.6 - - - +
267J SER 2.7 18.8 + - - +
268J GLU* 3.4 16.9 + - - +
270J GLN* 1.4 68.2 - - - +
272J THR* 1.3 88.1 + - - +
274J LEU* 3.1 25.8 + - + +
275J GLU* 3.2 47.4 + - - +
304J ALA* 5.0 16.6 - - + -
305J LEU* 4.4 13.5 - - + -
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Residues in contact with THR 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I VAL* 4.1 10.3 - - + -
251I VAL* 4.2 14.6 - - + -
254I GLU* 3.3 30.5 - - + -
231J VAL* 3.9 18.4 - - + -
268J GLU 3.2 9.1 + - - -
269J VAL* 3.4 10.9 + - - -
270J GLN 3.3 0.4 - - - -
271J ARG* 1.3 100.6 + - - +
273J MET* 1.4 56.2 + - - +
275J GLU* 3.2 6.6 + - - +
276J LEU* 3.0 32.2 + - + +
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Residues in contact with MET 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231J VAL* 5.2 7.8 - - + +
234J LEU* 4.5 14.8 - - + -
235J PHE* 3.7 40.8 - - + +
246J ILE* 3.6 32.1 - - + -
269J VAL 3.6 5.7 + - - +
270J GLN* 3.1 16.2 + - - +
272J THR* 1.4 76.3 - - - +
274J LEU* 1.4 58.4 + - + +
276J LEU* 3.4 11.3 + - + +
277J LEU* 3.0 41.9 + - + +
291J VAL* 4.3 17.9 - - + -
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Residues in contact with LEU 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184J LYS* 5.5 12.9 - - + +
185J GLY* 6.3 1.8 - - - -
270J GLN* 3.3 17.0 + - + +
271J ARG* 3.1 21.9 + - + +
273J MET* 1.4 75.9 - - + +
275J GLU* 1.3 68.2 + - - +
277J LEU* 3.3 9.4 + - + +
278J ASN* 3.0 31.4 + - - +
291J VAL* 5.2 17.0 - - + -
293J MET* 5.1 15.3 - - + -
304J ALA 5.6 1.3 - - - +
305J LEU* 4.1 22.4 - - + -
310J ARG* 4.6 31.0 - - + +
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Residues in contact with GLU 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249I ARG* 3.9 12.0 + - - +
251I VAL* 4.5 15.9 - - + -
285I ASP* 3.7 20.8 - - - +
271J ARG* 3.2 42.2 + - - +
272J THR* 3.2 7.3 + - - +
274J LEU* 1.3 80.2 - - - +
276J LEU* 1.4 65.0 + - - +
278J ASN* 3.3 35.1 + - - +
279J GLN* 3.5 14.7 + - - +
310J ARG* 4.5 15.8 + - - -
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Residues in contact with LEU 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I VAL* 3.6 33.9 - - + -
174I MET 5.6 0.2 - - - -
175I LYS* 3.5 41.3 + - + +
231J VAL* 4.8 6.3 - - + +
232J ARG* 4.7 9.9 - - + -
235J PHE* 4.1 36.8 - - + -
272J THR* 3.0 25.5 + - + +
273J MET* 3.4 14.5 + - + +
275J GLU* 1.4 75.1 - - + +
277J LEU* 1.4 62.9 - - - +
279J GLN* 3.4 11.2 + - - +
280J LEU* 3.3 16.7 + - - +
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Residues in contact with LEU 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184J LYS* 4.9 19.7 - - + +
235J PHE* 3.8 26.5 - - + -
273J MET* 3.0 28.1 + - + +
274J LEU* 3.6 9.9 - - + +
275J GLU 3.2 0.4 - - - -
276J LEU* 1.4 76.4 - - - +
278J ASN* 1.3 52.6 + - - +
280J LEU* 3.2 16.7 + - + +
281J ASP* 2.6 43.9 + - - +
287J LYS* 5.3 8.5 - - + -
289J ILE* 4.5 20.9 - - + +
291J VAL* 3.5 32.3 - - + -
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Residues in contact with ASN 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I THR* 5.1 8.1 + - - +
237I LYS* 3.6 17.1 + - + +
249I ARG* 4.9 10.4 - - - +
184J LYS* 4.5 15.1 - - - +
274J LEU* 3.0 24.5 + - - +
275J GLU* 3.4 35.5 + - - +
276J LEU 3.3 0.6 - - - -
277J LEU* 1.3 72.8 - - - +
279J GLN* 1.3 65.2 + - + +
281J ASP* 3.5 24.5 + - - +
282J GLY 3.6 4.0 + - - -
309J GLY 5.3 1.9 - - - +
310J ARG* 4.4 20.9 - - - +
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Residues in contact with GLN 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I LYS* 3.9 34.6 + - - +
177I GLU* 4.3 17.4 + - - +
237I LYS* 4.9 8.4 - - + +
247I PHE* 5.0 5.4 - - + -
249I ARG* 3.6 58.2 + - - +
275J GLU* 3.5 17.0 - - - +
276J LEU* 3.4 17.9 + - - +
277J LEU 3.3 0.2 - - - -
278J ASN* 1.3 73.4 - - - +
280J LEU* 1.4 58.7 + - - +
282J GLY* 3.1 16.3 + - - -
283J PHE* 3.5 14.4 + - - +
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Residues in contact with LEU 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I LYS* 3.7 15.0 - - - +
235J PHE* 4.3 13.7 - - + -
239J ARG* 3.9 23.6 - - + +
276J LEU 3.3 10.6 + - - +
277J LEU* 3.2 22.4 + - + +
279J GLN* 1.4 74.8 - - - +
281J ASP* 1.3 63.7 + - - +
282J GLY 3.1 1.6 - - - -
283J PHE* 3.2 9.8 + - + +
284J GLU* 3.1 61.6 + - + +
286J THR 5.1 0.2 - - - +
287J LYS* 4.5 20.6 - - + -
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Residues in contact with ASP 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I GLU* 4.0 4.0 - - - +
237I LYS* 4.8 5.2 + - - +
182J GLN 5.3 0.3 - - - +
184J LYS* 3.8 21.7 - - - +
277J LEU* 2.6 30.6 + - - +
278J ASN* 3.5 13.9 - - - +
279J GLN 3.3 0.2 - - - -
280J LEU* 1.3 79.2 - - - +
282J GLY* 1.3 54.8 + - - +
283J PHE 3.5 0.4 - - - -
284J GLU 3.2 17.3 - - - +
285J ALA* 5.2 0.4 - - - +
287J LYS* 3.5 30.0 + - - -
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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
------------------------------------------------------------
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