Contacts of the helix formed by residues 243 - 259 (chain B) in PDB entry 5INQ
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 HIS 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B LYS* 4.7 20.9 + - + +
214B MET* 3.5 23.2 - - + +
238B GLU* 3.8 20.3 - - + +
239B SER 3.3 16.9 + - - +
240B THR* 3.0 27.5 + - + +
241B ARG 3.1 1.2 + - - -
242B GLU* 1.3 86.9 - - + +
244B SER* 1.3 63.2 + - - +
245B ALA* 3.3 3.8 + - - -
246B GLU* 3.3 9.4 + - + +
247B ARG* 3.1 22.3 + - - +
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Residues in contact with SER 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.3 16.1 + - - -
242B GLU 3.4 2.0 + - - -
243B HIS* 1.3 77.9 - - - +
245B ALA* 1.3 58.9 + - - +
247B ARG* 3.2 15.1 + - - +
248B ILE* 2.8 42.4 + - - +
279B GLU* 2.7 28.4 + - - +
282B LYS* 5.4 2.6 - - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU 5.1 0.8 + - - -
243B HIS* 3.3 1.2 - - - +
244B SER* 1.3 79.9 - - - +
246B GLU* 1.3 62.9 + - - +
248B ILE* 3.4 9.9 + - - +
249B ARG* 3.1 42.0 + - - +
282B LYS* 6.4 0.2 - - - +
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASN* 3.5 13.4 - - - +
212B THR 3.3 7.1 + - - -
238B GLU* 3.8 21.1 - - + +
243B HIS* 3.3 13.9 + - + +
244B SER 3.3 0.2 - - - -
245B ALA* 1.3 75.1 - - - +
247B ARG* 1.3 61.7 + - - +
249B ARG* 2.6 52.2 + - - +
250B GLN* 2.9 54.2 + - - +
403B GOL 2.3 30.6 + - - -
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 4.0 7.0 - - + +
238B GLU* 2.7 43.5 + - - +
239B SER* 3.7 6.1 + - - +
240B THR 2.9 32.3 + - - +
241B ARG* 3.9 4.6 - - - +
243B HIS 3.1 11.1 + - - +
244B SER* 3.4 17.6 - - - +
246B GLU* 1.3 76.4 - - - +
248B ILE* 1.3 56.7 + - - +
250B GLN* 3.1 7.9 + - - +
251B LEU* 2.9 26.5 + - - +
273B THR 3.2 26.9 - - - +
274B ASN* 3.2 17.7 + - - +
275B LEU* 4.1 11.7 - - + +
276B ARG* 3.5 12.3 - - - +
279B GLU* 2.9 38.0 + - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER* 2.8 34.9 + - - +
245B ALA* 3.7 8.3 - - - +
247B ARG* 1.3 74.8 - - - +
249B ARG* 1.3 66.5 + - + +
251B LEU* 3.2 9.0 + - - +
252B LYS* 3.1 35.4 + - - +
275B LEU* 5.5 1.3 - - + -
279B GLU* 4.0 25.4 - - + +
282B LYS* 3.9 40.4 - - + +
283B CYS* 4.1 24.5 - - + +
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASN* 4.3 11.4 + - - +
245B ALA* 3.1 36.4 + - - +
246B GLU* 2.6 41.3 + - - +
248B ILE* 1.3 77.4 - - + +
250B GLN* 1.3 62.9 + - - +
252B LYS* 3.3 13.5 + - + +
253B THR* 3.2 21.8 + - - -
403B GOL 2.8 35.5 + - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B PHE* 3.3 35.5 - - + -
212B THR* 3.8 5.1 - - - -
216B ARG* 4.3 0.6 - - - +
237B LEU* 3.4 19.8 - - + +
238B GLU* 2.9 52.3 + - - +
246B GLU* 2.9 41.4 + - - +
247B ARG* 3.1 6.4 + - - +
249B ARG* 1.3 74.1 - - - +
251B LEU* 1.3 67.1 + - - +
253B THR* 3.1 6.9 + - - -
254B VAL* 3.0 26.4 + - - +
403B GOL 3.9 7.2 - - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 4.2 14.0 - - + +
247B ARG 2.9 12.5 + - - +
248B ILE* 3.2 10.7 + - - +
250B GLN* 1.3 78.1 - - - +
252B LYS* 1.3 56.3 + - - +
254B VAL* 3.2 10.2 + - + +
255B LEU* 2.9 45.4 + - + +
273B THR* 5.9 0.2 - - + -
275B LEU* 3.8 32.3 - - + -
279B GLU 4.9 0.7 - - - +
280B VAL* 4.4 13.7 - - + -
283B CYS* 3.9 25.6 - - + -
286B LEU* 5.5 1.3 - - + -
329B PHE* 3.8 29.2 - - + -
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.1 25.0 + - + +
249B ARG* 3.5 13.9 - - + +
250B GLN 3.2 0.2 - - - -
251B LEU* 1.3 75.5 - - - +
253B THR* 1.3 58.1 + - - +
255B LEU* 3.5 5.9 + - + +
256B GLY* 2.9 26.2 + - - -
282B LYS 5.1 3.6 + - - -
283B CYS* 3.3 41.5 + - - +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.2 22.4 - - + -
208B PRO 4.8 1.3 - - - +
209B PHE* 4.0 19.3 - - + -
218B LEU* 4.8 2.9 - - + -
249B ARG 3.2 7.8 + - - -
250B GLN 3.1 9.7 + - - -
252B LYS* 1.3 76.5 - - - +
254B VAL* 1.3 62.1 + - - +
256B GLY* 3.3 2.6 + - - -
257B LYS* 3.0 22.8 + - + +
403B GOL 2.5 28.5 + - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.3 12.1 - - + -
218B LEU* 4.1 25.6 - - + -
233B MET* 3.8 8.4 - - + +
237B LEU* 4.4 9.0 - - + -
250B GLN 3.0 20.5 + - - +
251B LEU* 3.2 13.9 + - + +
253B THR* 1.3 73.3 - - - +
255B LEU* 1.3 66.4 + - - +
257B LYS* 3.1 5.0 + - - +
258B MET* 3.0 30.2 + - - +
269B PHE* 3.7 38.8 - - + -
329B PHE* 5.0 5.4 - - + -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 2.9 44.5 + - + +
252B LYS* 4.0 5.4 - - + +
254B VAL* 1.3 77.5 - - + +
256B GLY* 1.3 62.9 + - - +
258B MET* 3.3 23.2 + - - +
259B GLN* 3.3 20.9 + - - +
283B CYS* 4.6 11.7 - - - -
285B GLY 4.8 6.3 - - - +
286B LEU* 3.9 26.9 - - + -
287B PRO* 4.1 24.5 - - + -
290B VAL* 4.1 17.3 - - + -
329B PHE* 4.6 4.9 - - + -
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Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LYS 2.9 18.0 + - - -
253B THR* 3.7 2.2 - - - -
255B LEU* 1.3 77.1 - - - +
257B LYS* 1.3 61.4 + - - +
259B GLN* 3.2 20.3 + - - +
260B GLU* 3.6 15.8 + - - +
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLU* 2.8 34.1 + - - -
207B ILE* 3.4 28.4 - - + +
218B LEU* 4.0 16.4 - - + -
220B CYS* 4.2 12.1 - - - -
231B CYS* 5.2 8.3 - - - -
233B MET* 4.1 12.6 - - + -
253B THR 3.0 14.1 + - - +
254B VAL 3.5 7.9 - - - +
256B GLY* 1.3 74.0 - - - +
258B MET* 1.3 65.4 + - - +
260B GLU* 3.0 48.2 + - + +
261B ALA* 3.9 4.0 + - - +
267B VAL* 5.5 0.2 - - - +
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Residues in contact with MET 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B MET* 3.8 18.8 - - + -
254B VAL* 3.0 21.6 + - - +
255B LEU* 3.5 24.7 - - - +
257B LYS* 1.3 76.6 - - - +
259B GLN* 1.3 57.5 + - - +
260B GLU 3.5 0.3 + - - -
261B ALA 3.9 1.2 + - - -
267B VAL* 3.8 28.6 - - + +
269B PHE* 4.2 11.4 - - - +
290B VAL* 4.2 14.8 - - + -
329B PHE* 3.7 45.3 - - + +
330B PHE* 3.9 12.3 - - - -
331B ARG* 3.0 38.4 + - + +
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Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU 3.3 14.6 - - - +
256B GLY* 3.2 11.2 + - - +
257B LYS 3.1 0.6 - - - -
258B MET* 1.3 78.7 - - - +
260B GLU* 1.3 61.2 + - - +
261B ALA 3.4 2.2 + - - +
287B PRO* 3.4 25.2 - - + +
289B ASN* 2.7 44.5 + - - -
290B VAL* 3.6 9.4 - - - +
331B ARG* 3.6 11.2 + - - +
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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