Contacts of the helix formed by residues 242 - 259 (chain B) in PDB entry 5HQ0
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 MET 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B VAL* 3.8 10.3 - - + -
239B PRO* 3.1 28.6 + - + +
241B LYS* 1.3 97.2 - - + +
243B LEU* 1.3 64.1 + - - +
244B GLN 3.3 2.5 - - - -
245B LEU* 3.1 29.9 + - - +
246B VAL* 3.0 23.0 + - - +
276B TYR* 3.9 11.4 - - + -
280B GLN* 4.5 13.2 - - - +
284B MET* 4.7 12.1 - - + -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 3.9 21.5 - - + -
200B MET* 4.0 34.8 - - + +
201B ARG* 4.5 2.7 - - + +
204B LEU* 3.6 26.8 - - + +
229B ILE* 5.5 1.6 - - + -
233B MET* 3.9 33.7 - - + -
238B VAL* 3.7 8.7 - - + -
239B PRO 3.4 7.5 + - - +
240B LYS 3.3 14.8 + - - +
242B MET* 1.3 77.6 - - - +
244B GLN* 1.3 63.7 + - - +
246B VAL* 3.2 6.8 + - + +
247B GLY 3.0 18.0 + - - -
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.8 12.8 - - + +
207B TRP* 3.3 50.0 - - + +
240B LYS 4.7 1.0 + - - -
241B LYS 4.7 0.2 + - - -
242B MET 3.3 0.4 - - - -
243B LEU* 1.3 80.4 - - - +
245B LEU* 1.3 61.1 + - - +
247B GLY* 3.3 1.4 + - - -
248B VAL* 3.0 23.2 + - - +
272B THR* 4.0 17.0 + - + +
275B THR* 4.3 12.1 + - - +
276B TYR* 3.4 25.6 + - + +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B MET* 3.1 28.6 + - - +
244B GLN* 1.3 74.9 - - - +
246B VAL* 1.3 60.0 + - - +
248B VAL* 3.3 6.4 - - + +
249B THR* 2.7 43.7 + - - +
276B TYR* 3.3 42.2 + - + -
280B GLN* 3.8 22.7 - - + +
281B ILE* 3.5 37.2 - - + +
284B MET* 4.1 16.6 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 4.5 22.7 - - + +
232B PHE* 4.1 23.1 - - + -
233B MET* 5.6 1.3 - - - -
238B VAL* 3.8 27.8 - - + -
242B MET 3.0 16.1 + - - +
243B LEU* 3.6 12.8 - - + +
245B LEU* 1.3 76.9 - - - +
247B GLY* 1.3 56.5 + - - +
249B THR* 3.5 1.6 + - - -
250B ALA* 2.8 28.3 + - + +
284B MET* 3.6 33.9 - - + -
288B ILE* 4.2 6.3 - - + +
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.1 6.7 - - - +
208B LEU* 3.8 17.8 - - - +
229B ILE* 3.8 20.9 - - - -
243B LEU 3.0 13.5 + - - -
244B GLN 3.3 2.9 + - - -
245B LEU 3.2 0.2 - - - -
246B VAL* 1.3 73.3 - - - +
248B VAL* 1.3 65.0 + - - +
250B ALA* 3.1 5.2 + - - +
251B MET* 2.9 22.3 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TRP* 3.4 37.0 - - + -
208B LEU* 4.2 3.7 - - + +
211B VAL* 5.8 1.1 - - + -
244B GLN 3.0 17.3 + - - +
245B LEU* 3.3 25.1 - - + +
247B GLY* 1.3 71.2 - - - -
249B THR* 1.3 64.4 + - - +
251B MET* 3.2 8.5 + - - +
252B PHE* 2.8 29.5 + - - +
268B PHE* 4.1 20.8 - - + +
271B VAL* 4.5 3.8 - - + -
272B THR* 3.5 22.0 - - + -
281B ILE* 4.4 11.7 - - + -
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 2.7 38.7 + - - +
246B VAL 3.8 1.6 - - - -
248B VAL* 1.3 74.9 - - - +
250B ALA* 1.4 57.0 + - - +
252B PHE* 3.2 7.8 + - + +
253B ILE* 2.9 35.9 + - + +
281B ILE* 3.6 17.2 - - + +
284B MET* 3.6 17.6 - - + +
285B GLU* 3.3 42.0 - - + +
288B ILE* 4.0 5.8 - - + -
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 3.7 13.9 - - + +
228B ILE* 3.9 23.5 - - + +
229B ILE* 3.5 23.8 - - + -
246B VAL 2.8 14.9 + - - +
247B GLY 3.3 8.5 - - - +
249B THR* 1.4 76.6 - - - +
251B MET* 1.3 57.0 + - - +
253B ILE* 3.4 7.0 + - - +
254B ALA* 2.9 29.6 + - - +
288B ILE* 4.6 2.8 - - + +
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Residues in contact with MET 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 3.4 23.1 - - + +
211B VAL* 3.6 30.1 - - - -
212B GLN* 4.3 4.3 - - + -
217B LEU* 3.8 24.0 - - + -
221B THR* 4.9 2.0 - - + -
222B MET* 3.3 41.3 - - + -
225B THR* 3.4 20.6 - - + +
247B GLY 2.9 12.3 + - - +
248B VAL* 3.6 8.5 - - - +
250B ALA* 1.3 74.4 - - - +
252B PHE* 1.3 53.9 + - - +
254B ALA* 3.7 0.3 - - - +
255B SER* 2.7 42.4 + - - -
268B PHE* 3.9 11.0 - - + -
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Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.4 26.0 - - - -
43A GLY* 5.3 0.2 - - - -
248B VAL 2.8 16.2 + - - +
249B THR* 3.4 8.3 - - - +
251B MET* 1.3 74.5 - - - +
253B ILE* 1.3 65.2 + - + +
255B SER* 3.6 1.5 - - - -
256B LYS* 3.1 51.3 + - + +
263B PRO 4.0 9.9 - - - -
265B ILE* 3.8 42.2 - - + -
268B PHE* 3.5 33.8 - + + -
281B ILE* 3.8 19.5 - - + -
282B ARG* 5.9 0.4 - - - -
285B GLU* 3.9 17.3 - - + -
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.6 6.1 - - + +
228B ILE* 4.1 10.3 - - + -
249B THR* 2.9 31.3 + - + +
250B ALA* 3.7 5.8 - - - +
252B PHE* 1.3 76.0 - - + +
254B ALA* 1.3 60.1 + - - +
256B LYS* 3.2 6.5 + - - +
257B TYR* 2.9 27.0 + - - +
285B GLU* 3.8 35.7 - - + +
288B ILE* 3.8 34.8 - - + -
289B LEU* 4.0 13.9 - - + -
296B LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 254 (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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221B THR* 3.5 17.5 - - + +
224B MET* 3.9 21.5 - - + -
225B THR* 3.5 22.0 - - - +
228B ILE* 4.3 2.7 - - + +
250B ALA 2.9 18.2 + - - +
251B MET 3.7 1.8 - - - +
253B ILE* 1.3 76.8 - - - +
255B SER* 1.3 56.2 + - - +
257B TYR* 3.2 6.4 + - - +
258B GLU* 2.8 34.7 + - - +
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Residues in contact with SER 255 (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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217B LEU* 3.7 15.6 - - - +
221B THR* 3.6 16.6 - - - +
251B MET 2.7 27.5 + - - -
252B PHE* 3.6 6.3 - - - -
254B ALA* 1.3 70.9 - - - +
256B LYS* 1.3 62.3 + - - +
259B GLU* 2.9 38.5 + - - +
262B PRO* 3.7 6.5 - - - +
263B PRO* 4.0 21.8 - - - -
268B PHE* 3.9 6.0 - - - -
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Residues in contact with LYS 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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42A GLU* 2.8 25.9 + - + +
44A VAL 2.6 29.1 + - - +
45A PRO* 5.2 0.4 - - + -
46A SER* 3.3 30.1 - - - +
49A ILE* 4.0 8.7 - - + -
50A ARG* 3.0 27.0 + - - -
252B PHE* 3.1 39.4 + - + +
253B ILE* 3.7 5.4 - - - +
255B SER* 1.3 76.9 - - - +
257B TYR* 1.3 56.8 + - - +
262B PRO* 4.1 19.7 - - + +
285B GLU* 2.7 30.8 + - - -
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Residues in contact with TYR 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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49A ILE* 3.8 20.6 - - + +
50A ARG* 3.3 34.8 + - + +
53A SER* 3.1 35.1 + - - -
155A ILE* 3.7 11.4 - - - +
224B MET* 3.8 16.6 - - + -
253B ILE 2.9 15.9 + - - +
254B ALA* 3.5 5.4 - - - +
256B LYS* 1.3 78.3 - - - +
258B GLU* 1.3 84.8 + - + +
296B LEU* 3.8 18.8 - - + -
297B GLY* 2.5 31.0 + - - -
298B ARG* 3.0 30.5 + - - -
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.1 1.8 - - - -
155A ILE* 3.4 37.6 - - - +
218B LEU* 4.3 10.9 - - + +
220B GLU* 4.0 10.6 - - + +
221B THR* 3.3 34.5 - - - +
224B MET* 3.8 6.8 - - + +
254B ALA 2.8 19.6 + - - +
257B TYR* 1.3 100.9 - - + +
259B GLU* 1.3 61.9 + - - +
260B MET 4.1 0.7 + - - -
298B ARG* 5.3 2.8 + - - -
299B PRO* 3.4 36.7 - - - +
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 2.7 26.4 + - - -
155A ILE* 6.1 0.2 - - - -
216B ARG 4.5 3.1 - - - +
217B LEU* 3.5 24.2 - - + +
218B LEU* 2.8 41.4 + - - +
221B THR* 2.6 27.2 + - - +
255B SER* 2.9 33.0 + - - +
258B GLU* 1.3 74.1 - - - +
260B MET* 1.3 62.5 + - - +
261B TYR 4.1 4.0 + - - +
262B PRO* 4.0 19.6 - - + +
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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
------------------------------------------------------------
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