Contacts of the helix formed by residues 235 - 249 (chain B) in PDB entry 3HS3
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 ASN 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASN* 5.7 3.2 + - - +
179B TRP* 3.6 27.4 - - + -
233B THR* 3.4 6.3 + - - +
234B VAL* 1.3 83.0 - - - +
236B ASP* 1.3 59.3 + - - +
237B LEU* 2.9 16.7 + - - +
238B TYR* 2.8 36.8 + - - +
239B ALA* 3.0 22.9 + - - +
261B GLY* 4.1 0.7 - - - -
262B TYR 3.2 24.2 - - - +
263B ASP* 3.5 17.4 + - - +
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Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASN* 1.3 73.6 - - - +
237B LEU* 1.3 60.2 + - - +
239B ALA* 3.5 6.8 - - - +
240B ALA* 2.8 29.6 + - - +
261B GLY* 3.4 4.3 - - - -
262B TYR 2.8 15.5 + - - -
264B ASN 2.7 28.8 + - - -
265B ASN* 2.7 29.3 + - + +
267B LEU* 3.8 8.8 - - + +
268B CYS* 3.0 22.9 - - - -
275B ILE* 4.0 4.3 - - + +
277B THR* 2.8 21.8 + - - -
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Residues in contact with LEU 237 (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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72A ARG* 4.4 13.2 - - - +
266A ILE* 3.9 27.4 - - + -
270A TYR* 4.2 7.6 + - + +
71B ASN* 4.1 10.3 - - - +
214B PRO* 4.7 9.9 - - + -
235B ASN* 2.9 14.4 + - - +
236B ASP* 1.3 72.3 - - - +
238B TYR* 1.3 70.8 + - + +
240B ALA* 3.3 7.7 + - - +
241B GLU* 3.0 27.7 + - - +
265B ASN* 3.5 30.7 - - - +
267B LEU* 4.2 16.2 - - + -
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Residues in contact with TYR 238 (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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179B TRP* 3.5 4.7 + + - -
209B THR* 4.1 4.3 - - + -
210B PRO 2.7 24.0 + - - -
211B GLU 3.2 21.5 + - - -
213B ASN 3.5 6.8 + - - -
214B PRO* 3.4 37.4 - - + +
217B SER* 3.1 37.2 - - - -
218B ALA* 5.0 0.5 - - - +
233B THR* 3.4 21.1 - - - +
234B VAL* 3.2 26.7 - - + -
235B ASN* 2.8 36.3 + - - +
237B LEU* 1.3 79.0 - - + +
239B ALA* 1.3 61.9 + - - +
241B GLU* 3.2 4.6 + - - +
242B ILE* 3.0 25.9 + - + +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR* 3.5 14.5 - - + +
235B ASN 3.0 14.5 + - - +
236B ASP* 3.5 13.2 - - - +
237B LEU 3.2 0.4 - - - -
238B TYR* 1.3 76.6 - - - +
240B ALA* 1.3 62.5 + - - +
242B ILE* 3.1 6.4 + - - +
243B ILE* 3.0 26.0 + - - +
259B LEU* 3.4 22.9 - - + +
261B GLY* 4.2 4.3 - - - -
275B ILE* 4.0 18.6 - - + -
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Residues in contact with ALA 240 (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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270A TYR* 3.6 35.8 - - + +
236B ASP 2.8 17.6 + - - +
237B LEU 3.6 5.8 - - - +
238B TYR 3.2 0.2 - - - -
239B ALA* 1.3 76.3 - - - +
241B GLU* 1.3 57.7 + - - +
243B ILE* 3.3 8.5 + - - +
244B LYS* 3.0 28.1 + - - +
267B LEU* 4.1 16.6 - - + -
271B THR* 4.5 3.4 - - + -
275B ILE* 4.2 7.4 - - + -
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Residues in contact with GLU 241 (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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270A TYR* 2.5 37.6 + - - +
214B PRO* 3.7 33.0 - - + +
215B TYR* 4.0 28.0 - - - -
218B ALA* 3.7 5.9 - - + +
237B LEU 3.0 13.0 + - - +
238B TYR 3.2 9.2 + - - +
240B ALA* 1.3 73.6 - - - +
242B ILE* 1.3 61.1 + - - +
244B LYS* 3.3 13.8 + - - +
245B GLU* 2.9 30.1 + - - +
248B ARG* 4.9 4.2 + - - -
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLN* 3.7 23.6 - - - +
217B SER 5.3 0.4 - - - -
218B ALA* 4.0 22.7 - - - -
221B ALA* 3.8 10.1 - - + -
222B LEU* 3.7 16.4 - - + +
231B ILE* 4.2 6.7 - - + -
233B THR* 4.1 11.0 - - + +
238B TYR* 3.0 17.3 + - + +
239B ALA* 3.1 8.0 + - - +
241B GLU* 1.3 74.9 - - - +
243B ILE* 1.3 59.8 + - - +
245B GLU 3.3 0.2 + - - -
246B ALA* 2.8 29.8 + - - +
253B ILE* 4.2 4.5 - - + -
257B PHE* 4.0 25.4 - - + -
259B LEU* 4.0 22.0 - - + -
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Residues in contact with ILE 243 (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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270A TYR 5.7 3.1 - - - +
272A SER* 6.1 0.4 - - - +
239B ALA 3.0 14.5 + - - +
240B ALA* 3.6 8.1 - - - +
241B GLU 3.3 0.2 - - - -
242B ILE* 1.3 75.2 - - - +
244B LYS* 1.3 58.4 + - - +
246B ALA* 3.3 2.9 + - - +
247B LYS* 3.0 28.8 + - + +
253B ILE* 3.9 15.3 - - + -
259B LEU* 3.7 15.7 - - + -
271B THR* 4.0 8.3 - - + +
272B SER 3.4 25.4 - - - +
273B PRO* 3.6 33.2 - - + +
275B ILE* 3.7 28.3 - - + -
317B SER* 5.6 0.4 - - - -
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Residues in contact with LYS 244 (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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269A GLY* 2.8 34.5 + - - +
270A TYR* 4.5 13.9 - - + -
274A THR* 4.0 14.5 - - - +
240B ALA 3.0 16.8 + - - +
241B GLU* 3.6 13.0 - - - +
242B ILE 3.2 0.2 - - - -
243B ILE* 1.3 79.1 - - - +
245B GLU* 1.3 60.4 + - - +
247B LYS* 3.3 10.0 + - + +
248B ARG* 3.2 55.5 + - + +
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Residues in contact with GLU 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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215B TYR* 4.3 2.6 + - - -
218B ALA* 4.3 4.5 - - + +
219B GLN* 2.9 40.3 + - - +
222B LEU* 3.1 32.0 - - + +
241B GLU 2.9 17.2 + - - +
242B ILE 3.9 2.5 - - - +
244B LYS* 1.3 73.2 - - - +
246B ALA* 1.3 66.0 + - - +
248B ARG* 2.7 54.7 + - - +
249B ARG* 2.9 35.5 + - - +
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Residues in contact with ALA 246 (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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222B LEU* 3.1 15.1 - - + +
242B ILE 2.8 18.6 + - - +
243B ILE 3.5 5.6 - - - +
245B GLU* 1.3 77.8 - - - +
247B LYS* 1.3 59.8 + - - +
249B ARG 3.2 6.9 + - - -
251B LEU* 2.8 46.8 + - + +
253B ILE* 4.1 20.2 - - + -
257B PHE* 4.4 7.4 - - + -
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Residues in contact with LYS 247 (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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272A SER* 4.4 24.8 + - - +
243B ILE* 3.0 15.4 + - + +
244B LYS* 3.5 12.1 - - + +
245B GLU 3.2 0.2 - - - -
246B ALA* 1.3 73.8 - - - +
248B ARG* 1.3 66.5 + - + +
250B ASN* 3.1 13.1 + - - +
251B LEU 4.1 6.5 + - - +
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Residues in contact with ARG 248 (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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215B TYR* 4.6 14.6 - - - -
219B GLN* 4.6 1.8 + - - -
241B GLU* 4.9 5.3 + - - -
244B LYS* 3.2 46.2 + - + +
245B GLU* 2.7 62.2 + - - +
247B LYS* 1.3 79.0 - - + +
249B ARG* 1.3 60.2 + - + +
250B ASN 3.4 0.8 + - - -
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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
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219B GLN* 3.1 32.1 + - - +
222B LEU* 3.4 39.2 + - - +
223B ASN* 2.8 34.3 + - - +
245B GLU* 2.9 25.9 + - - +
246B ALA 3.2 4.0 + - - +
247B LYS 3.1 0.8 - - - -
248B ARG* 1.3 80.8 - - - +
250B ASN* 1.3 68.7 + - - +
251B LEU* 3.3 22.4 + - + +
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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