Contacts of the strand formed by residues 227 - 238 (chain B) in PDB entry 3HN3
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 TYR 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 4.1 3.1 - - - +
118B ARG* 3.4 47.1 + - - -
223B THR* 3.7 13.2 - - + +
224B PRO 3.6 15.0 - - - +
225B THR 3.5 19.5 - - - -
226B THR* 1.3 76.3 - - - +
228B ILE* 1.3 72.4 + - - +
229B ASP* 3.3 30.4 + - + -
250B VAL* 3.4 3.8 - - - -
251B LYS* 3.0 54.6 + - + +
252B GLY 5.0 0.4 - - - -
307B LEU* 3.8 8.5 - - - -
318B ASP* 3.3 13.0 - - - +
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Residues in contact with ILE 228 (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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28B LEU* 4.2 10.8 - - + +
36B ARG* 2.9 22.2 + - - +
227B TYR* 1.3 72.7 - - - +
229B ASP* 1.3 60.5 + - - +
230B ASP 4.1 1.3 - - - +
231B ILE* 4.0 32.1 - - + -
248B ILE* 4.0 15.5 - - + -
249B SER 3.8 3.6 - - - -
250B VAL* 4.7 2.2 - - + +
258B LEU* 4.8 3.8 - - + -
305B VAL* 3.5 41.1 - - + +
307B LEU* 4.0 15.7 - - + -
318B ASP* 2.7 33.1 + - - +
320B TYR* 3.9 15.9 - - + +
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Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY* 3.5 1.6 - - - -
26B GLY* 2.7 47.0 + - - +
28B LEU* 3.9 11.8 + - - +
118B ARG* 5.1 1.6 + - - -
150B GLU* 5.5 2.3 - - - +
227B TYR* 3.3 25.3 + - + -
228B ILE* 1.3 73.5 - - - +
230B ASP* 1.3 55.5 + - - +
249B SER* 2.7 23.5 + - - +
251B LYS* 3.1 44.2 + - + -
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Residues in contact with ASP 230 (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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25B GLY 4.7 3.0 - - - +
26B GLY* 3.7 22.8 + - - +
27B MET 4.8 1.4 + - - -
28B LEU* 4.2 8.8 - - - +
228B ILE* 3.7 0.7 - - - +
229B ASP* 1.3 79.2 - - - +
231B ILE* 1.3 77.8 + - - +
232B THR* 4.5 2.0 + - - -
247B GLN 4.5 0.4 - - - -
248B ILE* 3.4 3.3 - - - +
249B SER* 2.9 43.5 + - - +
435B ARG* 5.4 2.7 - - - +
438B LYS* 2.7 35.2 + - - -
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Residues in contact with ILE 231 (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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28B LEU* 4.0 11.5 - - + +
228B ILE* 4.0 16.4 - - + -
230B ASP* 1.3 91.3 + - - +
232B THR* 1.3 65.6 + - - +
233B VAL* 3.8 12.8 - - + -
246B TYR* 5.4 0.7 - - + -
247B GLN 3.4 8.1 - - - +
248B ILE* 4.5 12.8 - - + -
303B LEU* 4.3 9.0 - - + -
305B VAL* 3.9 20.6 - - + -
320B TYR* 3.7 32.3 - - + -
322B LEU* 3.6 29.6 - - + -
438B LYS* 3.4 2.9 - - - -
439B ASN* 2.9 20.5 + - - -
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Residues in contact with THR 232 (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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230B ASP* 4.4 2.6 + - - -
231B ILE* 1.3 71.6 - - - +
233B VAL* 1.3 67.7 + - - +
234B THR* 4.3 9.8 + - + +
245B ASN 3.7 1.0 - - - +
246B TYR* 3.5 3.5 - - - -
247B GLN* 2.8 47.4 + - + +
438B LYS* 3.0 37.2 + - + -
439B ASN* 3.6 3.6 - - - +
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Residues in contact with VAL 233 (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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231B ILE* 3.8 4.0 - - + -
232B THR* 1.3 78.6 - - - +
234B THR* 1.3 74.6 + - - +
235B THR* 4.0 11.2 - - + -
244B VAL* 3.6 26.7 - - + -
245B ASN 3.2 7.2 - - - +
246B TYR* 4.7 2.0 - - + -
303B LEU* 3.6 31.4 - - + -
322B LEU* 3.8 19.5 - - + -
324B VAL* 4.3 12.1 - - + -
438B LYS 4.4 7.8 - - - +
439B ASN* 2.9 22.2 + - + +
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Residues in contact with THR 234 (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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232B THR* 4.3 12.7 + - + -
233B VAL* 1.3 80.5 - - - +
235B THR* 1.3 68.0 + - - +
244B VAL* 3.7 0.2 - - - -
245B ASN* 2.8 54.0 + - - +
474B ASP* 5.5 1.8 - - - +
476B SER* 4.7 22.0 - - - +
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Residues in contact with THR 235 (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 VAL* 4.0 8.7 - - + -
234B THR* 1.3 83.0 - - - +
236B SER* 1.3 62.6 + - - +
243B LEU 3.2 10.3 - - - +
244B VAL* 4.4 2.9 - - + -
245B ASN* 4.8 1.3 - - - +
324B VAL* 4.0 21.3 - - + -
325B GLY 3.6 15.8 + - - +
326B ILE* 3.9 17.3 - - + -
327B ARG* 2.9 40.0 + - - +
328B THR* 3.9 4.3 - - - +
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Residues in contact with SER 236 (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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235B THR* 1.3 74.8 - - - +
237B VAL* 1.3 70.1 + - - +
242B GLY* 3.6 3.8 - - - -
243B LEU* 2.9 52.2 + - - +
245B ASN* 4.8 7.8 + - - +
279B GLN* 5.3 0.5 + - - -
326B ILE* 3.9 3.3 - - - +
328B THR* 3.9 11.4 - - - -
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Residues in contact with VAL 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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236B SER* 1.3 84.8 + - - +
238B GLU* 1.3 64.0 + - - +
239B GLN 3.4 22.7 - - - +
241B SER 3.5 10.5 - - - +
243B LEU* 5.0 1.2 - - - +
285B VAL* 5.2 1.3 - - + -
287B LEU* 3.6 41.3 - - + -
326B ILE* 4.6 3.8 - - + -
327B ARG* 5.4 0.9 - - - -
328B THR* 4.2 17.5 - - + +
339B ASN* 5.1 4.9 - - + +
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Residues in contact with GLU 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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237B VAL* 1.3 72.8 - - - +
239B GLN* 1.3 76.4 + - + +
241B SER* 2.8 46.0 + - - +
243B LEU* 3.9 30.8 - - + +
281B LYS* 4.9 13.7 + - - +
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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
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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