Contacts of the strand formed by residues 227 - 238 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ARG* 4.1 2.7 - - - +
118E ARG* 3.2 49.0 + - - -
223E THR* 3.7 13.2 - - + +
224E PRO 3.6 21.1 - - - +
225E THR 3.6 12.6 - - - -
226E THR* 1.3 76.1 - - - +
228E ILE* 1.3 73.8 + - - +
229E ASP* 3.3 29.6 + - + -
250E VAL* 3.3 4.2 - - - +
251E LYS* 2.9 54.9 + - + +
252E GLY* 5.0 0.7 - - - -
307E LEU* 3.8 8.7 - - - -
318E ASP* 3.3 13.2 - - - +
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Residues in contact with ILE 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 3.9 14.1 - - + +
36E ARG* 3.0 18.5 + - - +
227E TYR* 1.3 73.2 - - - +
229E ASP* 1.3 59.6 + - - +
230E ASP 4.4 1.1 - - - +
231E ILE* 4.0 30.1 - - + -
248E ILE* 4.2 11.7 - - + -
249E SER 3.9 3.6 - - - -
250E VAL* 4.7 2.5 - - + -
258E LEU* 4.7 4.9 - - + -
305E VAL* 3.6 39.0 - - + +
307E LEU* 4.1 15.7 - - + -
318E ASP* 2.8 31.4 + - - +
320E TYR* 3.7 20.0 - - + +
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Residues in contact with ASP 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLY* 3.5 10.0 - - - -
26E GLY* 2.8 43.4 + - - +
28E LEU* 3.7 11.0 + - - +
118E ARG* 5.2 1.2 + - - -
150E GLU* 5.5 3.1 - - - +
227E TYR* 3.3 28.3 + - + -
228E ILE* 1.3 74.7 - - - +
230E ASP* 1.3 58.2 + - - +
249E SER* 2.8 21.6 + - - +
251E LYS* 3.8 29.0 - - + +
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Residues in contact with ASP 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLY 4.4 4.0 - - - +
26E GLY* 3.7 25.3 + - - +
27E MET 4.8 1.2 + - - -
28E LEU* 4.0 8.7 - - - +
228E ILE 3.7 0.8 - - - -
229E ASP* 1.3 81.2 - - - +
231E ILE* 1.3 74.2 + - - +
232E THR* 5.0 0.4 - - - -
247E GLN 4.5 0.2 - - - -
248E ILE* 3.4 4.9 - - - +
249E SER* 2.9 42.4 + - - +
435E ARG* 5.2 3.3 - - - +
438E LYS* 2.8 33.3 + - - -
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Residues in contact with ILE 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 3.9 11.0 - - + +
228E ILE* 4.0 17.3 - - + -
230E ASP* 1.3 82.6 + - - +
232E THR* 1.3 66.6 + - - +
233E VAL* 4.0 14.1 - - + -
246E TYR* 5.3 0.2 - - + -
247E GLN 3.3 11.2 - - - +
248E ILE* 4.4 11.2 - - + -
303E LEU* 4.2 9.6 - - + -
305E VAL* 4.0 20.4 - - + -
320E TYR* 3.6 33.7 - - + -
322E LEU* 3.9 29.2 - - + -
438E LYS* 3.2 12.0 + - - -
439E ASN* 2.9 20.2 + - - -
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Residues in contact with THR 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ASP* 5.0 1.0 - - - -
231E ILE* 1.3 71.6 - - - +
233E VAL* 1.3 71.5 + - - +
234E THR* 4.7 10.1 - - + -
245E ASN 3.6 0.5 - - - +
246E TYR* 3.4 4.7 - - - -
247E GLN* 2.8 58.8 + - - +
438E LYS* 2.8 37.0 + - + +
439E ASN* 3.6 4.0 - - - +
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Residues in contact with VAL 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E ILE* 4.0 8.7 - - + -
232E THR* 1.3 80.4 - - - +
234E THR* 1.3 72.6 + - - +
235E THR* 3.9 16.4 - - + -
244E VAL* 3.7 21.1 - - + -
245E ASN 3.2 11.0 - - - +
246E TYR* 4.4 3.6 - - + -
303E LEU* 3.8 28.7 - - + -
322E LEU* 4.2 11.0 - - + -
324E VAL* 4.3 14.1 - - + -
438E LYS 4.4 8.0 - - - +
439E ASN* 2.9 21.3 + - + +
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Residues in contact with THR 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E THR* 4.3 11.9 - - + -
233E VAL* 1.3 79.3 - - - +
235E THR* 1.3 65.8 + - - +
245E ASN* 2.8 54.7 + - - +
474E ASP* 5.2 3.1 - - - +
475E PRO* 5.4 9.6 - - + -
476E SER* 4.3 25.6 - - - +
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Residues in contact with THR 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E VAL* 3.9 16.8 - - + -
234E THR* 1.3 82.4 - - - +
236E SER* 1.3 62.2 - - - +
243E LEU 3.2 11.7 - - - +
244E VAL* 4.2 3.4 - - + -
245E ASN* 4.7 1.3 - - - -
324E VAL* 3.9 21.1 - - + -
325E GLY 3.5 8.5 + - - +
326E ILE* 3.9 17.0 - - + -
327E ARG* 3.0 40.1 + - - +
328E THR* 3.7 5.4 - - - +
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Residues in contact with SER 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E THR* 1.3 75.4 - - - +
237E VAL* 1.3 67.3 + - - +
242E GLY* 3.7 3.6 - - - -
243E LEU* 2.9 52.1 + - - +
245E ASN* 4.7 4.7 + - - -
279E GLN* 5.5 0.2 + - - -
326E ILE* 3.9 4.4 - - - +
328E THR* 3.6 14.1 - - - -
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Residues in contact with VAL 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E SER* 1.3 84.6 + - - +
238E GLU* 1.3 62.6 + - - +
239E GLN 3.5 18.2 - - - +
240E ASP* 5.1 0.4 - - - -
241E SER 3.2 19.5 - - - +
243E LEU* 4.9 2.3 - - - +
285E VAL* 5.0 1.3 - - + -
287E LEU* 3.9 37.7 - - + -
326E ILE* 4.8 2.5 - - + -
327E ARG* 5.4 0.4 - - - -
328E THR* 4.2 19.5 - - + +
339E ASN* 5.0 5.6 - - - +
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Residues in contact with GLU 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E VAL* 1.3 74.1 - - - +
239E GLN* 1.3 92.9 + - - +
241E SER* 2.8 28.4 + - - -
243E LEU* 4.1 31.4 - - + +
281E LYS* 3.9 23.2 + - - +
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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
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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