Contacts of the strand formed by residues 227 - 238 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 4.1 2.7 - - - +
118A ARG* 3.3 47.0 + - - -
223A THR* 3.7 13.5 - - + +
224A PRO 3.4 21.3 - - - +
225A THR 3.5 12.8 - - - -
226A THR* 1.3 75.1 - - - +
228A ILE* 1.3 73.2 + - - +
229A ASP* 3.3 27.0 + - + -
250A VAL* 3.3 2.9 - - - +
251A LYS* 3.0 60.9 + - + +
252A GLY 5.0 0.4 - - - -
307A LEU* 3.8 8.7 - - - -
318A ASP* 3.3 12.8 - - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.2 10.8 - - + +
36A ARG* 3.0 19.4 + - - +
227A TYR* 1.3 72.9 - - - +
229A ASP* 1.3 61.3 + - - +
230A ASP 4.1 1.3 - - - +
231A ILE* 3.9 32.5 - - + -
248A ILE* 4.0 13.9 - - + -
249A SER 3.7 4.3 - - - -
250A VAL* 4.6 2.2 - - + +
258A LEU* 4.6 3.8 - - + -
305A VAL* 3.6 41.3 - - + +
307A LEU* 4.1 15.3 - - + -
318A ASP* 2.7 33.0 + - - +
320A TYR* 3.9 14.6 - - + +
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY* 3.5 8.7 - - - -
26A GLY* 2.6 46.0 + - - +
28A LEU* 3.9 12.7 + - - +
118A ARG* 5.0 1.6 + - - -
150A GLU* 5.5 2.3 - - - +
227A TYR* 3.3 30.8 + - + -
228A ILE* 1.3 73.9 - - - +
230A ASP* 1.3 55.2 + - - +
249A SER* 2.7 24.3 + - - +
251A LYS* 3.6 30.6 + - + +
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Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 4.4 3.8 - - - +
26A GLY* 3.7 23.5 + - - +
27A MET 4.8 1.6 + - - -
28A LEU* 4.4 7.6 - - - +
228A ILE* 3.8 0.7 - - - +
229A ASP* 1.3 76.3 - - - +
231A ILE* 1.3 78.5 + - - +
232A THR* 4.9 0.9 - - - -
248A ILE* 3.5 3.5 - - - +
249A SER* 2.8 45.8 + - - +
435A ARG* 5.1 3.7 - - - +
438A LYS* 2.9 34.0 + - - -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.9 17.1 - - + +
228A ILE* 3.9 13.9 - - + -
230A ASP* 1.3 91.5 + - - +
232A THR* 1.3 66.2 + - - +
233A VAL* 4.1 5.4 - - + -
246A TYR* 5.4 0.2 - - + -
247A GLN 3.3 10.5 - - - +
248A ILE* 4.7 10.5 - - + -
303A LEU* 4.1 16.2 - - + -
305A VAL* 4.1 18.8 - - + -
320A TYR* 3.6 33.0 - - + -
322A LEU* 3.7 29.2 - - + -
438A LYS* 3.4 4.2 - - - -
439A ASN* 2.9 19.3 + - - -
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASP* 4.6 1.2 + - - -
231A ILE* 1.3 73.0 - - - +
233A VAL* 1.3 70.1 + - - +
234A THR* 4.7 9.6 - - + -
245A ASN 3.6 1.6 - - - +
246A TYR* 3.5 4.2 - - - +
247A GLN* 2.9 54.3 + - - +
438A LYS* 2.9 35.2 + - + +
439A ASN* 3.6 6.1 - - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ILE* 4.1 2.2 - - + -
232A THR* 1.3 79.3 - - - +
234A THR* 1.3 70.1 + - - +
235A THR* 3.9 15.7 - - + -
244A VAL* 3.8 24.9 - - + -
245A ASN 3.3 2.7 - - - -
246A TYR* 4.4 9.0 - - + -
303A LEU* 3.8 29.2 - - + -
322A LEU* 3.8 17.5 - - + -
324A VAL* 4.2 14.1 - - + -
438A LYS 4.4 8.0 - - - +
439A ASN* 2.8 22.9 + - + +
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A THR* 4.7 11.7 - - + -
233A VAL* 1.3 79.0 - - - +
235A THR* 1.3 67.1 + - - +
244A VAL* 3.8 0.5 - - - -
245A ASN* 2.9 49.5 + - - +
474A ASP* 5.3 2.9 - - - +
475A PRO* 5.3 10.1 - - + -
476A SER* 4.3 25.8 - - - +
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Residues in contact with THR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 3.9 17.3 - - + -
234A THR* 1.3 82.7 - - - +
236A SER* 1.3 63.7 + - - +
243A LEU 3.3 10.5 - - - +
244A VAL* 4.5 3.1 - - + -
245A ASN* 5.0 0.7 - - - +
324A VAL* 4.0 13.5 - - + -
325A GLY 3.5 15.5 + - - +
326A ILE* 4.0 16.6 - - + -
327A ARG* 2.8 47.4 + - - +
328A THR* 3.7 5.5 - - - +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A THR* 1.3 76.2 - - - +
237A VAL* 1.3 65.9 + - - +
242A GLY* 3.7 2.6 - - - -
243A LEU* 2.8 55.8 + - - +
245A ASN* 4.4 6.0 + - - +
279A GLN* 5.2 0.2 + - - -
326A ILE* 4.3 3.6 - - - +
328A THR* 3.7 13.0 - - - -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 1.3 84.0 - - - +
238A GLU* 1.3 70.5 + - - +
239A GLN 3.7 20.6 - - - +
241A SER 3.5 11.7 - - - +
243A LEU* 4.8 0.9 - - - -
285A VAL* 5.2 2.2 - - + -
287A LEU* 3.8 39.3 - - + -
326A ILE* 4.6 4.0 - - + -
327A ARG* 5.5 0.4 - - - -
328A THR* 4.3 19.5 - - + +
339A ASN* 5.1 4.5 - - + +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 1.3 75.9 - - - +
239A GLN* 1.3 82.0 + - - +
240A ASP 2.7 18.0 + - - -
241A SER* 2.8 30.8 + - - +
243A LEU* 3.6 32.9 - - + +
281A LYS* 5.6 8.0 - - - -
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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