Contacts of the strand formed by residues 227 - 238 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ARG* 4.1 2.0 - - - +
118D ARG* 3.4 47.8 + - - -
223D THR* 3.6 14.6 - - + +
224D PRO* 3.4 21.5 - - + +
225D THR 3.6 13.5 - - - -
226D THR* 1.3 74.5 - - - +
228D ILE* 1.3 76.7 + - - +
229D ASP* 3.2 27.6 + - + -
250D VAL* 3.5 4.3 - - - +
251D LYS* 3.0 69.6 + - + +
252D GLY* 4.8 0.4 - - - -
307D LEU* 3.8 8.1 - - - -
318D ASP* 3.3 12.3 - - - +
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Residues in contact with ILE 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 4.1 11.3 - - + +
36D ARG* 2.9 23.2 + - - +
227D TYR* 1.3 73.7 - - - +
229D ASP* 1.3 59.3 + - - +
230D ASP 4.3 1.3 - - - +
231D ILE* 3.9 31.9 - - + -
248D ILE* 4.1 13.0 - - + -
249D SER 3.9 3.4 - - - -
250D VAL* 4.9 1.6 - - + +
258D LEU* 4.7 4.0 - - + -
305D VAL* 3.4 42.4 - - + +
307D LEU* 4.1 16.6 - - + -
318D ASP* 2.7 29.7 + - - +
320D TYR* 3.8 17.5 - - + +
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Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLY* 3.5 9.8 - - - -
26D GLY* 2.8 47.3 + - - +
27D MET 4.0 0.2 + - - -
28D LEU* 4.0 9.7 + - - +
118D ARG* 5.0 2.1 + - - -
150D GLU* 5.4 3.5 - - - +
227D TYR* 3.2 29.1 + - + -
228D ILE* 1.3 73.9 - - - +
230D ASP* 1.3 57.0 + - - +
249D SER* 2.8 23.4 + - - +
251D LYS* 3.7 29.6 - - + +
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Residues in contact with ASP 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLY 4.5 3.1 - - - +
26D GLY* 3.7 25.1 + - - +
27D MET 4.8 1.2 + - - -
28D LEU* 4.1 8.9 - - - +
228D ILE* 3.7 1.1 - - - +
229D ASP* 1.3 81.7 - - - +
231D ILE* 1.3 79.9 + - - +
232D THR* 4.7 0.9 - - - -
247D GLN 4.5 0.9 - - - -
248D ILE* 3.5 3.3 - - - +
249D SER* 2.9 42.4 + - - +
435D ARG* 5.2 3.4 - - - +
438D LYS* 2.9 31.4 + - - -
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Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 3.9 14.5 - - + +
228D ILE* 3.9 17.3 - - + -
230D ASP* 1.3 88.2 + - - +
232D THR* 1.3 69.4 + - - +
233D VAL* 4.1 11.9 - - + -
246D TYR* 5.4 0.2 - - + -
247D GLN 3.4 9.6 - - - +
248D ILE* 4.6 12.1 - - + -
303D LEU* 4.3 9.6 - - + -
305D VAL* 3.8 20.9 - - + -
320D TYR* 3.7 31.9 - - + -
322D LEU* 3.7 26.9 - - + -
438D LYS* 3.4 1.6 - - - -
439D ASN* 2.9 21.2 + - - -
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Residues in contact with THR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ASP* 4.3 1.2 + - - -
231D ILE* 1.3 72.2 - - - +
233D VAL* 1.3 70.2 + - - +
234D THR* 4.9 9.0 - - + -
245D ASN 3.7 0.5 - - - +
246D TYR* 3.3 4.9 - - - -
247D GLN* 2.9 58.5 + - - +
438D LYS* 2.5 39.8 + - + +
439D ASN* 3.6 3.4 - - - +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ILE* 4.1 2.2 - - + -
232D THR* 1.3 79.1 - - - +
234D THR* 1.3 76.4 + - - +
235D THR* 4.0 11.2 - - + -
244D VAL* 3.8 21.1 - - + -
245D ASN 3.2 11.2 - - - +
246D TYR* 4.4 3.4 - - + -
303D LEU* 3.9 28.9 - - + -
322D LEU* 3.9 18.4 - - + -
324D VAL* 4.3 12.8 - - + -
438D LYS 4.3 9.4 - - - +
439D ASN* 2.9 20.8 + - + +
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Residues in contact with THR 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D THR* 4.9 10.5 - - + -
233D VAL* 1.3 79.2 - - - +
235D THR* 1.3 67.7 + - - +
243D LEU 3.8 0.2 - - - +
245D ASN* 2.9 47.3 + - - +
474D ASP* 5.0 4.3 - - - +
475D PRO* 5.0 12.3 - - + -
476D SER* 4.4 26.7 - - - +
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D VAL* 4.0 8.5 - - + -
234D THR* 1.3 83.3 - - - +
236D SER* 1.3 62.2 - - - +
243D LEU 3.2 7.6 - - - +
244D VAL* 4.5 3.6 - - + -
324D VAL* 4.0 19.1 - - + -
325D GLY 3.5 17.2 + - - +
326D ILE* 3.7 22.2 - - + -
327D ARG* 2.8 47.8 + - - +
328D THR* 3.8 4.9 - - - +
476D SER* 6.0 0.9 - - - -
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Residues in contact with SER 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D THR* 1.3 75.5 - - - +
237D VAL* 1.3 64.4 + - - +
238D GLU* 4.9 1.4 + - - -
242D GLY* 3.8 2.9 - - - -
243D LEU* 2.9 54.4 + - - +
245D ASN* 5.4 1.4 + - - -
326D ILE* 3.9 7.3 - - - +
328D THR* 3.8 13.5 - - - -
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER* 1.3 79.4 + - - +
238D GLU* 1.3 67.7 + - - +
239D GLN 3.2 26.3 + - - +
240D ASP* 4.8 1.8 - - - -
241D SER 3.2 15.7 - - - +
242D GLY* 5.4 0.2 - - - -
243D LEU* 5.0 0.2 - - - -
285D VAL* 4.9 0.4 - - + -
287D LEU* 4.7 27.4 - - + -
326D ILE* 5.8 0.4 - - + -
328D THR* 4.3 15.6 - - + +
339D ASN* 6.1 5.4 - - - +
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Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER* 4.9 1.4 + - - -
237D VAL* 1.3 76.4 - - - +
239D GLN* 1.3 76.7 + - - +
240D ASP 2.8 0.5 + - - -
241D SER* 2.6 49.1 + - - -
243D LEU* 3.2 36.3 - - + +
281D LYS* 6.0 1.8 - - - -
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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