Contacts of the strand formed by residues 230 - 239 (chain D) in PDB entry 3H90
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 GLY 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D THR* 5.0 4.7 - - - -
228D VAL* 3.4 9.8 - - - +
229D SER* 1.3 82.4 - - - +
231D ALA* 1.3 59.6 + - - +
249D LEU* 3.6 5.7 - - - +
250D GLU* 2.7 49.3 + - - +
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Residues in contact with ALA 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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219D ILE* 5.7 7.5 - - + +
222D VAL* 3.7 28.7 - - + -
223D THR* 4.2 17.5 - - + +
230D GLY* 1.3 75.0 - - - +
232D HIS* 1.3 64.4 + - - +
247D ILE* 3.7 14.1 - - + -
248D HIS 3.1 13.9 - - - +
249D LEU* 4.4 0.4 - - + +
250D GLU* 3.8 4.0 + - - +
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Residues in contact with HIS 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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219D ILE* 5.4 2.8 - - - +
231D ALA* 1.3 77.0 - - - +
233D ASP* 1.3 82.4 + - + +
234D LEU* 3.0 11.4 + - - +
247D ILE* 5.0 0.4 - - - -
248D HIS* 3.1 21.6 + - + -
250D GLU* 2.9 29.2 + - + +
285D ASP* 2.9 18.2 - - + -
289D VAL* 3.9 20.5 - - + +
292D ZN 1.9 37.5 - - - -
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Residues in contact with ASP 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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232D HIS* 1.3 90.8 - - + +
234D LEU* 1.3 60.2 + - - +
235D ARG* 3.0 42.0 + - - +
246D GLN 3.7 1.2 - - - +
247D ILE* 3.1 23.6 - - - -
248D HIS* 3.2 28.7 + - + +
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Residues in contact with LEU 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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72B SER* 4.8 4.3 + - - -
215D ARG* 3.7 37.5 - - + +
218D ILE* 4.4 9.6 - - + -
219D ILE* 3.7 23.1 - - + -
232D HIS 3.0 8.6 + - - +
233D ASP* 1.3 75.0 + - - +
235D ARG* 1.3 63.2 + - - +
236D THR* 3.9 19.3 + - + +
245D ILE* 4.1 11.9 - - + -
246D GLN 3.0 24.5 - - - +
247D ILE* 3.8 30.1 - - + -
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Residues in contact with ARG 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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72B SER* 3.5 39.4 + - - +
73B PHE* 3.7 26.7 - - + -
244B PHE* 4.5 2.0 - - - -
279B ASP* 2.9 42.2 + - - -
280B VAL 5.4 0.2 + - - -
281B ILE* 5.6 2.2 - - - +
233D ASP* 3.0 33.8 + - - +
234D LEU* 1.3 72.5 - - - +
236D THR* 1.3 61.3 + - - +
244D PHE 4.0 0.5 - - - +
245D ILE* 3.6 2.8 - - - -
246D GLN* 2.9 67.7 + - + +
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Residues in contact with THR 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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72B SER* 3.7 7.1 + - - -
73B PHE* 3.6 8.6 - - - -
209D ALA* 3.4 20.3 + - - +
210D LEU* 3.2 42.9 + - + +
215D ARG* 4.3 10.7 + - + -
218D ILE* 4.2 10.1 - - + -
234D LEU* 3.9 30.4 + - + -
235D ARG* 1.3 79.4 - - - +
237D ARG* 1.3 69.5 + - - +
244D PHE 3.4 5.2 - - - -
245D ILE* 4.3 6.1 - - + -
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Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B PHE* 3.6 24.9 - - + -
207B ASP* 2.7 28.8 + - - -
237B ARG* 3.0 26.0 - - - +
246B GLN* 5.3 2.4 - - - +
73D PHE* 4.1 20.0 - - - +
77D LYS* 5.3 1.2 - - - +
207D ASP* 3.3 36.8 + - + +
208D ARG 3.6 17.5 - - - +
210D LEU* 3.8 8.5 - - - +
236D THR* 1.3 80.4 - - - +
238D GLN* 1.3 57.7 + - - +
239D SER* 4.7 4.8 - - - -
243D ARG* 3.6 0.5 - - - -
244D PHE* 2.6 75.5 + - + +
246D GLN* 5.5 0.8 - - - +
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Residues in contact with GLN 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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77D LYS* 4.5 8.7 - - - +
204D SER* 4.7 15.0 + - - +
208D ARG 4.3 4.2 + - - -
210D LEU* 3.8 13.2 - - + +
211D PRO* 5.3 4.9 - - - +
214D GLU* 4.8 0.5 - - - +
237D ARG* 1.3 79.6 - - - +
239D SER* 1.3 57.5 + - - +
240D GLY 3.0 25.0 + - - +
241D PRO* 3.4 16.6 + - - +
242D THR 3.1 14.6 - - - +
243D ARG* 3.5 35.4 + - + +
244D PHE* 4.3 0.9 - - - +
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Residues in contact with SER 239 (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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207B ASP* 4.9 1.1 - - - -
74D GLY* 3.9 9.9 - - - -
76D GLY* 3.6 22.4 + - - -
77D LYS* 3.7 32.8 + - - +
237D ARG* 4.7 6.3 - - - -
238D GLN* 1.3 72.4 - - - +
240D GLY* 1.3 62.3 + - - +
241D PRO* 3.4 8.1 - - - +
242D THR* 3.1 17.3 + - - +
244D PHE* 3.8 24.3 - - - -
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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