Contacts of the strand formed by residues 236 - 243 (chain D) in PDB entry 2HU4
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 SER 236 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D CYS* 3.0 2.1 - - - +
233D VAL 2.6 46.4 + - - +
234D ASN 4.0 5.0 + - - -
235D GLY* 1.3 76.6 - - - +
237D CYS* 1.3 63.3 + - - +
238D PHE* 3.3 24.3 - - - -
256D LYS* 3.7 13.7 + - - -
257D MET 3.5 8.5 - - - -
258D GLU* 3.0 22.9 + - - -
308D GLN* 5.5 2.8 + - - -
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Residues in contact with CYS 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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183D CYS* 3.8 8.7 - - - -
185D ASP* 3.7 19.5 - - - -
190D LEU* 3.8 29.8 - - + -
207D TYR* 6.2 0.7 - - - -
231D ALA 3.3 4.3 - - - -
232D CYS* 2.0 44.0 - - - -
235D GLY 5.4 0.2 - - - -
236D SER* 1.3 74.1 - - - +
238D PHE* 1.3 67.1 + - - +
256D LYS* 3.6 0.2 - - - -
257D MET* 2.9 40.5 + - + +
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Residues in contact with PHE 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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226D GLN* 4.1 0.5 + - - -
230D CYS* 3.1 20.1 - - - +
231D ALA* 2.8 28.2 + - - +
233D VAL* 4.3 10.1 - - + -
236D SER* 3.3 35.9 - - - -
237D CYS* 1.3 75.7 - - - +
239D THR* 1.3 60.1 + - - +
255D PHE 3.3 13.2 - - - +
256D LYS* 3.7 22.9 - - + -
257D MET* 4.3 1.6 - - - -
280D CYS* 5.4 3.0 - - - +
287D ILE* 3.8 21.0 - - + +
305D PHE* 3.8 27.8 - + + -
306D ASN 4.4 1.8 - - - -
308D GLN* 4.0 29.4 - - + -
310D LEU* 3.8 26.0 - - + -
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Residues in contact with THR 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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181D SER* 3.7 4.3 + - - -
192D ILE* 3.9 11.9 - - + -
225D THR* 3.4 15.1 + - - +
226D GLN* 2.7 25.7 + - - +
230D CYS* 4.2 1.6 - - - -
238D PHE* 1.3 75.1 - - - +
240D VAL* 1.3 70.2 + - - +
241D MET* 4.7 9.0 - - + -
254D ILE* 3.6 7.0 - - - +
255D PHE* 3.2 40.7 + - + +
257D MET* 3.3 30.1 - - + -
280D CYS* 5.5 1.3 - - - -
305D PHE* 6.0 0.2 - - - -
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Residues in contact with VAL 240 (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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225D THR* 3.0 23.4 + - - -
226D GLN* 3.8 8.7 + - + +
239D THR* 1.3 83.5 + - - +
241D MET* 1.3 73.1 + - - +
242D THR* 5.3 1.6 - - - +
252D TYR* 5.1 7.9 - - + -
253D LYS 3.4 16.4 - - - +
254D ILE* 4.6 14.4 - - + -
268D LEU* 5.6 3.8 - - + -
275D TYR* 5.2 5.4 - - + -
278D CYS* 4.3 25.7 + - + -
280D CYS* 4.0 4.9 - - - -
289D CYS* 3.9 28.0 - - - -
303D VAL* 5.3 4.7 - - + -
305D PHE* 4.8 5.2 - - + -
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Residues in contact with MET 241 (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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192D ILE* 3.5 32.1 - - + -
194D ILE* 3.9 14.4 - - + -
203D ALA* 3.6 21.3 - - + -
215D ILE* 4.3 11.0 - - + -
218D TRP* 4.1 3.7 - - + -
223D LEU* 4.1 20.9 - - + -
224D ARG 3.3 9.9 - - - +
225D THR* 3.6 12.6 - - - +
239D THR* 4.7 8.7 - - + -
240D VAL* 1.3 83.2 - - - +
242D THR* 1.3 66.2 + - - +
251D SER 4.0 0.2 - - - +
252D TYR* 3.5 2.9 - - - -
253D LYS 3.1 30.5 + - - -
255D PHE* 3.8 32.3 - - + -
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Residues in contact with THR 242 (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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218D TRP* 4.4 0.7 - - - -
222D ILE 3.7 0.9 - - - +
223D LEU* 3.5 5.1 - - - +
224D ARG* 3.0 52.2 + - - +
240D VAL* 5.3 1.9 - - - +
241D MET* 1.3 77.0 + - - +
243D ASP* 1.3 67.8 + - - +
250D ALA* 4.1 10.1 - - + -
251D SER 3.4 10.8 - - - +
252D TYR* 4.0 10.6 - - + +
274D HIS* 5.7 0.2 - - - +
275D TYR* 2.8 27.6 + - - +
276D GLU* 3.6 25.1 - - - +
277D GLU 5.3 0.3 + - - -
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Residues in contact with ASP 243 (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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217D SER* 2.4 28.4 + - - -
218D TRP* 2.9 31.6 + - + -
219D ARG* 2.8 25.4 + - + +
221D ASN 3.0 34.3 + - - +
222D ILE 3.9 0.6 + - - -
223D LEU* 4.3 5.2 - - + -
224D ARG* 4.4 0.2 - - - +
242D THR* 1.3 79.9 - - - +
244D GLY* 1.3 64.3 + - - +
251D SER* 2.9 34.7 + - - +
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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