Contacts of the strand formed by residues 236 - 243 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E CYS* 3.1 1.0 - - - -
233E VAL 2.7 38.1 + - - +
234E ASN 4.3 3.8 + - - -
235E GLY* 1.3 78.3 - - - +
237E CYS* 1.3 60.8 + - - +
238E PHE* 3.4 26.7 - - - -
256E LYS* 3.4 16.0 - - - -
257E MET 3.9 4.3 - - - -
258E GLU* 2.8 28.8 + - - +
308E GLN* 5.4 3.1 + - - -
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Residues in contact with CYS 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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183E CYS* 3.8 16.4 - - - -
185E ASP* 3.7 17.9 - - - -
190E LEU* 3.8 19.7 - - + -
207E TYR* 6.4 1.6 - - - -
230E CYS* 4.8 0.2 - - - -
231E ALA 3.2 3.4 - - - -
232E CYS* 2.1 44.9 - - - -
235E GLY 5.3 0.9 - - - -
236E SER* 1.3 72.9 - - - +
238E PHE* 1.3 66.9 + - - +
256E LYS* 3.7 0.9 - - - -
257E MET* 3.0 42.3 + - - +
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Residues in contact with PHE 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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226E GLN* 3.9 0.9 + - - -
230E CYS* 3.0 20.6 - - - +
231E ALA* 2.6 30.0 + - - +
233E VAL* 4.3 11.4 - - + -
236E SER* 3.4 34.8 - - - -
237E CYS* 1.3 77.3 - - - +
239E THR* 1.3 60.2 + - - +
255E PHE 3.4 14.8 - - - +
256E LYS* 3.5 22.2 - - + -
257E MET* 4.3 0.7 - - - -
280E CYS* 5.2 4.1 - - - +
287E ILE* 3.3 30.5 - - + -
305E PHE* 3.9 28.0 - + + -
306E ASN 4.5 0.4 - - - -
308E GLN* 3.8 27.6 - - + -
310E LEU* 3.9 15.7 - - + -
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Residues in contact with THR 239 (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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181E SER* 4.0 4.9 + - - -
192E ILE* 4.3 8.8 - - + +
225E THR* 3.3 15.0 + - - +
226E GLN* 2.7 25.6 + - - +
230E CYS* 4.3 3.1 - - - -
238E PHE* 1.3 75.3 - - - +
240E VAL* 1.3 68.5 + - - +
241E MET* 4.5 10.5 - - + -
254E ILE* 3.5 6.1 - - - +
255E PHE* 3.0 47.2 + - + +
257E MET* 3.3 26.5 - - + -
280E CYS* 5.5 1.1 - - - -
305E PHE* 5.7 0.9 - - - -
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Residues in contact with VAL 240 (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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225E THR* 3.1 23.7 + - - -
226E GLN* 3.8 9.3 + - + +
239E THR* 1.3 81.4 + - - +
241E MET* 1.3 71.0 + - - +
242E THR* 5.2 4.3 - - - +
252E TYR* 5.3 6.3 - - + -
253E LYS 3.3 14.8 - - - +
254E ILE* 4.7 6.5 - - + -
268E LEU* 5.6 4.9 - - + -
275E TYR* 5.3 4.5 - - + -
278E CYS* 3.9 29.3 + - + -
280E CYS* 3.9 23.8 - - - -
289E CYS* 3.9 8.7 - - - -
303E VAL* 5.9 4.0 - - + -
305E PHE* 4.7 12.3 - - + -
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Residues in contact with MET 241 (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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192E ILE* 3.7 30.7 - - + -
194E ILE* 4.1 6.3 - - + -
203E ALA* 3.8 16.2 - - + -
215E ILE* 4.4 19.3 - - + -
218E TRP* 4.0 10.2 - - + -
223E LEU* 4.1 17.5 - - + -
224E ARG 3.4 9.2 - - - +
225E THR* 3.9 17.0 - - - +
239E THR* 4.5 8.5 - - + -
240E VAL* 1.3 81.0 - - - +
242E THR* 1.3 63.1 + - - +
252E TYR* 3.4 4.3 - - - +
253E LYS* 2.9 33.7 + - - -
255E PHE* 3.7 32.5 - - + -
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Residues in contact with THR 242 (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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218E TRP* 4.3 0.9 - - - -
223E LEU* 3.5 5.3 - - - +
224E ARG* 3.0 68.7 + - - +
240E VAL* 5.2 2.8 - - - +
241E MET* 1.3 75.4 + - - +
243E ASP* 1.3 67.3 + - - +
250E ALA* 4.3 6.5 - - + -
251E SER 3.3 10.1 - - - +
252E TYR* 3.5 13.6 - - + +
275E TYR* 2.7 29.5 + - - +
276E GLU* 4.0 9.0 - - - +
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Residues in contact with ASP 243 (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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217E SER* 2.4 26.6 + - - -
218E TRP* 2.8 31.0 + - + -
219E ARG* 2.7 28.6 + - + +
221E ASN 3.0 34.1 + - - +
223E LEU* 3.7 7.4 + - + -
224E ARG* 3.9 3.8 - - - +
242E THR* 1.3 77.1 - - - +
244E GLY* 1.3 60.3 + - - +
251E SER* 2.9 34.0 + - - -
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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