Contacts of the strand formed by residues 236 - 243 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H CYS* 3.1 2.3 - - - +
233H VAL 2.7 41.1 + - - -
234H ASN* 3.2 5.6 + - - -
235H GLY* 1.3 78.6 - - - +
237H CYS* 1.3 60.9 + - - +
238H PHE* 3.4 21.1 - - - -
256H LYS* 3.6 16.1 - - - -
257H MET 3.7 5.2 - - - -
258H GLU* 3.1 25.8 + - - -
308H GLN* 5.1 4.3 + - - -
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Residues in contact with CYS 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H CYS* 4.0 7.4 - - - -
185H ASP* 3.5 22.0 - - - -
190H LEU* 3.9 25.8 - - + -
207H TYR* 6.3 0.2 - - - -
231H ALA 3.5 3.4 - - - -
232H CYS* 2.1 45.5 - - - -
235H GLY 5.1 0.9 - - - -
236H SER* 1.3 74.4 - - - +
238H PHE* 1.3 63.9 + - - +
256H LYS* 3.4 2.4 - - - -
257H MET* 2.7 47.5 + - - +
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Residues in contact with PHE 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H GLN* 4.0 0.2 + - - -
230H CYS* 2.9 23.7 - - - +
231H ALA 2.8 30.5 + - - +
233H VAL* 4.2 10.3 - - + -
236H SER* 3.4 35.7 - - - -
237H CYS* 1.3 73.6 - - - +
239H THR* 1.3 63.3 + - - +
255H PHE 3.2 5.6 - - - +
256H LYS* 3.4 37.2 - - + -
257H MET* 4.1 1.1 - - - -
280H CYS* 5.6 2.9 - - - +
287H ILE* 3.5 27.4 - - + -
305H PHE* 3.9 28.9 - + + -
306H ASN 4.5 1.1 - - - -
308H GLN* 3.9 33.0 - - + -
310H LEU* 4.0 7.0 - - + -
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Residues in contact with THR 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H SER* 3.8 6.4 + - - -
192H ILE* 3.9 11.9 - - + -
215H ILE* 6.5 0.2 - - + -
225H THR* 3.6 11.4 + - - -
226H GLN* 2.4 27.9 + - - +
230H CYS* 4.1 5.4 - - - -
238H PHE* 1.3 76.6 - - - +
240H VAL* 1.3 68.2 + - - +
241H MET* 4.8 7.9 - - + -
254H ILE* 3.6 4.5 - - - +
255H PHE* 2.8 45.7 + - + +
257H MET* 3.2 25.4 - - + -
280H CYS* 5.4 1.3 - - - -
305H PHE* 5.8 0.4 - - - -
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Residues in contact with VAL 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H THR* 2.8 19.9 + - - -
226H GLN* 3.3 12.1 + - + +
239H THR* 1.3 82.5 + - - +
241H MET* 1.3 71.7 + - - +
242H THR* 5.1 3.4 - - - +
252H TYR* 5.1 8.3 - - + -
253H LYS 3.4 15.0 - - - +
254H ILE* 4.5 15.7 - - + -
268H LEU* 5.6 4.0 - - + -
275H TYR* 5.4 4.0 - - + -
278H CYS* 4.1 27.8 - - + -
280H CYS* 3.9 4.7 - - - -
289H CYS* 3.9 27.4 - - - -
303H VAL* 5.8 3.8 - - + -
305H PHE* 4.8 4.7 - - + -
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Residues in contact with MET 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H ILE* 3.5 37.0 - - + -
194H ILE* 4.1 9.9 - - + -
203H ALA* 3.7 17.7 - - + -
215H ILE* 4.6 12.3 - - + -
218H TRP* 4.1 9.1 - - + -
223H LEU* 4.4 21.1 - - + -
224H ARG 3.4 7.0 - - - +
225H THR* 3.5 19.7 - - - +
239H THR* 4.8 5.2 - - + -
240H VAL* 1.3 75.7 - - - +
242H THR* 1.3 63.9 + - - +
251H SER 4.0 0.2 - - - +
252H TYR* 3.5 3.1 - - - -
253H LYS 2.9 32.4 + - - +
255H PHE* 3.7 33.2 - - + -
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Residues in contact with THR 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H TRP* 4.4 1.3 - - - -
223H LEU* 3.7 2.1 - - - +
224H ARG* 3.0 62.4 + - - +
240H VAL* 5.1 2.8 - - - +
241H MET* 1.3 76.9 + - - +
243H ASP* 1.3 66.6 + - - +
250H ALA* 4.0 7.4 - - + -
251H SER 3.2 12.3 - - - +
252H TYR* 3.7 15.0 - - + +
275H TYR* 2.8 31.1 + - - +
276H GLU* 4.2 12.0 - - - +
277H GLU 5.4 0.2 + - - -
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Residues in contact with ASP 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H SER* 2.4 26.0 + - - -
218H TRP* 2.9 32.9 + - + +
219H ARG* 2.7 26.8 + - + +
221H ASN 3.0 32.9 + - - +
223H LEU* 3.8 9.1 + - + -
224H ARG* 4.5 0.2 - - - +
242H THR* 1.3 77.1 - - - +
244H GLY* 1.3 61.0 + - - +
251H SER* 2.9 36.6 + - - -
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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
------------------------------------------------------------
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