Contacts of the strand formed by residues 236 - 243 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C CYS* 3.0 1.0 - - - -
233C VAL 2.6 49.9 + - - +
234C ASN 3.2 4.4 + - - -
235C GLY* 1.3 73.8 - - - +
237C CYS* 1.3 60.1 + - - +
238C PHE* 3.4 25.8 - - - -
256C LYS* 3.4 13.9 - - - -
257C MET 3.3 8.5 - - - -
258C GLU* 2.9 25.9 + - - +
308C GLN* 5.2 3.4 + - - -
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Residues in contact with CYS 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C CYS* 3.8 8.1 - - - -
185C ASP* 3.6 20.2 - - - -
190C LEU* 3.7 29.4 - - + -
207C TYR* 6.1 0.9 - - - -
230C CYS* 4.9 0.2 - - - -
231C ALA 3.2 4.3 - - - -
232C CYS* 2.0 45.3 - - - -
235C GLY 5.1 0.7 - - - -
236C SER* 1.3 73.0 - - - +
238C PHE* 1.3 63.5 + - - +
256C LYS 3.6 0.5 - - - -
257C MET* 2.7 40.8 + - - +
258C GLU* 6.4 0.2 - - - -
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Residues in contact with PHE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C GLN* 4.0 0.3 + - - -
230C CYS* 3.2 20.4 - - - +
231C ALA* 2.7 29.1 + - - +
233C VAL* 4.4 9.2 - - + -
236C SER* 3.4 37.0 - - - -
237C CYS* 1.3 75.0 - - - +
239C THR* 1.3 61.6 + - - +
255C PHE 3.1 7.4 - - - +
256C LYS* 3.4 28.5 - - + -
257C MET* 4.3 0.9 - - - -
280C CYS* 5.5 2.7 - - - +
287C ILE* 3.6 20.8 - - + +
305C PHE* 3.7 29.2 - + + -
306C ASN 4.5 1.1 - - - -
308C GLN* 3.9 28.3 - - + -
310C LEU* 3.6 27.1 - - + -
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C SER* 4.0 3.3 + - - -
192C ILE* 3.9 10.3 - - + +
215C ILE* 6.2 1.3 - - + -
225C THR* 3.4 14.3 + - - +
226C GLN* 2.7 25.7 + - - +
230C CYS* 4.2 3.6 - - - -
238C PHE* 1.3 73.5 - - - +
240C VAL* 1.3 71.2 + - - +
241C MET* 4.8 7.9 - - + -
254C ILE* 3.4 7.0 - - - +
255C PHE* 2.9 44.4 + - + +
257C MET* 3.1 28.7 - - + -
280C CYS* 5.4 1.6 - - - -
305C PHE* 5.6 0.9 - - - -
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C THR* 2.7 30.3 + - - -
226C GLN* 3.7 7.4 + - + +
239C THR* 1.3 85.2 + - - +
241C MET* 1.3 71.1 + - - +
242C THR* 5.2 1.6 - - - +
252C TYR* 5.0 8.1 - - + -
253C LYS 3.3 14.8 - - - +
254C ILE* 4.8 13.2 - - + -
268C LEU* 5.5 4.5 - - + -
275C TYR* 5.2 6.3 - - + -
278C CYS* 4.2 24.9 - - + -
280C CYS* 4.1 4.0 - - - -
289C CYS* 4.0 27.4 - - - -
303C VAL* 5.7 4.3 - - + -
305C PHE* 4.8 4.5 - - + -
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE* 3.6 24.7 - - + -
194C ILE* 3.9 17.0 - - + -
203C ALA* 3.6 28.9 - - + -
215C ILE* 4.3 17.0 - - + -
218C TRP* 4.1 11.0 - - + -
223C LEU* 4.3 14.8 - - + -
224C ARG 3.2 9.0 - - - +
225C THR* 3.8 11.2 - - - +
239C THR* 4.8 4.9 - - + -
240C VAL* 1.3 82.8 - - - +
242C THR* 1.3 64.1 + - - +
251C SER 4.0 0.2 - - - +
252C TYR* 3.5 3.5 - - - -
253C LYS 2.9 31.3 + - - -
255C PHE* 3.6 32.8 - - + -
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Residues in contact with THR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C TRP* 4.6 0.4 - - - -
223C LEU* 3.5 2.8 - - - +
224C ARG* 2.9 69.1 + - - +
225C THR* 5.0 0.2 - - - +
240C VAL* 5.2 2.1 - - - +
241C MET* 1.3 75.6 - - - +
243C ASP* 1.3 66.3 + - - +
245C PRO 5.3 0.2 - - - +
250C ALA* 4.2 7.2 - - + -
251C SER 3.4 11.2 - - - +
252C TYR* 3.6 15.9 - - + +
274C HIS* 5.7 0.4 - - - +
275C TYR* 2.6 32.3 + - - +
276C GLU* 3.8 6.5 - - - +
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C SER* 2.4 26.8 + - - -
218C TRP* 2.6 34.1 + - + -
219C ARG* 2.6 28.7 + - + +
221C ASN 3.0 33.3 + - - +
223C LEU* 3.9 7.1 + - + -
224C ARG* 4.2 0.4 - - - +
242C THR* 1.3 76.9 - - - +
244C GLY* 1.3 62.3 + - - +
250C ALA* 3.6 0.3 - - - +
251C SER* 2.9 33.3 + - - +
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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