Contacts of the helix formed by residues 230 - 238 (chain C) in PDB entry 1USK
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 ASN 230 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLN* 2.6 41.8 + - - +
18C TRP* 3.6 33.6 - - + -
21C MET* 4.2 4.6 - - - +
203C TYR* 3.7 34.4 - - + -
228C VAL 3.0 4.9 + - - -
229C GLY* 1.3 73.4 - - - -
231C ALA* 1.3 64.3 + - - +
232C SER* 3.1 20.5 + - - +
233C LEU* 3.2 15.8 + - - +
336C TRP* 3.5 15.2 + - - -
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASN* 3.9 13.0 - - - +
17C GLN* 3.4 14.9 - - - +
21C MET* 6.2 0.2 - - - +
230C ASN* 1.3 77.0 - - - +
232C SER* 1.3 60.2 + - - +
233C LEU 3.4 0.3 + - - -
234C SER* 3.8 11.5 + - - -
235C ASN* 3.2 18.9 - - - +
271C ASP* 5.0 10.8 - - - +
336C TRP* 5.3 1.6 - - - -
340C GLY* 5.4 7.4 - - - -
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Residues in contact with SER 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASN* 3.5 13.2 + - - +
17C GLN* 3.3 17.9 + - - +
203C TYR* 3.5 23.4 - - - -
230C ASN* 3.1 16.9 + - - -
231C ALA* 1.3 77.2 - - - +
233C LEU* 1.3 64.5 + - - +
234C SER 3.4 0.2 - - - -
235C ASN* 3.2 11.0 + - - +
236C ILE* 3.0 33.2 + - - +
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Residues in contact with LEU 233 (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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203C TYR* 4.0 13.4 - - + +
206C MET* 3.9 25.8 - - + -
207C GLY* 4.0 15.5 - - - +
210C LEU* 4.3 4.5 - - + -
228C VAL 3.2 25.1 - - - +
230C ASN* 3.2 17.0 + - - +
231C ALA 3.2 0.8 - - - -
232C SER* 1.3 78.3 - - - +
234C SER* 1.3 59.1 + - - +
236C ILE* 3.3 4.8 + - - +
237C ALA* 3.0 27.9 + - - +
241C ALA* 4.8 6.1 - - + -
244C MET* 3.2 33.7 - - + -
336C TRP* 3.8 20.2 - - + +
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Residues in contact with SER 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 5.6 0.3 - - - +
20B ASP* 5.0 0.2 - - - +
230C ASN 4.4 0.6 + - - -
231C ALA 3.8 7.8 + - - -
232C SER 3.4 0.2 - - - -
233C LEU* 1.3 76.8 - - - +
235C ASN* 1.3 69.5 + - - +
238C GLY* 3.0 28.2 + - - +
241C ALA* 4.0 15.3 - - - -
336C TRP* 4.3 3.6 - - - -
337C HIS 3.7 16.6 - - - -
338C ALA* 3.4 21.2 + - - +
339C ASP 4.0 1.4 - - - -
340C GLY* 3.4 22.9 + - - -
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Residues in contact with ASN 235 (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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17B GLN* 3.5 33.7 + - + +
20B ASP* 4.4 0.3 - - - +
231B ALA* 3.9 23.4 - - - +
232B SER* 3.8 21.3 + - - +
235B ASN* 2.7 28.8 - - + +
211C ARG* 4.0 8.8 + - - -
231C ALA* 3.2 11.1 + - - +
232C SER* 3.2 8.9 + - - +
234C SER* 1.3 86.3 + - - +
236C ILE* 1.3 60.5 + - + +
238C GLY 4.2 0.2 + - - -
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Residues in contact with ILE 236 (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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203C TYR* 4.1 26.5 - - + +
204C PRO* 4.1 17.5 - - + +
207C GLY* 3.6 26.2 - - - +
208C GLN* 3.7 25.5 + - - +
211C ARG* 2.9 26.2 + - - -
232C SER* 3.0 25.2 + - - +
233C LEU 3.8 3.4 - - - +
235C ASN* 1.3 81.0 - - + +
237C ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 237 (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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207C GLY* 3.4 23.6 - - - +
210C LEU* 3.8 21.5 - - + -
211C ARG* 3.7 15.7 + - - +
233C LEU 3.0 16.6 + - - +
236C ILE* 1.3 77.0 - - - +
238C GLY* 1.3 63.6 + - - +
239C ASP 3.6 0.3 + - - -
240C ALA* 3.3 16.8 + - - +
241C ALA* 4.0 17.5 - - + +
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Residues in contact with GLY 238 (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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20B ASP* 3.3 27.1 + - - -
211C ARG* 3.5 4.3 - - - +
234C SER 3.0 20.4 + - - +
236C ILE 3.4 2.6 - - - -
237C ALA* 1.3 78.5 - - - +
239C ASP* 1.3 63.4 + - - -
240C ALA 3.1 1.2 + - - -
241C ALA* 3.3 13.2 + - - +
338C ALA* 4.1 10.2 - - - +
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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