Contacts of the helix formed by residues 234 - 241 (chain X) in PDB entry 1T6B
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 234 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156X LEU 4.8 1.0 + - - -
181X ASP* 4.1 5.2 + - - +
226X TRP* 3.1 52.6 - - - -
233X TYR* 1.3 75.6 - - - +
235X ASP* 1.3 64.8 + - - +
236X PHE* 3.2 9.1 + - - +
237X GLU* 2.8 35.5 + - - +
238X LYS* 2.9 23.0 + - - +
464X PHE* 5.5 0.3 - - - -
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Residues in contact with ASP 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X ASP* 3.5 10.7 + - - +
183X ILE* 3.9 13.2 - - + +
188X GLU* 3.2 3.8 - - - +
221X SER* 3.2 10.7 - - - +
225X LYS 3.1 1.2 - - - +
226X TRP 2.8 13.6 + - - -
227X SER* 3.6 1.6 + - - -
228X THR* 2.6 41.2 + - - -
234X SER* 1.3 73.3 - - - +
236X PHE* 1.3 56.3 + - - +
238X LYS* 3.5 6.3 + - - +
239X VAL* 3.1 33.1 + - - +
254X PRO* 3.6 22.5 - - + +
801X CA 2.3 26.7 - - - -
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Residues in contact with PHE 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X LEU* 3.6 30.1 - - + -
35X VAL* 4.7 8.1 - - + -
36X THR* 6.3 0.7 - - - -
153X LEU* 5.0 2.0 - - + -
156X LEU* 3.8 20.4 - - + -
181X ASP* 2.8 31.1 - - - +
182X GLY 4.4 5.4 - - - -
183X ILE* 3.7 23.9 - - + +
203X LEU* 4.4 14.6 - - + -
234X SER* 3.1 2.6 + - - +
235X ASP* 1.3 76.9 - - - +
237X GLU* 1.3 63.5 + - - +
239X VAL* 3.5 2.1 + - - +
240X THR* 2.8 44.0 + - + -
242X ARG* 3.3 31.9 - - - -
464X PHE* 4.5 15.0 - + - -
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Residues in contact with GLU 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X LYS* 3.1 23.1 + - - -
226X TRP* 3.5 10.8 - - - -
232X PRO 4.3 1.2 - - - +
233X TYR* 3.5 18.2 - - + +
234X SER* 2.8 39.6 + - - +
236X PHE* 1.3 73.1 - - - +
238X LYS* 1.3 63.5 + - - +
240X THR* 4.3 5.2 - - - -
241X GLY* 3.0 21.7 + - - -
242X ARG* 3.1 29.3 + - + +
243X ILE* 3.9 2.8 - - + +
462X TYR* 3.9 15.4 + - + +
464X PHE* 3.2 31.3 - - + -
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Residues in contact with LYS 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227X SER* 4.7 1.3 + - - -
229X ALA* 4.0 7.1 - - - +
231X ASP* 2.4 39.4 + - - -
233X TYR* 3.8 16.2 - - + +
234X SER 2.9 17.2 + - - +
235X ASP* 3.5 7.4 - - - +
237X GLU* 1.3 79.9 - - - +
239X VAL* 1.3 59.4 + - + +
240X THR 3.1 4.2 + - - -
241X GLY* 3.5 6.9 + - - -
243X ILE* 4.0 19.5 - - + +
251X ALA 3.3 20.5 + - - +
252X ARG* 3.3 31.6 - - - +
253X HIS 3.8 11.0 + - - +
254X PRO* 3.9 11.7 + - + -
256X VAL 2.7 27.3 + - - -
258X ALA* 4.0 1.9 - - - +
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Residues in contact with VAL 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X ILE* 4.5 10.3 - - + -
192X TYR* 4.4 6.1 - - + -
194X VAL* 3.6 34.1 - - + +
201X THR* 3.8 16.5 - - + +
203X LEU* 4.5 7.4 - - + -
219X TYR* 4.1 16.6 - - + -
235X ASP 3.1 11.8 + - - +
236X PHE* 3.9 9.9 - - - +
238X LYS* 1.3 75.8 - - - +
240X THR* 1.3 60.9 + - - +
241X GLY 3.6 0.2 - - - -
252X ARG 3.9 10.1 - - - +
254X PRO* 3.7 31.9 - - + -
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Residues in contact with THR 240 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201X THR* 4.0 28.2 + - - +
203X LEU* 5.7 1.6 - - - +
236X PHE* 2.8 35.7 + - + +
238X LYS 3.1 0.2 - - - -
239X VAL* 1.3 83.0 + - - +
241X GLY* 1.4 62.4 + - - +
242X ARG* 2.8 57.7 + - + +
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Residues in contact with GLY 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X SER* 5.7 0.5 + - - -
237X GLU 3.0 5.8 + - - -
238X LYS 3.5 5.7 + - - -
239X VAL 3.6 0.4 - - - -
240X THR* 1.4 79.5 - - - +
242X ARG* 1.3 61.7 + - - +
243X ILE* 3.1 23.2 + - - +
252X ARG* 4.9 8.1 + - - -
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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