Contacts of the helix formed by residues 239 - 254 (chain E) in PDB entry 3TMP
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 MET 239 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ALA* 3.7 4.3 - - + -
234E TYR* 3.9 35.9 - - + -
236E ASP* 2.9 33.6 + - + +
238E ASP* 1.3 97.8 - - + +
240E HIS* 1.3 63.4 + - - +
241E GLU 3.2 4.0 + - - -
242E VAL* 3.3 29.3 + - + +
243E VAL* 3.3 13.0 + - - +
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Residues in contact with HIS 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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221E ASP* 5.6 0.2 - - - -
223E ALA* 3.4 21.8 - - + +
226E PHE* 3.6 16.0 - - + +
227E ARG* 3.6 56.0 + - + +
237E GLN 3.0 23.9 + - - +
238E ASP* 3.1 13.3 - - - -
239E MET* 1.3 78.1 - - - +
241E GLU* 1.3 83.5 + - + +
243E VAL* 3.3 2.9 + - - +
244E ARG* 2.9 32.5 + - - +
276E ASN* 4.7 11.2 + - + +
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Residues in contact with GLU 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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238E ASP 4.8 3.3 + - - +
239E MET 3.2 1.2 - - - -
240E HIS* 1.3 100.5 - - + +
242E VAL* 1.3 59.2 + - + +
244E ARG* 3.4 7.1 + - - +
245E LYS* 2.9 30.5 + - - +
276E ASN* 3.3 35.3 + - + +
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Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E TYR* 4.0 20.6 - - + +
239E MET* 3.4 29.2 - - + +
241E GLU* 1.3 75.9 - - + +
243E VAL* 1.3 64.4 + - - +
245E LYS* 3.5 4.7 + - - +
246E HIS* 3.1 49.9 + - + +
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Residues in contact with VAL 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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226E PHE* 3.9 13.2 - - + +
229E VAL* 3.8 13.2 - - + -
230E ALA* 3.7 35.0 - - + +
233E VAL* 5.4 0.2 - - + -
234E TYR* 3.9 10.8 - - + -
239E MET 3.3 3.3 + - - +
240E HIS 3.3 7.5 + - - +
242E VAL* 1.3 78.7 - - - +
244E ARG* 1.3 58.3 + - - +
246E HIS* 3.8 2.8 - - - +
247E CYS* 3.0 27.5 + - - +
288E MET* 3.5 28.0 - - - -
291E MET* 4.6 0.9 - - - +
292E TYR* 3.3 27.0 + - - +
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Residues in contact with ARG 244 (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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222E GLY 3.6 6.9 + - - -
223E ALA* 3.6 5.1 - - - +
226E PHE* 3.4 45.1 - - + +
240E HIS* 2.9 20.0 + - - +
241E GLU* 3.8 6.7 - - - +
242E VAL 3.3 0.2 - - - -
243E VAL* 1.3 77.1 - - - +
245E LYS* 1.3 63.0 + - - +
247E CYS* 3.3 2.6 + - - +
248E MET* 3.1 37.7 + - + +
273E LYS* 2.8 32.9 + - - +
274E ARG* 3.4 25.4 - - - -
275E LYS 3.0 13.2 + - - -
276E ASN* 2.8 33.5 + - - +
278E CYS* 2.9 31.5 + - - +
279E HIS 5.2 0.2 - - - -
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Residues in contact with LYS 245 (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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60B ASN* 6.2 1.1 - - - +
62B GLN* 4.1 8.3 - - - +
241E GLU 2.9 17.7 + - - +
242E VAL* 4.0 4.9 - - - +
244E ARG* 1.3 76.0 - - - +
246E HIS* 1.3 66.1 + - + +
248E MET* 3.3 1.1 + - - -
249E ASP* 2.8 62.7 + - - +
274E ARG* 3.9 16.3 + - - +
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Residues in contact with HIS 246 (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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234E TYR* 4.1 13.2 + - - -
242E VAL* 3.1 41.0 + - + +
243E VAL* 3.8 4.3 - - - +
245E LYS* 1.3 85.1 - - + +
247E CYS* 1.3 57.8 + - - +
249E ASP* 3.7 10.8 - - + +
250E TYR* 2.9 24.8 + - - +
291E MET* 3.2 30.1 - - + +
292E TYR* 4.6 8.0 + - - +
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Residues in contact with CYS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E PHE* 4.3 2.5 - - + -
243E VAL 3.0 17.5 + - - +
244E ARG* 3.4 7.4 - - - +
245E LYS 3.3 0.2 - - - -
246E HIS* 1.3 77.8 - - - +
248E MET* 1.3 63.9 + - + +
250E TYR* 3.2 3.5 + - - +
251E LEU* 2.9 37.1 + - - +
284E GLU* 3.7 51.1 - - - -
287E ALA* 4.2 4.6 - - - +
288E MET* 3.8 16.2 - - + -
291E MET* 3.6 10.7 - - - +
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Residues in contact with MET 248 (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 PHE* 3.8 17.9 - - + -
244E ARG* 3.1 18.6 + - + +
245E LYS* 5.0 0.2 - - - -
247E CYS* 1.3 78.4 - - - +
249E ASP* 1.3 66.4 + - - +
251E LEU* 3.4 20.8 + - - +
252E MET* 3.1 27.5 + - - +
270E ILE* 3.9 11.1 - - + +
273E LYS* 3.5 40.4 - - + +
274E ARG* 3.6 42.2 - - + +
284E GLU* 3.6 26.5 - - + -
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Residues in contact with ASP 249 (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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60B ASN* 3.9 4.3 + - - -
62B GLN* 3.0 34.0 + - - +
245E LYS* 2.8 48.7 + - - +
246E HIS* 3.7 9.3 - - + +
248E MET* 1.3 77.9 - - - +
250E TYR* 1.3 57.0 + - - +
252E MET* 3.3 5.0 + - - +
253E LYS* 3.0 28.5 + - - +
274E ARG* 2.8 30.5 + - - +
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Residues in contact with TYR 250 (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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170C HIS* 5.6 0.3 - - - -
246E HIS 2.9 19.0 + - - +
247E CYS* 3.6 4.3 - - - +
249E ASP* 1.3 75.7 - - - +
251E LEU* 1.3 65.1 + - - +
253E LYS* 3.3 10.7 + - + -
254E ASN* 2.9 54.4 + - - +
258E PHE* 3.9 13.2 - + - -
287E ALA* 3.8 24.7 - - + +
290E GLU* 2.7 42.2 + - + +
291E MET* 3.6 33.9 - - + -
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Residues in contact with LEU 251 (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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247E CYS* 2.9 26.2 + - - +
248E MET* 3.7 22.2 - - - +
249E ASP 3.4 0.2 - - - -
250E TYR* 1.3 77.8 - - - +
252E MET* 1.3 57.2 + - - +
254E ASN 3.2 3.3 - - - -
255E ALA* 3.0 27.4 + - - -
258E PHE* 3.5 34.9 - - + -
266E PHE* 3.5 8.5 - - + -
269E TYR* 4.8 0.4 - - + -
270E ILE* 3.7 26.0 - - + -
283E ILE* 3.7 18.4 - - + -
284E GLU* 4.1 16.4 - - + +
287E ALA* 3.6 20.4 - - + -
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Residues in contact with MET 252 (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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45B PHE* 3.7 41.5 - - + -
46B ALA* 3.6 24.0 - - + +
59B TYR 5.2 3.8 - - - +
60B ASN* 6.0 2.9 - - + +
62B GLN* 5.9 0.9 - - - +
248E MET 3.1 20.1 + - - +
249E ASP* 3.6 7.2 - - - +
251E LEU* 1.3 72.9 - - - +
253E LYS* 1.3 66.8 + - - +
254E ASN 3.2 0.5 + - - -
255E ALA* 3.3 16.5 + - - +
266E PHE* 4.0 13.7 - - - -
267E THR* 4.1 17.9 - - + +
270E ILE* 3.7 35.9 - - + -
274E ARG* 4.0 9.4 - - - +
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Residues in contact with LYS 253 (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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45B PHE* 5.5 2.0 - - - -
62B GLN* 5.7 2.7 - - - +
63B LYS* 4.5 11.1 + - - +
64B GLU* 3.5 52.9 + - - +
65B SER* 5.0 11.0 - - - +
66B THR* 4.9 13.5 + - - -
249E ASP 3.0 17.0 + - - +
250E TYR* 3.3 13.9 + - + +
252E MET* 1.3 77.5 - - - +
254E ASN* 1.3 69.8 + - - +
255E ALA 3.5 1.7 + - - -
256E ASP 5.5 0.2 + - - -
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Residues in contact with ASN 254 (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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170C HIS* 5.6 5.7 - - + -
250E TYR* 2.9 58.3 + - - +
251E LEU 3.2 5.2 - - - -
252E MET 3.1 0.2 - - - -
253E LYS* 1.3 92.3 - - - +
255E ALA* 1.3 64.6 + - - +
256E ASP* 3.3 3.1 - - - -
257E TYR* 3.0 18.9 + - + +
258E PHE* 3.1 32.0 + - + -
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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