Contacts of the helix formed by residues 246 - 260 (chain E) in PDB entry 3SZ9
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 246 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243E PHE* 3.6 4.2 - - - -
245E GLY* 1.3 73.3 - - - -
247E THR* 1.3 65.2 + - - +
248E GLU* 3.7 11.0 + - - +
249E ILE* 3.2 29.0 + - - +
250E GLY 3.0 18.5 + - - -
269E LEU* 3.6 4.4 - - - +
270E GLY* 4.8 2.7 - - - +
399E GLU* 5.5 4.3 - - - -
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Residues in contact with THR 247 (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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245E GLY 3.8 1.6 + - - -
246E SER* 1.3 69.6 - - - +
248E GLU* 1.3 63.2 + - - +
250E GLY* 3.1 10.7 + - - -
251E ARG* 3.2 22.3 + - + +
269E LEU* 3.4 19.0 - - - +
270E GLY* 3.5 4.0 + - - +
425E TYR* 3.4 27.1 - - + -
470E MET* 3.0 40.8 + - + +
262F LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 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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246E SER* 3.1 10.7 + - - +
247E THR* 1.3 81.4 - - - +
249E ILE* 1.3 72.6 + - + +
251E ARG* 3.4 25.0 + - - +
252E VAL* 3.6 9.4 + - + +
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Residues in contact with ILE 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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243E PHE* 3.3 36.1 - - + -
246E SER* 3.1 17.4 + - - +
248E GLU* 1.3 88.3 - - + +
250E GLY* 1.3 67.3 + - - +
251E ARG 3.0 2.2 - - - -
252E VAL* 2.8 28.4 + - + +
253E ILE* 2.9 20.8 + - + +
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Residues in contact with GLY 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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243E PHE* 3.7 4.3 - - - -
246E SER 3.0 13.5 + - - -
247E THR 3.1 6.2 + - - -
249E ILE* 1.3 77.1 - - - +
251E ARG* 1.3 59.8 + - - +
253E ILE* 3.4 3.7 + - - +
254E GLN* 3.1 19.1 + - - +
267E LEU* 3.7 21.9 - - - +
269E LEU* 3.9 20.2 - - - -
262F LEU* 4.2 6.1 - - - -
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Residues in contact with ARG 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 THR* 3.2 21.0 + - - +
248E GLU* 3.6 14.6 - - - +
249E ILE 3.0 0.8 - - - -
250E GLY* 1.3 74.5 - - - +
252E VAL* 1.3 64.7 + - + +
254E GLN* 3.3 2.4 + - - +
255E VAL* 3.0 30.4 + - + +
470E MET* 4.3 17.4 - - - +
236F GLU* 5.3 0.6 + - - -
258F GLY 3.4 18.8 + - - +
259F SER* 2.6 25.2 + - - +
260F SER 2.5 31.5 + - - -
261F ASN* 5.0 0.2 - - - +
262F LEU* 3.8 17.8 - - + +
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Residues in contact with VAL 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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230E ALA* 5.7 9.4 - - + -
233E ALA* 6.1 0.9 - - + -
248E GLU* 4.0 11.7 - - + +
249E ILE* 2.8 28.3 + - + +
251E ARG* 1.3 74.0 - - + +
253E ILE* 1.3 67.0 + - + +
255E VAL* 3.9 5.9 - - - +
256E ALA* 3.0 27.6 + - + +
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Residues in contact with ILE 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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165E ILE* 4.1 11.9 - - + -
229E GLY 5.1 2.5 - - - +
230E ALA* 6.1 0.4 - - - -
233E ALA* 4.0 19.5 - - + +
241E VAL* 3.8 32.7 - - + +
243E PHE* 3.6 36.6 - - + -
249E ILE* 2.9 26.7 + - + +
250E GLY 3.6 7.0 - - - +
251E ARG 3.3 0.2 - - - -
252E VAL* 1.3 79.6 - - + +
254E GLN* 1.3 56.3 + - - +
256E ALA* 3.4 5.5 + - - +
257E ALA* 3.0 26.3 + - - +
265E VAL* 4.6 3.1 - - + -
267E LEU* 3.8 17.3 - - + -
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Residues in contact with GLN 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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250E GLY 3.1 13.2 + - - +
251E ARG 3.3 0.6 + - - +
253E ILE* 1.3 80.2 - - - +
255E VAL* 1.3 61.4 + - - +
257E ALA* 3.6 6.8 + - - +
258E GLY* 3.2 16.6 + - - -
265E VAL* 4.5 15.6 - - + +
267E LEU* 3.9 10.1 - - + +
254F GLN* 3.8 25.1 + - + +
257F ALA* 3.1 35.1 - - - +
258F GLY* 3.3 17.4 - - - +
262F LEU* 3.6 23.0 - - + +
263F LYS 3.5 12.0 + - - +
265F VAL* 3.9 8.7 - - - +
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Residues in contact with VAL 255 (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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251E ARG* 3.0 23.1 + - + +
252E VAL* 3.9 5.8 - - - +
254E GLN* 1.3 73.0 - - - +
256E ALA* 1.3 62.0 + - - +
258E GLY* 3.2 2.6 + - - +
259E SER* 2.8 44.6 + - - +
255F VAL* 3.8 21.0 - - + +
258F GLY 4.0 13.2 - - - -
259F SER* 3.8 23.3 - - - +
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Residues in contact with ALA 256 (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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233E ALA* 3.7 21.0 - - + +
234E SER* 3.7 22.5 + - - +
252E VAL* 3.0 22.2 + - + +
253E ILE 3.5 4.9 - - - +
255E VAL* 1.3 76.9 - - - +
257E ALA* 1.3 55.3 + - - +
259E SER* 3.3 6.8 + - - -
260E SER* 2.8 35.4 + - - -
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Residues in contact with ALA 257 (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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233E ALA 3.9 2.1 + - - -
241E VAL* 5.1 0.2 - - + -
253E ILE 3.0 10.4 + - - +
254E GLN 3.6 7.9 - - - +
255E VAL 3.3 0.2 - - - -
256E ALA* 1.3 75.7 - - - +
258E GLY* 1.3 60.4 + - - +
259E SER 3.4 0.2 + - - -
260E SER* 3.4 6.2 + - - -
262E LEU* 2.9 28.6 + - - -
263E LYS* 3.6 23.1 - - + +
265E VAL* 3.3 33.9 - - + -
254F GLN* 3.6 7.6 - - - +
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Residues in contact with GLY 258 (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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254E GLN 3.2 7.9 + - - -
255E VAL 3.2 3.3 + - - -
257E ALA* 1.3 79.4 - - - +
259E SER* 1.3 60.1 + - - +
260E SER 4.2 1.9 - - - +
262E LEU* 4.2 4.8 - - - +
251F ARG* 3.0 30.6 + - - +
254F GLN* 3.9 29.1 - - - -
255F VAL* 3.8 12.6 - - - -
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Residues in contact with SER 259 (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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236E GLU* 5.0 0.5 - - - +
255E VAL* 2.8 27.8 + - - +
256E ALA* 3.8 6.7 - - - -
257E ALA 3.3 0.4 - - - -
258E GLY* 1.3 76.8 - - - +
260E SER* 1.3 57.3 + - - +
251F ARG* 3.1 16.1 + - - +
255F VAL* 3.7 12.5 - - - +
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Residues in contact with SER 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ALA 3.7 0.9 + - - -
234E SER* 3.2 28.3 + - - -
236E GLU* 3.4 19.9 - - - +
256E ALA 2.8 20.2 + - - -
257E ALA 3.5 2.1 + - - -
258E GLY 3.3 1.1 - - - +
259E SER* 1.3 76.7 - - - +
261E ASN* 1.3 67.6 + - - -
262E LEU 3.4 2.9 + - - -
263E LYS* 3.1 20.1 + - - -
251F ARG* 2.4 32.8 + - - -
470F MET* 4.8 0.5 - - - +
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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