Contacts of the helix formed by residues 243 - 256 (chain E) in PDB entry 2Q5E
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 THR 243 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144E PRO 5.6 0.2 - - - -
145E TYR* 3.8 28.3 - - + +
241E ALA 3.2 14.9 + - - +
242E ASP* 1.3 75.9 - - - +
244E GLU* 1.3 59.2 + - - +
245E LEU 3.2 2.5 - - - -
246E LEU* 2.8 32.0 + - + -
247E ASN* 3.1 31.9 + - - -
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Residues in contact with GLU 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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143E ARG* 3.5 21.8 - - - +
233E VAL* 4.4 9.9 - - + -
234E GLN* 3.6 31.5 + - + +
242E ASP* 3.0 20.6 + - - +
243E THR* 1.3 80.9 + - - +
245E LEU* 1.3 61.4 + - - +
247E ASN* 3.4 22.1 + - - +
248E LEU* 3.2 26.4 + - + +
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Residues in contact with LEU 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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111E THR* 4.4 10.1 - - + +
112E LEU* 4.3 11.0 - - + -
143E ARG* 3.7 30.5 - - + +
144E PRO 4.0 12.1 - - - +
145E TYR* 4.4 0.9 - - - +
146E VAL* 3.7 40.4 - - + -
149E PHE* 3.4 54.3 - - + -
216E LEU* 4.6 6.1 - - + -
233E VAL* 5.0 2.7 - - + -
242E ASP* 4.2 1.2 + - - -
243E THR 3.2 1.0 - - - -
244E GLU* 1.3 79.3 - - - +
246E LEU* 1.3 61.0 + - - +
248E LEU* 3.3 21.6 + - + +
249E ILE* 3.6 4.0 + - - +
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Residues in contact with LEU 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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145E TYR* 3.5 51.3 - - + +
148E GLU* 5.6 3.6 - - + -
243E THR* 2.8 14.4 + - + +
245E LEU* 1.3 75.8 - - - +
247E ASN* 1.3 63.3 + - - +
248E LEU 2.9 10.4 + - - -
249E ILE* 3.2 30.1 + - + +
250E PRO* 3.5 7.8 - - - +
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Residues in contact with ASN 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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243E THR* 3.1 34.2 + - - +
244E GLU* 3.4 26.3 + - - +
246E LEU* 1.3 79.3 - - - +
248E LEU* 1.3 59.4 + - - +
249E ILE 3.5 0.2 - - - -
250E PRO* 3.5 15.6 - - - +
251E ILE* 3.7 16.0 - - + +
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Residues in contact with LEU 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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149E PHE* 4.4 3.4 - - + -
216E LEU* 3.8 25.1 - - + -
231E VAL* 3.8 20.0 - - + -
232E PRO 5.0 3.8 - - - +
233E VAL* 4.4 13.9 - - + -
244E GLU* 3.2 15.9 + - + +
245E LEU* 3.6 27.1 - - + +
246E LEU 2.9 1.6 + - - -
247E ASN* 1.3 80.3 - - + +
249E ILE* 1.3 66.1 + - - +
250E PRO* 3.3 1.6 - - - -
251E ILE* 3.0 28.3 + - + +
252E PHE* 3.1 42.8 + - + -
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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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145E TYR 5.2 0.9 - - - +
148E GLU* 4.4 9.2 - - + +
149E PHE* 3.9 38.4 - - + +
152E ARG* 3.3 34.3 - - + -
153E MET* 5.4 3.5 - - + +
156E LEU* 5.3 0.3 - - - +
245E LEU 3.6 13.4 + - - +
246E LEU* 3.2 24.6 + - + +
248E LEU* 1.3 78.1 - - - +
250E PRO* 1.4 65.5 - - + +
252E PHE* 3.4 5.6 + - - +
253E GLU* 2.8 38.0 + - - +
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Residues in contact with PRO 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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246E LEU 3.5 11.4 - - - +
247E ASN* 3.5 11.0 - - - +
248E LEU 3.4 2.7 - - - -
249E ILE* 1.4 96.6 - - + +
251E ILE* 1.3 54.8 + - + +
253E GLU* 3.2 19.5 - - + +
254E GLU* 2.7 34.0 + - - +
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Residues in contact with ILE 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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231E VAL* 4.9 8.1 - - + -
247E ASN* 3.7 20.4 - - + +
248E LEU* 3.0 29.7 + - + +
250E PRO* 1.3 76.4 - - + +
252E PHE* 1.3 69.7 + - + +
254E GLU* 3.3 8.5 + - - +
255E LEU* 3.2 33.7 + - + +
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Residues in contact with PHE 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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104E VAL* 4.2 15.3 - - + -
149E PHE* 4.5 6.3 - + - -
153E MET* 3.7 34.5 - - + -
156E LEU* 5.4 0.2 - - + -
157E PHE* 3.4 26.4 - + + -
214E LEU* 4.1 13.0 - - + -
216E LEU* 4.1 20.9 - - + -
231E VAL* 4.0 33.0 - - + -
248E LEU* 3.1 57.0 + - + -
249E ILE 4.1 2.7 - - - +
251E ILE* 1.3 74.3 - - + +
253E GLU* 1.3 56.2 + - - +
255E LEU* 2.9 7.6 + - + +
256E SER* 2.6 36.6 + - - -
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Residues in contact with GLU 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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152E ARG* 2.7 35.8 + - - +
156E LEU* 3.5 22.6 - - + +
249E ILE* 2.8 25.3 + - + +
250E PRO* 3.1 25.9 + - + +
252E PHE* 1.3 75.1 - - - +
254E GLU* 1.3 60.9 + - - +
256E SER* 2.1 29.9 + - - -
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Residues in contact with GLU 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 PRO 2.7 16.0 + - - +
251E ILE* 3.6 10.8 - - - +
253E GLU* 1.3 74.3 - - - +
255E LEU* 1.3 64.2 + - + +
257E GLY 4.6 2.8 + - - -
258E ALA* 5.1 2.8 + - - +
264E SER* 6.0 0.3 - - - -
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Residues in contact with LEU 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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102E ILE* 3.1 13.5 - - + +
157E PHE* 4.6 1.1 - - + -
214E LEU* 3.8 33.0 - - + -
231E VAL* 5.0 6.1 - - + -
251E ILE* 3.2 25.7 + - + +
252E PHE* 2.9 13.5 + - + +
254E GLU* 1.3 81.0 - - + +
256E SER* 1.3 67.2 + - - +
257E GLY 2.9 4.8 + - - -
258E ALA* 3.0 19.7 + - + +
261E VAL* 5.4 4.7 - - + +
264E SER* 3.3 40.6 - - - +
265E LEU* 4.7 15.3 - - + +
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Residues in contact with SER 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ARG* 5.4 2.6 - - - +
102E ILE* 3.6 17.7 + - - +
156E LEU* 3.8 38.6 - - - +
157E PHE* 3.7 15.0 - - - -
212E LYS* 5.8 0.2 + - - -
252E PHE 2.6 14.6 + - - -
253E GLU* 2.1 32.8 + - - -
255E LEU* 1.3 69.3 - - - +
257E GLY* 1.3 57.2 + - - +
258E ALA 4.5 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