Contacts of the helix formed by residues 240 - 253 (chain D) in PDB entry 7CE1
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 PRO 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238D GLU 3.6 6.7 - - - +
239D THR* 1.3 93.1 - - + +
241D LEU* 1.3 61.0 + - - +
242D ASP* 3.1 18.4 - - - +
243D LYS* 3.1 12.7 + - + +
244D ILE* 3.1 21.3 + - - +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C TRP* 3.7 35.0 - - + -
90D LEU* 4.1 33.7 - - + -
237D ILE 5.6 2.2 - - - +
239D THR 4.3 3.8 - - - +
240D PRO* 1.3 69.7 - - - +
242D ASP* 1.3 65.4 + - - +
244D ILE* 3.3 23.9 + - + +
245D ARG* 3.0 24.6 + - - +
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Residues in contact with ASP 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C TRP* 4.1 11.7 - - + -
240D PRO* 3.1 23.1 - - - +
241D LEU* 1.3 75.0 + - - +
243D LYS* 1.3 73.5 + - - +
245D ARG* 3.4 8.9 + - - +
246D ASP* 3.2 22.3 + - - +
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ILE* 4.7 0.3 - - - +
239D THR* 3.7 16.8 - - + -
240D PRO* 3.1 17.0 + - + +
242D ASP* 1.3 87.0 + - - +
244D ILE* 1.3 65.0 + - - +
246D ASP* 3.5 6.8 + - - +
247D PHE* 3.2 21.5 + - - +
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Residues in contact with ILE 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ILE* 5.2 13.9 - - + -
235D ILE* 3.8 24.2 - - + +
236D THR 3.9 9.9 - - - +
237D ILE* 4.7 4.5 - - - +
239D THR* 3.5 44.2 - - + +
240D PRO 3.1 7.2 + - - +
241D LEU* 3.3 23.3 + - + +
243D LYS* 1.3 73.8 - - - +
245D ARG* 1.3 62.8 + - - +
247D PHE* 3.1 3.0 + - + +
248D GLY* 2.9 27.3 + - - -
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Residues in contact with ARG 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C TRP* 4.6 20.6 - - + -
241D LEU 3.0 17.7 + - - +
242D ASP* 3.5 7.9 - - - +
244D ILE* 1.3 77.1 - - - +
246D ASP* 1.3 67.7 + - - +
248D GLY* 3.3 2.9 + - - -
249D LYS* 3.1 40.5 + - - +
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Residues in contact with ASP 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ASP 3.2 11.2 + - - +
243D LYS* 3.7 10.3 - - - +
244D ILE 3.3 0.2 - - - -
245D ARG* 1.3 85.0 - - - +
247D PHE* 1.3 57.3 + - - +
249D LYS* 3.3 14.5 + - - +
250D ARG* 3.0 57.1 + - - +
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Residues in contact with PHE 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 5.9 0.4 - + - -
232D LEU* 3.3 37.2 - - + -
233D ASP* 5.3 3.1 - - - -
234D ALA* 3.6 30.5 - - + -
235D ILE* 3.3 34.3 - - + -
243D LYS 3.2 7.8 + - - +
244D ILE* 3.1 3.7 + - + +
246D ASP* 1.3 75.5 - - - +
248D GLY* 1.3 65.2 + - - +
250D ARG* 3.1 11.2 + - + +
251D LEU* 2.8 51.2 + - + +
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Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE* 2.9 14.3 + - - -
245D ARG* 3.3 4.7 + - - -
246D ASP 3.3 0.2 - - - -
247D PHE* 1.3 82.1 - - - +
249D LYS* 1.3 60.2 + - - +
251D LEU* 3.4 4.8 + - - +
252D MET* 3.2 30.7 + - - +
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Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ARG* 3.1 32.7 + - - +
246D ASP* 3.7 17.0 - - - +
247D PHE 3.2 0.2 - - - -
248D GLY* 1.3 76.1 - - - +
250D ARG* 1.3 61.3 + - - +
252D MET* 3.6 3.6 + - - +
253D GLN* 3.1 66.3 + - + +
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Residues in contact with ARG 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ASP* 3.0 52.6 + - - +
247D PHE* 3.1 12.1 + - + +
249D LYS* 1.3 78.9 - - - +
251D LEU* 1.3 65.2 + - - +
253D GLN* 3.4 14.3 + - - +
254D SER* 3.2 22.0 + - - -
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.7 35.9 - - + -
232D LEU* 4.5 4.5 - - + -
247D PHE* 2.8 46.0 + - + +
248D GLY* 3.9 4.7 - - - +
249D LYS 3.3 0.2 - - - -
250D ARG* 1.3 76.5 - - - +
252D MET* 1.3 91.6 + - + +
254D SER* 3.2 18.7 + - - -
256D ASP 4.0 1.1 - - - +
257D ARG* 3.6 22.6 - - + +
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Residues in contact with MET 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D GLY* 3.2 18.3 + - - +
249D LYS* 4.2 4.0 - - - +
251D LEU* 1.3 96.5 - - + +
253D GLN* 1.3 62.0 + - + +
254D SER 3.1 2.0 - - - +
257D ARG* 3.3 38.1 - - + +
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Residues in contact with GLN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D LYS* 3.1 58.6 + - + +
250D ARG* 3.6 14.6 - - - +
251D LEU 3.3 0.4 - - - -
252D MET* 1.3 77.6 - - + +
254D SER* 1.3 57.4 + - - +
255D ASP* 4.2 1.2 + - - +
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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