Contacts of the helix formed by residues 244 - 252 (chain C) in PDB entry 6DVD
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 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242C GLY 5.0 4.7 - - - +
243C TRP* 1.3 78.1 - - - +
245C SER* 1.3 63.6 + - - +
246C GLU* 3.2 8.9 + - - +
247C GLN* 3.2 30.3 + - - +
248C ILE* 3.2 21.4 + - - +
270C THR* 5.7 3.8 - - - +
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Residues in contact with SER 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C LYS* 3.7 13.0 + - - +
243C TRP 3.9 0.4 + - - -
244C THR* 1.3 72.6 - - - +
246C GLU* 1.3 65.1 - - - +
248C ILE* 4.1 9.9 - - - -
249C VAL* 3.3 25.3 + - - +
262C LEU* 3.6 17.2 - - - +
268C VAL* 3.4 29.3 - - - +
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C THR* 3.1 7.5 + - - +
245C SER* 1.3 82.8 - - - +
247C GLN* 1.3 64.3 + - - +
248C ILE 3.1 2.0 - - - -
249C VAL* 3.2 10.3 + - + +
250C GLU* 3.2 19.8 + - - +
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Residues in contact with GLN 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLY 5.3 0.7 - - - +
243C TRP* 4.2 44.7 - - + +
244C THR* 3.2 25.4 + - - +
246C GLU* 1.3 78.4 - - - +
248C ILE* 1.3 61.8 + - - +
250C GLU* 3.5 25.5 + - - +
251C ARG* 3.4 20.4 + - - +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C THR* 4.2 14.4 - - + -
238C LEU* 3.7 35.0 - - + -
239C LYS* 4.3 14.6 - - + -
243C TRP* 4.0 28.5 - - + +
244C THR 3.2 19.2 + - - +
245C SER* 4.1 9.2 - - - +
246C GLU 3.1 0.4 - - - -
247C GLN* 1.3 75.2 - - - +
249C VAL* 1.3 64.9 + - - +
251C ARG 3.2 1.2 + - - -
252C PHE* 3.1 47.3 + - + +
258C MET* 4.8 3.8 - - + -
262C LEU* 4.5 17.5 - - + -
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C SER 3.3 18.4 - - - +
246C GLU* 3.2 11.5 + - + +
248C ILE* 1.3 74.3 - - - +
250C GLU* 1.3 61.6 + - - +
252C PHE* 4.7 1.8 - - - +
253C GLY* 3.3 21.1 + - - +
259C ARG* 3.3 41.1 + - - +
262C LEU* 3.6 19.5 - - + -
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU 3.2 12.4 + - - +
247C GLN* 3.6 30.2 + - - +
248C ILE 3.2 0.8 - - - -
249C VAL* 1.3 78.8 - - - +
251C ARG* 1.3 59.3 + - + +
253C GLY* 4.6 1.9 + - - -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C TRP* 3.9 17.4 - - + -
247C GLN* 3.4 11.1 + - + +
248C ILE 3.2 1.6 + - - -
250C GLU* 1.3 83.4 - - + +
252C PHE* 1.3 89.8 + - + +
253C GLY 3.5 0.7 - - - -
254C PHE* 3.3 22.0 - - - -
336C GLU 5.7 0.4 + - - -
339C VAL* 3.5 28.3 - - + +
340C ALA 4.7 2.6 - - - +
343C GLU* 3.0 36.7 + - + +
357C VAL* 4.4 6.9 - - - +
358C PRO* 3.3 31.5 - - - +
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Residues in contact with PHE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LEU* 4.0 23.8 - - + -
243C TRP* 4.3 8.7 - + - -
248C ILE* 3.1 29.1 + - + +
249C VAL* 4.0 2.9 - - - -
251C ARG* 1.3 98.0 - - + +
253C GLY* 1.3 62.8 + - - +
254C PHE* 3.4 10.4 + + - -
255C SER* 3.6 10.0 + - - +
258C MET* 3.5 50.5 - - + +
259C ARG* 4.7 3.4 + - - -
339C VAL* 4.1 15.7 - - + -
342C ILE* 3.7 33.7 - - + -
343C GLU* 4.3 13.2 - - + -
346C VAL* 4.6 11.2 - - + -
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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