Contacts of the helix formed by residues 246 - 257 (chain D) in PDB entry 1DGH
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D ILE* 5.1 0.2 - - - -
245D LEU* 1.3 75.6 - - - +
247D VAL* 1.3 60.3 + - - +
248D GLU* 3.8 18.9 + - - -
249D ASP* 3.1 34.2 + - - +
250D ALA* 2.8 28.2 + - - +
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Residues in contact with VAL 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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127D ARG* 3.7 18.8 - - - +
205D ILE* 4.6 6.3 - - + +
245D LEU 3.9 0.8 + - - -
246D SER* 1.3 72.9 - - - +
248D GLU* 1.3 70.4 + - + +
250D ALA* 3.5 5.4 + - - +
251D ALA* 3.0 29.8 + - + +
462D ASN* 3.6 25.4 - - - +
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Residues in contact with GLU 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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246D SER* 3.8 15.1 + - - +
247D VAL* 1.3 92.5 + - + +
249D ASP* 1.3 68.2 + - - +
251D ALA* 3.3 6.0 + - - +
252D ARG* 3.0 23.7 + - - +
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Residues in contact with ASP 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 LEU* 4.4 15.3 - - + +
246D SER* 3.1 27.3 + - - +
248D GLU* 1.3 81.2 - - - +
250D ALA* 1.3 56.7 + - - +
252D ARG* 2.8 35.1 + - - +
253D LEU* 2.9 37.6 + - + +
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Residues in contact with ALA 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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125D THR* 2.9 39.6 + - - +
205D ILE* 3.6 41.3 - - + -
245D LEU* 4.3 6.0 - - + +
246D SER 2.8 20.4 + - - +
247D VAL 3.8 2.9 - - - +
249D ASP* 1.3 74.1 - - - +
251D ALA* 1.3 56.5 + - - +
253D LEU* 4.6 0.9 - - - -
254D SER* 3.0 12.8 + - - -
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Residues in contact with ALA 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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255B GLN* 3.0 42.8 - - - +
247D VAL* 3.0 19.5 + - + +
248D GLU* 3.7 7.0 - - - +
250D ALA* 1.3 75.4 - - - +
252D ARG* 1.3 65.4 + - - +
254D SER* 2.9 21.3 + - - -
255D GLN* 3.5 1.2 + - - +
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Residues in contact with ARG 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 GLU 3.0 16.6 + - - +
249D ASP* 2.8 37.7 + - - +
251D ALA* 1.3 76.4 - - - +
253D LEU* 1.3 79.2 + - - +
255D GLN* 3.0 14.9 + - - +
256D GLU* 2.8 61.5 + - + +
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Residues in contact with LEU 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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125D THR* 3.7 13.5 - - + +
245D LEU* 4.0 32.1 - - + -
249D ASP* 2.9 22.4 + - + +
252D ARG* 1.3 94.5 - - - +
254D SER* 1.3 56.6 + - - +
255D GLN 2.9 5.2 - - - -
256D GLU* 4.0 16.2 - - + +
257D ASP* 2.7 40.6 + - + +
260D TYR* 3.9 37.2 - - + -
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Residues in contact with SER 254 (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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254B SER 5.3 3.3 - - - +
255B GLN* 3.4 18.7 + - - +
123D ALA* 3.6 28.8 - - - +
125D THR* 3.4 13.4 + - - +
126D VAL* 4.8 4.3 - - - -
250D ALA 3.0 16.9 + - - -
251D ALA* 2.9 17.0 + - - -
253D LEU* 1.3 76.4 - - - +
255D GLN* 1.3 56.1 + - - +
257D ASP 4.7 1.8 - - - -
258D PRO* 3.6 19.7 - - - +
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Residues in contact with GLN 255 (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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251B ALA* 3.2 43.9 + - + +
252B ARG* 5.4 1.0 - - - +
254B SER* 3.4 14.8 + - - +
255B GLN* 4.0 18.2 - - + +
251D ALA 4.0 1.6 - - - +
252D ARG* 3.0 14.0 + - - +
253D LEU 2.9 0.2 - - - -
254D SER* 1.3 80.8 + - - +
256D GLU* 1.3 87.0 + - - +
257D ASP 3.5 0.4 + - - -
258D PRO* 4.1 7.7 - - - +
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Residues in contact with GLU 256 (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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252D ARG* 2.8 53.2 + - - +
253D LEU* 4.0 14.9 - - + +
255D GLN* 1.3 97.1 + - - +
257D ASP* 1.3 61.5 + - + +
258D PRO* 4.0 2.5 - - - +
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Residues in contact with ASP 257 (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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124D ASP 5.3 0.3 + - - -
125D THR* 5.2 0.9 + - - -
253D LEU* 2.7 24.8 + - + +
254D SER* 4.7 0.3 - - - -
256D GLU* 1.3 77.3 - - + +
258D PRO* 1.3 61.6 - - - +
259D ASP* 3.0 27.7 + - - +
260D TYR* 3.1 40.8 + - + +
263D ARG* 2.9 42.3 + - - -
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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