Contacts of the helix formed by residues 246 - 257 (chain B) in PDB entry 1D2G
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 CYS 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B HIS* 4.4 0.2 - - - -
177B TYR 4.7 0.4 - - - -
178B ASP* 3.6 27.4 - - - +
181B LEU* 3.8 30.1 - - - -
244B PRO 3.5 4.8 + - - -
245B HIS* 1.3 76.9 - - - +
247B LEU* 1.3 61.4 + - - +
248B ALA* 3.3 4.7 - - + +
249B SER* 3.2 16.3 + - - +
250B PHE* 2.8 30.1 + - - +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B HIS* 4.0 12.9 + - + -
178B ASP* 3.1 20.4 + - - +
246B CYS* 1.3 71.5 - - - +
248B ALA* 1.3 54.1 + - - +
251B THR* 2.6 43.9 + - - +
266B VAL* 4.2 9.2 - - + -
273B TYR* 3.7 21.3 - - + +
284B PHE* 3.5 41.5 - - + -
286B HIS* 3.4 31.2 - - + +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP* 5.2 1.4 + - - +
246B CYS* 3.3 3.6 - - + +
247B LEU* 1.3 76.5 - - - +
249B SER* 1.3 66.9 + - - +
251B THR* 3.7 6.6 - - - -
252B GLU* 3.2 21.1 + - - +
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 4.5 17.7 + - - -
243B TYR* 6.0 0.5 - - - -
245B HIS* 4.8 4.7 - - - -
246B CYS* 3.2 19.6 + - - +
248B ALA* 1.3 74.6 - - - +
250B PHE* 1.3 69.5 + - - +
252B GLU* 3.0 8.9 + - - +
253B LEU* 2.9 28.1 + - - +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PHE* 3.9 27.4 - + + -
157B LEU* 4.9 7.0 - - + -
172B ILE* 4.0 37.5 - - + -
173B ASP 4.6 4.0 - - - -
174B HIS* 3.4 26.2 - - + -
245B HIS* 3.4 29.6 - + + -
246B CYS 2.8 15.5 + - - +
247B LEU 4.0 0.2 - - - +
249B SER* 1.3 80.3 + - - +
251B THR* 1.3 63.8 + - - +
253B LEU* 3.0 9.4 + - + +
254B VAL* 2.9 35.6 + - + +
286B HIS* 3.4 38.8 - + - -
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LEU* 2.6 36.3 + - - +
248B ALA* 3.7 7.4 - - - +
250B PHE* 1.3 73.8 - - - +
252B GLU* 1.3 59.7 + - - +
254B VAL* 3.6 1.3 - - - +
255B GLN* 3.1 37.9 + - - +
264B HIS* 4.1 25.6 + - + +
266B VAL* 5.0 2.3 - - - +
286B HIS* 3.5 16.2 + - - -
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 5.1 8.0 + - - -
248B ALA 3.2 12.0 + - - +
249B SER* 3.0 13.3 + - - +
251B THR* 1.3 76.4 - - - +
253B LEU* 1.3 62.9 + - + +
255B GLN* 3.3 7.4 + - - +
256B GLU* 2.9 46.8 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLN* 3.5 26.9 - - + +
153B HIS* 4.1 13.7 - - + -
154B ARG* 3.6 41.3 - - + +
157B LEU* 3.8 25.7 - - + +
245B HIS* 4.7 11.9 - - + +
249B SER* 2.9 19.7 + - - +
250B PHE* 3.0 8.7 + - + +
252B GLU* 1.3 81.7 - - - +
254B VAL* 1.3 63.2 + - - +
256B GLU* 3.2 18.3 + - - +
257B ALA* 3.1 21.5 + - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 4.3 14.9 - - + +
170B LEU* 4.2 11.0 - - + -
172B ILE* 4.1 18.8 - - + -
250B PHE* 2.9 26.3 + - + +
251B THR* 3.6 7.0 - - - +
253B LEU* 1.3 74.3 - - - +
255B GLN* 1.3 63.3 + - - +
257B ALA* 3.4 10.4 + - + +
258B PHE* 3.1 26.6 - - + -
264B HIS* 3.4 36.1 - - + +
286B HIS* 4.7 3.6 - - - +
288B LEU* 3.8 23.1 - - + -
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B THR* 3.1 27.1 + - - +
252B GLU* 3.3 6.8 + - - +
253B LEU 3.2 0.8 - - - -
254B VAL* 1.3 77.3 - - - +
256B GLU* 1.3 61.8 + - - +
257B ALA 3.0 1.8 - - - -
258B PHE* 3.0 18.0 + - - +
260B GLY* 3.1 24.2 + - - -
262B CYS* 4.4 16.2 - - - +
264B HIS* 3.1 41.8 - - + +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 3.3 48.3 + - - +
252B GLU* 2.9 30.1 + - - +
253B LEU* 3.2 14.5 + - - +
255B GLN* 1.3 77.0 - - - +
257B ALA* 1.3 62.8 + - - +
258B PHE 3.2 0.2 - - - -
259B GLY* 3.2 13.6 + - - +
260B GLY 4.7 2.7 - - - +
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG 5.4 0.4 - - - +
157B LEU* 3.5 39.7 - - + +
158B LYS* 4.1 13.4 - - - +
161B ALA* 3.9 15.6 - - + +
170B LEU* 6.4 0.2 - - + -
253B LEU 3.1 11.7 + - - +
254B VAL* 3.5 13.9 - - + +
255B GLN 3.0 1.0 - - - -
256B GLU* 1.3 79.3 - - - +
258B PHE* 1.3 61.2 + - + +
259B GLY 3.2 1.4 + - - -
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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