Contacts of the helix formed by residues 246 - 257 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A HIS* 4.4 0.4 - - - -
177A TYR 4.7 0.4 - - - -
178A ASP* 3.5 29.2 - - - +
181A LEU* 3.6 31.2 - - - -
244A PRO 3.5 5.7 + - - -
245A HIS* 1.3 75.9 - - - +
247A LEU* 1.3 60.5 + - - +
248A ALA* 3.4 4.0 - - + +
249A SER* 3.1 16.9 + - - +
250A PHE* 2.8 28.9 + - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A HIS* 4.0 14.1 + - + -
178A ASP* 3.0 19.1 + - - +
246A CYS* 1.3 70.0 - - - +
248A ALA* 1.3 56.8 + - - +
251A THR* 2.6 49.8 + - - +
266A VAL* 4.4 10.3 - - + -
273A TYR* 3.8 21.3 - - + +
284A PHE* 3.3 42.6 - - + -
286A HIS* 3.6 23.1 - - + +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 5.3 1.2 + - - -
246A CYS* 3.4 3.2 - - + +
247A LEU* 1.3 79.2 - - - +
249A SER* 1.3 63.4 + - - +
251A THR* 3.5 5.6 + - - -
252A GLU* 3.3 21.5 + - - +
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLN* 4.2 14.7 + - - -
243A TYR* 5.9 0.9 - - - -
245A HIS* 4.9 5.5 - - - -
246A CYS* 3.1 20.9 + - - +
248A ALA* 1.3 76.9 - - - +
250A PHE* 1.3 67.1 + - - +
252A GLU* 3.3 7.2 + - - +
253A LEU* 3.0 25.6 + - - +
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.8 28.3 - + + -
157A LEU* 4.6 11.7 - - + -
172A ILE* 3.8 34.1 - - + -
173A ASP 5.0 4.0 - - - -
174A HIS* 3.5 33.2 - - + -
245A HIS* 3.4 30.5 - + + -
246A CYS 2.8 19.0 + - - +
247A LEU 4.1 0.2 - - - +
249A SER* 1.3 74.4 + - - +
251A THR* 1.3 57.3 + - - +
253A LEU* 3.1 8.7 + - + +
254A VAL* 2.8 43.2 + - + +
286A HIS* 3.7 24.9 - + - -
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 2.6 32.9 + - - +
248A ALA* 3.7 6.7 - - - +
249A SER 3.3 0.2 - - - -
250A PHE* 1.3 78.1 - - - +
252A GLU* 1.3 61.2 + - - +
254A VAL* 3.8 0.9 - - - +
255A GLN* 3.2 37.5 + - - +
264A HIS* 4.1 25.4 + - + +
266A VAL* 4.6 3.3 - - + +
286A HIS* 3.4 15.6 - - - -
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 4.7 12.0 + - - -
248A ALA 3.3 10.9 + - - +
249A SER* 3.7 9.2 - - - +
250A PHE 3.2 0.6 - - - -
251A THR* 1.3 77.8 - - - +
253A LEU* 1.3 70.5 + - - +
255A GLN* 4.0 6.4 - - - +
256A GLU* 3.3 36.4 + - - +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLN* 3.8 23.3 - - + +
153A HIS* 4.0 24.0 - - + -
154A ARG* 3.7 44.6 - - + +
157A LEU* 3.9 19.5 - - + +
245A HIS* 4.6 14.6 - - + +
249A SER* 3.0 17.2 + - - +
250A PHE* 3.1 10.5 + - + +
252A GLU* 1.3 84.7 - - - +
254A VAL* 1.3 62.0 + - - +
255A GLN 3.3 1.0 + - - -
256A GLU* 3.4 13.5 + - - +
257A ALA* 3.4 18.2 + - - +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 4.1 19.7 - - + +
170A LEU* 4.1 25.1 - - + -
172A ILE* 4.3 15.5 - - + -
250A PHE* 2.8 27.0 + - + +
251A THR 3.8 4.3 - - - +
253A LEU* 1.3 73.2 - - - +
255A GLN* 1.3 62.2 + - - +
257A ALA* 3.7 5.3 - - + +
258A PHE* 3.3 22.1 - - + -
264A HIS* 3.2 38.1 - - + +
286A HIS* 4.3 4.3 - - - +
288A LEU* 3.8 8.1 - - + +
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Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A THR* 3.2 28.2 + - - +
252A GLU* 4.0 6.1 - - - +
253A LEU 3.2 0.8 - - - -
254A VAL* 1.3 73.9 - - - +
256A GLU* 1.3 61.4 + - - +
257A ALA 3.0 4.9 - - - -
258A PHE* 3.1 10.4 + - - +
260A GLY* 3.0 27.1 + - - -
262A CYS* 4.3 15.4 - - - -
264A HIS* 3.2 42.5 - - + +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.4 46.7 + - - +
252A GLU* 3.3 28.7 + - - +
253A LEU* 3.4 15.7 + - - +
255A GLN* 1.3 79.0 - - - +
257A ALA* 1.3 57.7 + - - +
258A PHE 3.1 1.1 - - - -
259A GLY* 3.0 18.3 + - - +
260A GLY* 4.4 3.1 - - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG 5.3 0.4 - - - +
157A LEU* 3.4 39.7 - - + +
158A LYS* 4.1 15.7 - - - +
161A ALA* 3.7 15.4 - - + +
253A LEU 3.4 11.4 + - - +
254A VAL* 3.7 13.9 - - + +
255A GLN 3.0 1.0 - - - -
256A GLU* 1.3 78.6 - - - +
258A PHE* 1.3 60.2 + - + +
259A GLY 3.3 1.3 - - - -
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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