Contacts of the helix formed by residues 232 - 243 (chain A) in PDB entry 2QJ3
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASP* 3.6 8.3 - - - -
217A PRO* 4.7 2.2 - - - -
230A VAL* 3.3 9.7 - - - +
231A THR* 1.3 79.9 + - - +
233A ALA* 1.3 64.4 + - - +
234A ALA* 3.5 7.0 + - - +
235A ALA* 3.0 26.6 + - - +
236A ALA* 3.1 15.8 + - - +
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Residues in contact with ALA 233 (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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103A VAL* 4.3 4.3 - - + -
214A THR* 3.6 30.3 - - + +
215A ALA 3.5 25.8 - - - +
216A ASP* 3.1 16.4 + - - +
217A PRO* 4.6 2.5 - - - +
231A THR 4.2 0.2 + - - -
232A SER* 1.3 70.5 - - - +
234A ALA* 1.3 66.4 + - - +
236A ALA* 3.0 9.0 + - - +
237A MET* 2.9 28.5 + - - +
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Residues in contact with ALA 234 (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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214A THR* 5.2 1.9 - - - +
232A SER* 3.4 7.0 + - - +
233A ALA* 1.3 76.8 - - - +
235A ALA* 1.3 60.5 + - - +
237A MET* 3.3 5.7 + - - +
238A ASP* 2.7 37.0 + - - +
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Residues in contact with ALA 235 (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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230A VAL* 4.0 10.5 - - + -
231A THR* 5.3 1.3 - - - +
232A SER* 3.0 26.5 + - - +
234A ALA* 1.3 76.4 - - - +
236A ALA* 1.3 63.5 + - - +
238A ASP* 3.1 11.1 + - - +
239A THR* 2.9 28.7 + - - +
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Residues in contact with ALA 236 (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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98A TYR* 2.7 42.4 + - + +
103A VAL* 4.6 8.7 - - + -
217A PRO* 6.4 0.2 - - + -
221A LEU* 4.8 5.2 - - + -
230A VAL* 3.5 24.6 - - + +
232A SER 3.1 4.9 + - - +
233A ALA* 3.0 12.8 + - - +
235A ALA* 1.3 78.8 - - - +
237A MET* 1.3 53.3 + - - +
239A THR* 3.2 3.3 + - - -
240A LEU* 2.8 24.6 + - - +
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Residues in contact with MET 237 (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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98A TYR* 4.0 21.5 - - - -
103A VAL* 4.3 3.6 - - + -
104A ILE* 4.1 24.2 - - + -
112A LEU* 4.5 6.3 - - + -
209A ALA* 3.8 35.2 - - + +
212A ILE* 5.2 3.1 - - + -
214A THR* 3.9 15.7 - - - +
233A ALA 2.9 20.4 + - - +
234A ALA* 3.8 5.4 - - - +
236A ALA* 1.3 71.8 - - - +
238A ASP* 1.3 65.2 + - - +
240A LEU* 3.6 24.7 - - + +
241A VAL* 3.1 31.0 + - + +
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Residues in contact with ASP 238 (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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234A ALA* 2.7 31.7 + - - +
235A ALA* 3.3 10.4 + - - +
237A MET* 1.3 76.6 - - - +
239A THR* 1.3 62.0 + - - +
241A VAL* 3.3 5.6 + - - +
242A SER* 2.9 26.9 + - - -
283B ARG* 3.6 18.8 + - - +
284B GLY* 3.6 30.1 + - - +
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Residues in contact with THR 239 (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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94A GLU* 5.8 0.9 - - - +
98A TYR* 4.4 3.6 - - - +
223A SER* 3.2 28.9 - - - +
225A ARG* 3.8 36.8 + - + +
230A VAL* 5.2 3.3 - - - +
235A ALA* 2.9 17.1 + - - +
236A ALA* 3.4 8.6 - - - -
238A ASP* 1.3 75.6 - - - +
240A LEU* 1.3 53.8 + - - +
242A SER* 3.2 8.4 + - - -
243A GLN* 2.7 41.6 + - + +
283B ARG* 4.3 5.9 + - - +
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Residues in contact with LEU 240 (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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91A SER 5.7 0.9 - - - +
94A GLU* 4.0 33.7 - - + +
95A ILE* 4.0 19.3 - - + +
98A TYR* 3.8 24.8 + - + +
104A ILE* 5.7 0.9 - - + -
112A LEU* 3.9 21.3 - - + -
116A ARG* 5.4 5.1 + - - +
205A PHE* 3.7 18.0 - - + -
209A ALA* 5.4 0.2 - - + -
236A ALA 2.8 20.1 + - - +
237A MET* 3.6 30.5 - - + +
239A THR* 1.3 74.2 - - - +
241A VAL* 1.3 64.5 + - + +
243A GLN* 3.3 15.6 - - - +
244A LEU* 3.8 2.6 + - - -
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Residues in contact with VAL 241 (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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202A LEU* 3.7 21.0 - - + +
205A PHE* 3.6 18.4 - - + -
206A ALA* 4.0 23.3 - - + +
209A ALA* 3.7 28.9 - - + -
237A MET 3.1 16.0 + - - +
238A ASP* 3.6 7.6 - - - +
240A LEU* 1.3 72.5 - - + +
242A SER* 1.3 58.2 + - - +
243A GLN 3.0 4.5 - - - -
244A LEU* 2.9 30.8 + - - +
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Residues in contact with SER 242 (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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202A LEU* 4.8 6.7 - - - -
225A ARG* 5.5 4.2 - - - -
238A ASP 2.9 18.2 + - - -
239A THR* 3.3 9.0 + - - +
241A VAL* 1.3 76.6 - - - +
243A GLN* 1.3 58.0 + - - +
244A LEU 3.1 2.3 + - - -
245A THR* 3.5 8.5 + - - -
246A GLN* 3.1 28.2 - - - +
283B ARG* 3.4 32.2 + - - -
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Residues in contact with GLN 243 (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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94A GLU* 3.7 21.1 - - - +
116A ARG* 4.8 2.0 - - - +
194A HIS* 2.8 34.8 + - + -
224A ASN* 3.6 21.9 + - + +
225A ARG* 3.4 30.7 - - + +
239A THR* 2.7 23.5 + - + +
240A LEU 3.3 10.3 - - - +
241A VAL 3.0 0.8 - - - -
242A SER* 1.3 72.4 - - - +
244A LEU* 1.3 60.0 + - - +
245A THR 3.2 0.4 - - - -
246A GLN* 3.3 22.8 + - - +
247A PRO 2.7 34.8 + - - -
248A VAL* 3.9 2.8 - - - +
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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