Contacts of the helix formed by residues 238 - 245 (chain B) in PDB entry 2CMG
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 ASN 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LEU 2.8 26.3 + - - -
249A PRO 3.6 0.4 - - - -
250A LYS* 3.3 22.9 - - + +
253A GLN* 3.3 17.7 + - - +
228B ILE* 4.3 6.3 - - - -
236B TYR 3.7 0.8 + - - -
237B TYR* 1.3 90.0 - - - +
239B GLU* 1.3 62.6 + - - +
240B ASP* 2.7 33.4 + - - +
241B ILE* 2.8 19.9 + - - +
242B HIS* 3.0 20.1 + - - +
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Residues in contact with GLU 239 (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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223B LEU* 4.0 10.8 - - + -
225B THR* 3.6 27.9 + - - -
228B ILE* 4.1 18.4 - - + +
238B ASN* 1.3 73.3 - - - +
240B ASP* 1.3 70.9 + - - +
242B HIS* 4.1 5.4 - - - -
243B ARG* 2.5 58.4 + - + +
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Residues in contact with ASP 240 (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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246A PHE 4.9 1.7 - - - +
247A ALA* 3.8 26.8 - - + +
248A LEU 4.5 3.1 + - - +
253A GLN* 3.9 15.9 + - - -
238B ASN* 2.7 20.9 + - - +
239B GLU* 1.3 77.3 - - - +
241B ILE* 1.3 60.2 + - - +
243B ARG* 3.9 5.3 - - - +
244B ALA* 3.0 24.8 + - - +
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Residues in contact with ILE 241 (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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247A ALA* 4.4 4.3 - - + -
248A LEU* 3.5 32.5 - - - +
249A PRO* 3.6 6.5 - - + -
61B LEU* 4.4 10.5 - - + -
201B PRO* 4.0 19.0 - - + +
202B LEU* 4.6 1.3 - - + -
236B TYR* 3.4 59.9 - - + +
237B TYR* 5.0 2.5 - - + -
238B ASN* 2.8 28.7 + - - +
240B ASP* 1.3 74.3 - - - +
242B HIS* 1.3 70.3 + - - +
244B ALA* 3.2 4.1 + - - +
245B ALA* 2.9 20.4 + - - +
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Residues in contact with HIS 242 (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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61B LEU* 5.2 0.7 - - - -
64B HIS 4.3 0.7 - - - -
65B MET* 3.2 49.8 - - - -
69B THR* 3.7 2.1 - - + +
219B PRO 2.8 27.9 + - - -
220B LEU* 4.4 4.9 - - + -
223B LEU* 3.3 33.8 - - + +
237B TYR* 2.5 41.6 + - + +
238B ASN 3.0 10.4 + - - +
239B GLU* 3.3 12.8 + - - +
241B ILE* 1.3 79.3 - - - +
243B ARG* 1.3 62.0 + - - +
245B ALA* 3.2 17.0 + - - +
246B PHE* 3.6 11.6 - + - -
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Residues in contact with ARG 243 (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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220B LEU* 4.0 42.3 + - + +
223B LEU* 3.1 27.6 - - + +
239B GLU* 2.5 51.2 + - + +
240B ASP* 4.0 4.9 - - - +
242B HIS* 1.3 75.4 - - - +
244B ALA* 1.3 62.9 + - - +
245B ALA 3.3 0.2 + - - -
246B PHE* 3.4 13.5 + - - +
247B ALA* 3.9 6.1 + - - +
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Residues in contact with ALA 244 (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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201A PRO* 6.1 0.2 - - - +
244A ALA* 3.8 26.6 - - + +
247A ALA* 3.6 22.2 - - + -
199B VAL* 5.6 1.4 - - - +
201B PRO* 4.0 14.9 - - + +
240B ASP 3.0 19.0 + - - +
241B ILE 3.7 3.6 - - - +
243B ARG* 1.3 77.3 - - - +
245B ALA* 1.3 63.1 + - - +
247B ALA* 3.0 20.9 + - - +
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Residues in contact with ALA 245 (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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61B LEU* 4.8 3.8 - - + -
65B MET* 4.2 13.7 - - + -
198B PHE* 3.1 16.9 - - + +
199B VAL* 3.1 50.1 + - - +
201B PRO* 3.7 10.0 - - + +
241B ILE 2.9 11.7 + - - +
242B HIS 3.2 15.5 - - - +
243B ARG 3.2 0.6 - - - -
244B ALA* 1.3 77.5 - - - +
246B PHE* 1.3 55.2 + - + +
247B ALA 3.4 2.0 + - - +
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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