Contacts of the helix formed by residues 249 - 257 (chain A) in PDB entry 2CXN
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LYS 4.3 0.7 - - - +
212A THR* 3.0 31.7 + - - +
214A THR* 4.6 3.8 - - - +
247A SER* 3.1 7.6 + - - +
248A THR* 1.3 77.9 + - - +
250A THR* 1.3 62.3 + - - +
251A ALA* 3.5 10.2 + - - +
252A LYS* 3.2 35.9 + - + +
253A VAL* 3.1 24.3 + - - +
263A MET* 3.7 3.1 - - - -
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Residues in contact with THR 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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248A THR 3.6 5.2 + - - -
249A ASN* 1.3 73.1 + - - +
251A ALA* 1.3 63.2 + - - +
253A VAL* 3.4 2.4 + - - +
254A LYS* 3.0 36.0 + - - +
260A PRO* 5.3 11.4 - - + -
263A MET* 3.6 29.6 - - - +
265A GLU* 4.2 13.1 + - - +
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Residues in contact with ALA 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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249A ASN* 3.3 8.8 + - - +
250A THR* 1.3 78.7 - - - +
252A LYS* 1.3 58.1 + - + +
254A LYS* 3.4 8.3 + - - +
255A GLU* 2.9 40.8 + - - +
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Residues in contact with LYS 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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213A PHE* 3.7 23.2 - - + +
214A THR* 4.1 21.2 - - + +
249A ASN* 3.2 33.3 + - - +
251A ALA* 1.3 77.7 - - + +
253A VAL* 1.3 60.9 + - - +
255A GLU* 3.2 34.5 + - + +
256A PHE* 3.0 28.4 + - - +
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Residues in contact with VAL 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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213A PHE* 3.7 35.7 - - + -
245A ALA* 3.8 20.4 - - + -
247A SER* 3.8 13.2 - - - -
249A ASN 3.1 21.1 + - - +
250A THR 3.6 4.5 - - - +
251A ALA 3.4 0.2 - - - -
252A LYS* 1.3 76.9 - - - +
254A LYS* 1.3 63.5 + - - +
256A PHE* 3.3 5.0 + - - +
257A GLY 3.3 4.9 + - - -
258A ILE* 3.2 41.7 + - + +
259A ASP 4.9 0.4 - - - +
260A PRO* 5.7 1.3 - - + -
263A MET* 4.0 22.7 - - + -
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Residues in contact with LYS 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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250A THR* 3.0 27.2 + - + +
251A ALA* 3.5 7.6 - - - +
253A VAL* 1.3 76.1 - - - +
255A GLU* 1.3 57.6 + - - +
257A GLY* 3.0 21.0 + - - -
258A ILE 3.9 12.5 - - - +
260A PRO* 5.1 20.2 - - + -
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Residues in contact with GLU 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 ALA* 2.9 30.7 + - - +
252A LYS* 3.2 44.9 + - + +
253A VAL 3.3 0.2 - - - -
254A LYS* 1.3 75.5 - - - +
256A PHE* 1.3 62.0 + - - +
257A GLY* 3.3 1.0 + - - -
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Residues in contact with PHE 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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208A ILE* 4.5 2.2 - - + -
213A PHE* 3.7 17.9 - + + -
219A ILE* 4.5 9.9 - - + -
222A ALA* 3.6 38.4 - - + -
223A GLU* 3.6 35.2 - - + -
226A LYS* 2.8 49.7 + - + -
239A VAL* 5.8 0.2 - - + -
243A PHE* 4.5 10.3 - + - -
252A LYS 3.0 16.8 + - - +
253A VAL 3.6 4.9 - - - +
254A LYS 3.2 0.4 - - - -
255A GLU* 1.3 75.4 - - - +
257A GLY* 1.3 57.4 + - - +
258A ILE* 3.7 35.0 - - + -
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Residues in contact with GLY 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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226A LYS* 4.5 4.2 + - - -
239A VAL* 4.1 18.4 - - - +
254A LYS 3.0 14.1 + - - -
255A GLU 3.1 1.5 - - - -
256A PHE* 1.3 79.8 - - - +
258A ILE* 1.3 64.6 + - - +
259A ASP 4.0 1.0 + - - -
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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