Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 2CN8
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 LYS 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.8 26.2 - - + +
237A ALA 3.6 5.4 - - - -
238A PHE* 3.6 27.4 - - + -
243A CYS 3.6 2.2 + - - +
244A LYS* 1.3 85.6 - - - +
246A VAL* 1.3 66.9 + - - +
289A LYS* 5.5 0.2 - - - -
303A LEU* 3.7 30.6 + - + +
305A GLU* 5.3 8.6 - - - +
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Residues in contact with VAL 246 (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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220A TYR* 3.9 16.8 - - + -
236A LEU* 3.8 8.3 - - - +
237A ALA* 2.9 46.9 + - + +
239A GLU* 4.2 14.8 - - + +
244A LYS* 3.8 14.1 - - + -
245A LYS* 1.3 80.1 - - - +
247A ALA* 1.3 62.5 + - - +
248A ILE* 4.3 0.7 - - + -
289A LYS* 3.8 25.8 - - + -
300A VAL* 3.7 22.7 - - + -
301A LEU 3.5 8.7 - - - +
303A LEU* 4.0 10.5 - - - +
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Residues in contact with ALA 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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226A LEU* 4.0 10.5 - - + -
234A VAL* 4.0 5.6 - - + -
235A LYS 3.3 9.6 - - - +
246A VAL* 1.3 73.0 - - - +
248A ILE* 1.3 65.6 + - - +
249A LYS 4.3 0.2 - - - -
300A VAL* 3.5 1.6 - - - +
301A LEU* 2.7 36.3 + - - +
302A GLU 3.9 6.1 - - - +
303A LEU* 4.2 2.8 - - + +
1506A DBQ 3.7 38.1 - - + +
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Residues in contact with ILE 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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216A LEU* 4.8 3.8 - - + -
220A TYR* 4.1 21.1 - - + -
222A MET* 3.5 24.5 - - + -
233A GLU 3.8 0.2 - - - +
234A VAL* 3.5 3.7 - - - -
235A LYS* 2.9 34.2 + - - +
237A ALA* 3.4 29.2 - - + -
246A VAL* 4.3 0.2 - - + -
247A ALA* 1.3 79.2 - - - +
249A LYS* 1.3 62.1 + - - +
250A ILE* 3.6 6.0 + - + +
298A TYR* 3.7 38.4 - - + -
299A ILE 3.3 6.7 - - - +
300A VAL* 3.8 18.8 - - + -
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Residues in contact with LYS 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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233A GLU 3.6 6.5 - - - +
234A VAL* 3.8 22.6 - - + +
247A ALA 4.3 0.6 - - - -
248A ILE* 1.3 71.0 - - - +
250A ILE* 1.3 63.2 + - - +
251A ILE* 3.9 29.7 + - + +
273A GLU* 4.8 11.8 + - - +
297A TYR 3.6 1.4 - - - +
298A TYR* 3.3 4.9 - - - -
299A ILE* 2.8 45.7 + - + +
301A LEU* 4.2 16.0 - - + +
368A ASP* 3.9 28.0 + - - +
1506A DBQ 3.4 33.8 + - - +
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Residues in contact with ILE 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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212A TYR* 4.1 12.1 - - + -
222A MET* 4.5 5.2 - - + -
233A GLU* 2.7 40.3 + - + +
235A LYS* 3.9 38.4 - - + +
248A ILE* 4.2 4.9 - - + +
249A LYS* 1.3 76.0 - - - +
251A ILE* 1.3 67.1 + - - +
252A SER* 4.2 2.3 + - - +
296A ASP* 4.2 19.1 - - - +
297A TYR 3.4 5.4 - - - +
298A TYR* 3.3 36.6 - - + -
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Residues in contact with ILE 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 LYS* 4.1 34.5 - - + +
250A ILE* 1.3 79.1 - - - +
252A SER* 1.3 73.2 + - - +
270A VAL* 4.1 27.6 - - + -
273A GLU* 4.2 13.7 - - - +
296A ASP* 3.6 3.1 - - - +
297A TYR* 2.9 44.6 + - + +
299A ILE* 4.3 9.9 - - + -
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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