Contacts of the helix formed by residues 240 - 248 (chain A) in PDB entry 1CEC
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 PRO 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A VAL* 3.2 8.5 - - + +
237A LYS 4.2 11.0 - - - +
238A ASN 3.5 9.4 - - - +
239A ASN* 1.3 83.3 - - - +
241A LYS* 1.3 63.6 + - + +
242A TYR 3.1 0.2 - - - -
243A SER* 3.1 27.5 + - - +
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Residues in contact with LYS 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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214A GLU* 3.8 23.5 + - - -
239A ASN* 3.0 2.4 + - + -
240A PRO* 1.3 82.1 - - + +
242A TYR* 1.3 84.4 + - + +
243A SER* 3.4 2.4 + - - -
244A PHE* 3.9 13.1 - - - -
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Residues in contact with TYR 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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214A GLU* 3.1 39.7 + - + +
215A SER* 3.9 23.1 - - - -
218A ALA* 3.6 21.0 - - + +
235A PHE* 3.7 33.4 - + + -
236A VAL* 3.8 5.6 - - - +
239A ASN* 2.9 24.4 + - + +
241A LYS* 1.3 104.4 - - + +
243A SER* 1.3 57.2 + - - +
244A PHE* 3.1 29.2 - + + -
245A MET* 2.9 31.7 + - - +
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Residues in contact with SER 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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236A VAL* 3.7 18.2 - - - -
240A PRO* 3.1 17.6 + - - -
241A LYS 3.4 2.2 + - - -
242A TYR* 1.3 76.1 - - - +
244A PHE* 1.3 64.7 + - - +
246A MET* 2.9 25.5 + - - +
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Residues in contact with PHE 244 (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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204A PHE* 5.4 4.0 - + - -
215A SER* 4.6 10.3 - - - -
241A LYS* 3.9 11.9 - - - -
242A TYR* 3.6 39.7 - + - -
243A SER* 1.3 81.5 + - - +
245A MET* 1.3 80.2 + - + +
246A MET 3.1 1.6 + - - -
247A GLU* 3.3 25.7 + - + +
248A LEU* 5.2 1.8 - - + +
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Residues in contact with MET 245 (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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204A PHE* 3.8 40.2 - - + -
215A SER* 4.5 8.7 - - - +
219A TYR* 4.1 15.9 - - + -
232A ILE* 3.4 35.1 - - + +
235A PHE* 3.8 21.5 - - + -
236A VAL* 4.3 8.1 - - + -
242A TYR* 2.9 21.9 + - - +
244A PHE* 1.3 94.8 - - + +
246A MET* 1.3 57.0 + - - +
247A GLU 3.0 2.9 - - - -
248A LEU* 2.8 39.9 + - + +
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Residues in contact with MET 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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232A ILE* 4.1 3.6 - - - -
233A GLU* 4.0 32.3 - - + +
236A VAL* 3.5 39.2 - - + +
237A LYS 5.4 0.2 - - - +
243A SER 2.9 16.9 + - - +
244A PHE 4.7 0.2 - - - +
245A MET* 1.3 78.2 - - - +
247A GLU* 1.3 62.2 + - + +
249A ASN* 3.0 34.5 + - - +
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Residues in contact with GLU 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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244A PHE* 3.3 17.2 + - - +
245A MET 3.0 0.4 + - - -
246A MET* 1.3 78.4 - - + +
248A LEU* 1.3 66.6 + - + +
249A ASN 3.7 2.4 + - - +
251A LEU* 5.6 2.8 - - - +
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Residues in contact with LEU 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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204A PHE* 3.7 35.9 - - + -
229A TYR* 3.5 21.2 - - + +
232A ILE* 4.2 5.8 - - + -
244A PHE* 5.2 1.8 - - + +
245A MET* 2.8 29.9 + - + +
247A GLU* 1.3 85.5 - - + +
249A ASN* 1.3 67.5 + - - +
250A ASN 3.1 0.9 + - - -
251A LEU* 2.9 42.5 + - + +
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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