Contacts of the helix formed by residues 242 - 246 (chain B) in PDB entry 3ECS
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 4.8 7.3 - - - +
305A LEU* 4.6 15.1 - - + +
240B PRO* 3.7 5.0 - - - +
241B LEU* 1.3 79.2 + - - +
243B GLN* 1.3 65.5 + - - +
244B GLN* 3.5 15.9 + - - +
245B ASP* 3.0 35.0 + - - +
246B VAL* 4.1 2.3 + - - +
275B TYR* 4.5 11.2 - - - -
188H GLU* 3.4 22.8 - - - +
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Residues in contact with GLN 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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213B ASN* 3.7 15.2 - - - +
242B ASN* 1.3 74.9 - - - +
244B GLN* 1.3 61.8 + - + +
246B VAL* 3.1 15.2 + - - +
251B LYS* 2.9 22.7 + - - -
274B ASP* 3.5 11.2 - - - +
275B TYR* 2.9 49.6 + - - +
184H GLY 4.7 2.2 + - - +
185H TYR* 3.4 48.5 - - + +
188H GLU* 3.4 22.7 + - - +
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ASN* 3.2 11.5 + - - +
243B GLN* 1.3 77.2 - - - +
245B ASP* 1.3 63.0 + - - +
246B VAL 3.1 8.3 + - - +
251B LYS* 3.8 9.3 + - - +
188H GLU* 3.8 5.8 + - - +
189H LYS* 3.2 31.4 + - - +
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Residues in contact with ASP 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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237A ARG* 4.0 17.2 + - - -
238B LEU* 5.3 4.2 - - - +
239B PHE 5.2 0.2 - - - +
240B PRO* 3.7 21.2 - - + +
241B LEU* 3.1 25.0 + - - +
242B ASN* 3.0 30.0 + - - +
244B GLN* 1.3 77.2 - - - +
246B VAL* 1.3 62.0 + - - +
247B PRO* 3.3 9.7 - - - +
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Residues in contact with VAL 246 (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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207B ILE* 4.0 23.6 - - + -
240B PRO* 4.6 5.8 - - + -
242B ASN 4.6 1.3 - - - +
243B GLN* 3.1 17.3 + - - +
244B GLN 3.7 3.5 - - - +
245B ASP* 1.3 76.9 - - - +
247B PRO* 1.3 80.9 - - + +
248B ASP* 3.4 2.6 + - - -
250B PHE* 4.4 3.1 - - + -
251B LYS* 3.2 26.6 + - - -
273B VAL* 4.2 20.4 - - + -
274B ASP* 5.0 1.3 - - - -
275B TYR* 3.6 37.2 - - + +
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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