Contacts of the helix formed by residues 241 - 249 (chain L) in PDB entry 4DVQ
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 241 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49G TRP* 4.7 31.4 - - + +
114L GLU* 3.6 16.8 - - - +
240L MET* 1.3 88.4 - - + +
242L ARG* 1.3 63.8 + - - +
243L SER* 4.3 12.1 - - - +
244L LEU* 3.0 21.0 + - + +
245L SER* 2.6 24.5 + - - -
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Residues in contact with ARG 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L GLU* 3.1 28.9 + - + +
118L ALA* 4.0 28.3 + - - +
121L GLN* 5.5 4.6 - - - +
122L HIS* 4.9 9.9 + - - +
240L MET 3.7 0.8 + - - -
241L PRO* 1.3 69.7 - - - +
243L SER* 1.3 63.6 + - - +
245L SER* 3.0 9.5 + - - -
246L ARG* 2.9 62.9 + - - +
253L TRP* 3.7 32.3 - - + -
257L PHE* 4.4 18.4 - - - -
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Residues in contact with SER 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G LEU* 4.0 18.1 - - - +
114L GLU* 5.4 1.0 + - - -
241L PRO* 4.6 12.1 - - - +
242L ARG* 1.3 78.1 - - - +
244L LEU* 1.3 57.8 + - - +
246L ARG* 4.0 17.2 + - - +
247L TRP* 3.1 29.1 + - - -
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Residues in contact with LEU 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G TRP* 4.2 24.7 - - + +
52G LEU* 3.9 24.9 - - + +
53G LEU* 3.5 42.4 - - + +
56G TRP* 5.7 5.2 - - + -
52L LEU* 5.2 7.0 - - + -
240L MET* 4.4 20.4 - - + -
241L PRO* 3.0 18.5 + - + +
243L SER* 1.3 75.4 - - - +
245L SER* 1.3 67.8 - - - +
246L ARG 3.0 3.7 + - - -
247L TRP* 3.0 15.9 + - + +
248L ILE* 3.4 24.3 + - + +
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Residues in contact with SER 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237L LEU* 4.1 10.9 + - - -
240L MET* 3.0 31.6 + - - +
241L PRO 2.6 29.8 + - - -
242L ARG* 3.0 4.7 + - - -
244L LEU* 1.3 71.8 - - - +
246L ARG* 1.3 57.3 + - - +
248L ILE* 3.2 9.2 + - - +
249L SER* 2.9 31.4 + - - -
253L TRP* 3.3 29.4 + - - -
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Residues in contact with ARG 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ARG* 6.0 2.0 - - - +
242L ARG* 2.9 58.1 + - + +
243L SER* 4.1 19.8 + - - +
245L SER* 1.3 76.8 - - - +
247L TRP* 1.3 91.6 + - + +
248L ILE 3.5 0.2 - - - -
250L PRO* 3.6 22.9 - - - +
253L TRP* 3.7 22.7 - - + +
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Residues in contact with TRP 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G LEU* 3.7 14.5 - - + +
56G TRP* 3.5 39.2 - - + +
57G ARG* 4.0 46.6 - - + +
243L SER 3.1 27.3 + - - -
244L LEU* 3.0 6.7 + - + +
246L ARG* 1.3 103.0 - - + +
248L ILE* 1.3 59.6 + - - +
250L PRO* 4.2 6.0 - - - +
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Residues in contact with ILE 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G TRP* 4.1 36.7 - - + +
248G ILE* 3.7 29.2 - - + -
52L LEU* 6.5 0.7 - - + -
56L TRP* 3.6 36.7 - - + +
240L MET* 3.7 26.7 - - + -
244L LEU* 3.4 25.0 + - + +
245L SER 3.2 9.9 - - - +
247L TRP* 1.3 77.9 - - - +
249L SER* 1.3 64.2 + - - +
250L PRO* 3.3 9.8 - - - +
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Residues in contact with SER 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L TRP* 3.0 31.5 + - - -
236L GLN 5.9 0.7 - - - -
237L LEU* 4.7 5.6 - - - -
240L MET* 3.9 10.4 - - - +
245L SER 2.9 14.5 + - - -
248L ILE* 1.3 80.2 - - - +
250L PRO* 1.4 58.9 - - - +
251L LYS* 3.2 4.3 - - - -
252L VAL* 2.9 38.9 + - - +
253L TRP* 3.2 13.6 + - - -
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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