Contacts of the helix formed by residues 340 - 345 (chain B) in PDB entry 3NSH
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 GLY 340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B ASP 3.2 8.3 - - - -
237B THR 3.1 14.1 - - - -
239B ASN 3.2 16.9 + - - -
338B VAL* 3.2 10.6 + - - -
339B MET* 1.3 76.9 - - - +
341B ALA* 1.3 67.2 + - - -
342B VAL 3.0 4.7 + - - -
343B ILE* 3.0 13.6 + - - +
344B MET* 3.0 11.3 + - - +
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Residues in contact with ALA 341 (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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20B TYR* 4.4 16.8 - - + -
160B LEU* 4.6 7.4 - - + -
234B ASP 3.8 2.6 + - - -
235B SER* 4.6 7.1 - - - +
237B THR 2.7 16.5 + - - +
238B THR* 3.2 13.0 + - + +
340B GLY* 1.3 70.8 - - - -
342B VAL* 1.3 58.9 + - + +
344B MET* 3.0 9.6 + - - +
345B GLU* 2.9 45.8 + - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B THR* 3.1 32.4 + - + +
239B ASN 3.9 0.7 - - - -
240B LEU* 3.6 26.0 - - + +
310B GLN* 3.2 52.9 + - - +
311B TYR* 5.0 3.4 - - + -
313B ARG* 4.5 11.4 - - + -
329B ALA* 3.9 19.3 - - + +
341B ALA* 1.3 74.6 - - + +
343B ILE* 1.3 69.4 + - + +
345B GLU* 4.0 19.3 + - - +
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.9 46.0 - - + -
291B LEU* 4.8 1.1 - - + -
304B ILE* 3.9 28.0 - - + -
306B ILE* 3.6 37.0 - - + -
310B GLN* 3.5 2.7 + - - +
311B TYR* 6.2 1.1 - - + -
339B MET* 3.9 30.7 - - + -
340B GLY 3.0 9.4 + - - +
342B VAL* 1.3 79.3 - - + +
344B MET* 1.3 67.2 + - + +
345B GLU 3.4 4.7 + - - +
347B PHE* 3.1 25.8 - - + -
360B PHE* 5.2 1.8 - - + -
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Residues in contact with MET 344 (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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158B LEU* 4.1 11.2 - - + +
160B LEU* 4.1 19.0 + - + +
233B VAL* 3.9 20.4 - - + -
234B ASP 4.1 2.7 - - - -
235B SER* 3.6 42.0 - - - -
339B MET* 4.3 3.8 - - + +
340B GLY 3.0 10.1 + - - +
341B ALA 3.0 8.5 + - - +
343B ILE* 1.3 82.7 - - + +
345B GLU* 1.3 59.5 + - - +
347B PHE* 2.9 34.5 + - - +
349B VAL* 4.1 21.2 - - + +
351B PHE* 3.9 31.6 - - + -
360B PHE* 5.7 2.0 - - + -
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Residues in contact with GLU 345 (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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16B SER* 6.1 1.0 - - - -
20B TYR* 2.7 33.0 + - + +
160B LEU* 3.0 20.4 - - + +
162B GLY* 3.8 24.0 - - - +
163B ALA 5.1 1.1 + - - -
176B VAL* 5.3 1.9 - - - +
309B GLN 5.6 0.7 - - - +
310B GLN* 3.4 30.0 + - + +
341B ALA* 2.9 29.6 + - - +
342B VAL* 4.0 20.0 - - - +
343B ILE 3.4 0.9 + - - +
344B MET* 1.3 73.1 - - - +
346B GLY* 1.3 65.3 + - - +
347B PHE 3.0 1.2 + - - -
367B VAL* 4.5 4.9 - - + -
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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