Contacts of the helix formed by residues 232 - 240 (chain B) in PDB entry 2NYM
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 GLU 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG* 2.7 38.2 + - - +
230B LYS* 4.4 15.6 - - + +
231B GLU* 1.3 77.7 - - - +
233B HIS* 1.3 77.4 + - + +
235B ILE* 3.4 10.9 + - - +
236B PHE* 3.0 23.2 + - - +
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Residues in contact with HIS 233 (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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191B ARG* 4.2 23.7 - - - -
225B PHE* 3.5 64.3 - + + -
229B LEU* 4.1 6.1 - - + -
230B LYS* 3.5 50.6 + - + +
231B GLU 3.2 0.2 - - - -
232B GLU* 1.3 89.5 + - + +
234B LYS* 1.3 55.5 + - - +
235B ILE 2.9 4.9 - - - -
236B PHE* 2.7 28.3 + - - +
237B LEU 2.8 12.5 + - - -
264B PHE* 3.5 12.3 - - + -
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Residues in contact with LYS 234 (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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229B LEU* 3.9 43.5 + - + -
230B LYS 3.9 7.7 + - - +
231B GLU* 3.9 26.4 + - + +
232B GLU 3.5 0.2 - - - -
233B HIS* 1.3 74.5 - - - +
235B ILE* 1.3 60.0 + - + +
237B LEU* 3.9 6.1 - - - -
238B LEU* 3.3 32.1 + - + +
264B PHE* 4.7 2.9 - - - -
268B ASP* 4.6 10.5 + - - -
270B THR* 5.9 5.0 - - - +
271B LEU* 4.3 24.4 - - + +
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Residues in contact with ILE 235 (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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140A TRP* 4.6 18.4 - - + +
195B ASN* 6.1 2.5 - - - +
199B TYR* 4.9 5.8 - - - +
231B GLU* 3.8 26.4 + - - +
232B GLU* 3.4 13.5 + - - +
233B HIS 2.9 0.4 - - - -
234B LYS* 1.3 76.4 - - + +
236B PHE* 1.3 71.8 + - - +
237B LEU 3.0 1.6 - - - -
238B LEU* 4.4 1.8 - - + +
239B LYS* 2.9 44.0 + - + +
240B VAL* 3.8 1.1 + - + +
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Residues in contact with PHE 236 (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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195B ASN* 3.5 33.4 - - - +
198B PHE* 5.1 2.7 - + - -
218B LEU* 3.5 47.3 - - + -
222B ILE* 4.4 10.1 - - + -
225B PHE* 5.0 7.6 - + - -
232B GLU 3.0 14.9 + - - +
233B HIS* 2.7 15.2 + - - +
235B ILE* 1.3 79.3 - - - +
237B LEU* 1.3 58.1 + - - +
240B VAL* 3.0 43.5 - - + +
241B LEU* 3.1 32.0 + - + -
264B PHE* 3.9 22.7 - + - -
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Residues in contact with LEU 237 (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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233B HIS 2.8 6.4 + - - +
234B LYS 4.0 3.1 - - - +
236B PHE* 1.3 77.0 - - - +
238B LEU* 1.3 79.3 + - + +
241B LEU* 3.2 31.4 + - + +
242B LEU* 3.2 28.3 + - + +
261B VAL* 4.7 9.0 - - + -
264B PHE* 3.2 56.3 - - + -
265B LEU* 5.8 0.4 - - + -
271B LEU* 3.7 15.5 - - + -
275B VAL* 3.7 30.5 - - + -
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Residues in contact with LEU 238 (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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100A GLU* 5.4 1.2 - - - +
234B LYS 3.3 20.4 + - - +
235B ILE* 4.4 1.8 - - + +
237B LEU* 1.3 101.9 - - + +
239B LYS* 1.3 66.0 + - + +
242B LEU* 4.2 19.6 - - + +
243B PRO* 3.3 17.7 - - - +
271B LEU* 4.5 15.0 - - + -
274B PRO* 4.0 28.7 - - + +
275B VAL* 5.1 0.7 - - + -
282B TYR* 5.6 0.3 + - - -
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Residues in contact with LYS 239 (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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100A GLU* 3.7 30.7 + - + +
140A TRP* 3.3 61.2 - - + +
199B TYR* 3.5 17.8 - - - +
203B TYR* 4.3 7.3 + - - -
235B ILE* 2.9 25.6 + - + +
238B LEU* 1.3 78.9 - - + +
240B VAL* 1.3 60.1 + - - +
243B PRO* 3.5 12.1 - - - +
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Residues in contact with VAL 240 (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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195B ASN* 4.3 15.0 - - - +
198B PHE* 4.1 35.4 - - + -
199B TYR* 3.2 43.7 - - + +
202B ILE* 3.7 10.1 - - + +
235B ILE* 4.5 4.0 - - + +
236B PHE* 3.0 30.0 + - + +
239B LYS* 1.3 77.2 - - - +
241B LEU* 1.3 64.4 + - + +
243B PRO* 2.9 18.0 - - - +
244B LEU* 3.4 11.7 + - + +
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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