Contacts of the helix formed by residues 232 - 241 (chain B) in PDB entry 3SJN
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 SER 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A TYR* 5.4 4.0 - - - -
228B VAL* 5.4 1.1 - - - -
229B LEU* 3.4 8.4 + - - +
230B ALA 3.3 3.3 - - - -
231B ASP* 1.3 75.7 - - - +
233B LEU* 1.3 63.4 + - - +
234B ILE* 4.0 6.4 + - - +
235B SER* 3.1 39.2 + - - -
236B TYR* 3.4 17.8 + - - -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLU* 5.0 8.1 - - - +
230B ALA 3.5 19.7 - - - +
231B ASP 3.3 6.9 + - - +
232B SER* 1.3 73.1 - - - +
234B ILE* 1.3 63.6 + - + +
236B TYR* 3.2 9.9 + - + +
237B GLU* 3.1 23.4 + - - +
261B GLU* 4.0 22.4 - - + +
262B PHE* 4.0 33.0 - - + +
265B LYS* 3.8 39.7 - - + +
266B SER* 4.0 4.7 - - - -
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN* 6.2 2.0 - - - +
232B SER* 3.2 6.4 - - - +
233B LEU* 1.3 77.8 - - + +
235B SER* 1.3 55.6 + - - +
237B GLU* 3.4 15.7 + - - +
238B LYS* 2.9 56.8 + - + +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B THR* 5.6 2.6 - - - +
206B CYS* 3.9 29.1 + - - +
228B VAL* 4.0 18.8 - - - +
232B SER* 3.1 33.4 + - - -
234B ILE* 1.3 75.7 - - - +
236B TYR* 1.3 61.3 + - - +
238B LYS* 3.7 1.7 + - - +
239B LEU* 3.2 29.3 + - - +
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Residues in contact with TYR 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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226B GLU* 3.4 23.6 - - - +
227B PRO* 4.1 10.1 - - + -
228B VAL* 3.3 26.4 + - + -
229B LEU 3.6 7.9 - - - -
230B ALA* 3.6 29.1 + - + +
232B SER 3.4 14.8 + - - -
233B LEU* 3.2 9.7 + - - +
235B SER* 1.3 76.0 - - - +
237B GLU* 1.3 66.2 + - - +
239B LEU* 3.0 18.5 + - + +
240B SER* 3.0 11.4 + - - -
247B ILE* 3.6 34.3 - - + +
248B ALA 4.0 9.4 + - - -
249B GLY* 4.3 2.1 - - - -
262B PHE* 4.1 24.7 - + - -
266B SER* 3.4 24.3 - - - +
268B ALA* 4.7 2.0 - - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU 3.1 5.6 + - - +
234B ILE* 3.4 21.2 + - - +
236B TYR* 1.3 78.1 - - - +
238B LYS* 1.3 64.5 + - + +
240B SER* 2.5 24.0 + - - -
241B ARG* 3.0 46.4 + - + +
265B LYS* 3.6 23.8 - - - +
266B SER 3.2 10.4 + - - +
267B ASN* 4.8 3.4 - - + -
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Residues in contact with LYS 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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206B CYS* 4.6 18.8 - - - -
234B ILE* 2.9 40.4 + - + +
235B SER* 3.9 4.7 - - - +
237B GLU* 1.3 77.7 - - + +
239B LEU* 1.3 60.9 + - - +
241B ARG* 3.5 15.2 + - - +
242B GLN* 3.3 26.7 + - - +
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Residues in contact with LEU 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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206B CYS* 3.7 17.5 - - + +
209B SER* 3.7 28.9 - - - +
210B ALA* 3.7 15.5 - - + +
227B PRO* 3.7 31.0 - - + -
228B VAL* 4.9 5.6 - - + -
235B SER 3.2 19.3 + - - +
236B TYR* 3.0 12.4 + - - +
238B LYS* 1.3 76.7 - - - +
240B SER* 1.3 58.2 + - - +
241B ARG 3.3 0.2 + - - -
242B GLN* 3.3 2.5 + - + -
243B VAL* 3.0 58.0 + - + +
247B ILE* 4.5 14.4 - - + -
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Residues in contact with SER 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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236B TYR 3.0 10.4 + - - -
237B GLU 2.5 19.4 + - - -
239B LEU* 1.3 75.3 - - - +
241B ARG* 1.3 62.9 + - - +
242B GLN 3.3 1.0 + - - -
243B VAL* 4.4 8.9 + - - +
247B ILE* 4.8 13.4 - - - +
267B ASN* 2.9 48.6 + - - +
269B ASP* 6.0 0.9 - - - -
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Residues in contact with ARG 241 (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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237B GLU* 3.0 46.3 + - + +
238B LYS* 3.9 11.0 - - + +
239B LEU 3.2 1.2 - - - -
240B SER* 1.3 81.7 + - - +
242B GLN* 1.3 58.9 + - + +
243B VAL 3.9 0.4 - - - -
267B ASN* 3.2 30.1 + - - +
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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
------------------------------------------------------------
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