Contacts of the helix formed by residues 228 - 242 (chain B) in PDB entry 3SN5
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 PHE 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B VAL* 3.8 28.3 - - + -
218B ALA* 3.7 31.4 - - + -
219B LEU* 4.3 7.0 - - + -
223B LEU* 4.0 22.4 - - + -
224B PRO 3.5 21.1 - - - -
225B ILE* 2.9 18.9 + - - +
226B HIS 4.0 1.1 - - - -
227B MET* 1.3 92.9 - - + +
229B ARG* 1.4 53.4 + - - +
230B THR 3.5 2.5 - - - -
231B ALA* 3.4 18.3 + - + +
232B HIS* 2.8 31.4 + - - +
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Residues in contact with ARG 229 (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 HIS 4.0 6.7 + - - +
227B MET 3.8 4.6 + - - -
228B PHE* 1.4 70.0 - - - +
230B THR* 1.4 64.3 + - - +
232B HIS* 3.1 8.8 + - - +
233B ASN* 3.0 36.9 + - - +
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Residues in contact with THR 230 (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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211B GLN* 3.4 35.9 - - + +
228B PHE 3.5 0.8 - - - -
229B ARG* 1.4 76.3 - - - +
231B ALA* 1.3 57.7 + - - +
233B ASN* 3.5 9.0 + - - +
234B ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 231 (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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211B GLN 3.4 26.5 - - - +
212B PHE* 4.3 3.9 - - - +
215B VAL* 3.6 35.2 - - + -
225B ILE* 3.9 5.4 - - + +
228B PHE* 3.4 11.7 + - + +
229B ARG 3.4 0.4 - - - -
230B THR* 1.3 75.9 - - - +
232B HIS* 1.3 58.5 + - - +
234B ALA* 3.7 5.0 - - - +
235B ARG* 3.0 29.3 + - - +
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Residues in contact with HIS 232 (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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225B ILE* 3.5 37.9 - - + +
226B HIS* 4.1 25.7 + - - +
228B PHE 2.8 22.1 + - - +
229B ARG* 3.1 8.3 + - - +
231B ALA* 1.3 72.8 - - - +
233B ASN* 1.4 62.8 + - - +
235B ARG* 3.3 17.4 + - - +
236B GLU* 3.1 38.3 + - + +
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Residues in contact with ASN 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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229B ARG* 3.0 32.2 + - - +
230B THR* 3.8 7.8 - - - +
232B HIS* 1.4 77.2 - - - +
234B ALA* 1.4 57.4 + - - +
236B GLU* 3.3 7.2 + - - +
237B LYS* 2.9 36.9 + - + +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 3.3 41.3 - - - +
211B GLN* 3.8 15.3 - - + -
212B PHE 4.2 1.6 - - - +
230B THR 3.0 18.4 + - - +
231B ALA* 3.7 6.1 - - - +
233B ASN* 1.4 73.2 - - - +
235B ARG* 1.3 58.5 + - - +
237B LYS* 3.4 2.1 + - - +
238B LEU* 3.0 36.1 + - - +
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Residues in contact with ARG 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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107B LYS 4.3 4.6 + - - -
108B ALA 3.1 21.7 + - - -
109B PHE 3.6 24.1 + - - +
110B GLY* 3.7 8.1 - - - +
212B PHE* 3.5 31.3 - - + +
225B ILE* 3.6 36.6 - - + +
231B ALA 3.0 18.3 + - - +
232B HIS* 3.3 11.1 + - - +
234B ALA* 1.3 73.7 - - - +
236B GLU* 1.3 83.4 + - - +
238B LEU* 3.4 11.0 + - - +
239B ALA* 3.0 27.0 + - - +
277B LYS* 3.8 13.5 - - - +
280B LEU* 3.5 19.3 - - + +
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Residues in contact with GLU 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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232B HIS* 3.1 30.2 + - + +
233B ASN* 3.8 6.1 - - - +
235B ARG* 1.3 112.0 + - - +
237B LYS* 1.4 60.2 + - + +
239B ALA* 3.4 4.0 + - - +
240B GLU* 3.0 35.4 + - + +
273B LEU* 3.8 18.2 - - - +
277B LYS* 3.5 23.0 + - - -
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Residues in contact with LYS 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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208B ASN* 3.5 24.9 - - - +
233B ASN* 2.9 23.3 + - + +
234B ALA 3.7 2.0 - - - +
235B ARG 3.4 0.2 - - - -
236B GLU* 1.4 73.9 - - + +
238B LEU* 1.4 63.1 + - - +
240B GLU* 3.4 9.2 + - - +
241B SER* 3.4 21.3 + - - -
2205B UNX 3.9 4.9 - - - -
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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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180B PHE* 5.1 0.4 - - + -
184B TYR* 5.4 0.9 - - + -
205B ASN* 3.7 29.6 - - + +
208B ASN* 3.8 8.3 - - + +
209B PHE* 3.8 26.7 - - + +
212B PHE* 4.1 15.0 - - + -
234B ALA 3.0 22.5 + - - +
235B ARG* 3.6 6.1 - - - +
237B LYS* 1.4 76.1 - - - +
239B ALA* 1.3 59.6 + - - +
241B SER* 2.9 19.4 + - - +
242B LEU* 3.3 17.6 - - + +
280B LEU* 3.9 24.2 - - + -
283B LEU* 4.0 22.2 - - + -
2205B UNX 3.9 10.3 - - - -
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Residues in contact with ALA 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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235B ARG 3.0 17.3 + - - +
236B GLU* 3.5 8.7 - - - +
237B LYS 3.3 0.2 - - - -
238B LEU* 1.3 75.4 - - - +
240B GLU* 1.3 61.2 + - - +
242B LEU* 3.0 10.8 + - - -
243B ARG 3.4 0.3 + - - -
273B LEU* 4.2 14.6 - - + -
276B ALA* 3.0 34.4 - - + +
277B LYS* 4.0 29.8 - - + +
280B LEU* 4.7 4.2 - - + +
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Residues in contact with GLU 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 GLU* 3.0 24.5 + - + +
237B LYS* 3.7 8.7 - - - +
238B LEU 3.4 0.4 - - - -
239B ALA* 1.3 75.0 - - - +
241B SER* 1.3 52.2 + - - +
242B LEU 3.3 0.9 + - - -
243B ARG* 2.9 57.4 + - - +
246B ASN* 2.6 29.6 + - - -
273B LEU* 3.8 9.0 - - + +
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B TYR* 3.7 13.2 + - - -
201B HIS* 6.4 2.5 - - - -
205B ASN* 3.4 25.2 + - - -
237B LYS 3.4 8.2 + - - -
238B LEU* 2.9 16.8 + - - +
240B GLU* 1.3 76.5 - - - +
242B LEU* 1.4 59.4 + - - +
243B ARG 3.4 1.6 - - - -
246B ASN* 3.4 24.2 - - - +
247B LEU* 4.5 5.5 - - - +
250B ARG* 5.6 3.3 + - - -
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Residues in contact with LEU 242 (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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184B TYR* 3.4 26.5 - - + +
188B PHE* 3.7 32.5 - - + -
238B LEU 3.3 16.2 - - - +
239B ALA 3.0 11.6 + - - +
241B SER* 1.4 74.5 - - - +
243B ARG* 1.3 63.7 + - - +
247B LEU* 3.4 23.7 - - + +
276B ALA* 3.4 22.2 - - - +
279B HIS* 3.5 12.5 - - + +
280B LEU* 3.7 37.5 - - + +
283B LEU* 4.3 15.3 - - + -
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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