Contacts of the helix formed by residues 253 - 262 (chain B) in PDB entry 3BUN
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 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B HIS* 4.7 1.8 - - - -
250B PRO* 3.2 11.8 + - - +
251B TRP 3.1 0.4 - - - -
252B SER* 1.3 80.2 + - - +
254B LEU* 1.3 65.9 + - - +
255B LEU 3.5 1.8 - - - -
256B ARG* 3.0 25.4 + - - -
257B ASN* 2.8 46.1 + - - -
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Residues in contact with LEU 254 (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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209B LEU* 4.3 10.1 - - + -
213B HIS* 3.8 17.3 - - + +
241B PHE* 6.0 0.4 - - + -
244B PHE* 3.8 26.0 - - + -
245B THR* 4.3 18.8 - - + +
248B PHE* 3.5 31.9 - - + +
249B GLN 4.6 0.2 - - - +
250B PRO 3.2 5.3 + - - -
251B TRP* 3.0 47.8 + - + +
252B SER 3.5 0.4 + - - -
253B SER* 1.3 76.6 - - - +
255B LEU* 1.3 71.4 + - + +
257B ASN* 3.1 5.9 + - - +
258B TRP* 3.1 21.0 + - - +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.3 6.7 - - + -
213B HIS* 3.4 43.5 + - + +
214B PRO 3.9 9.9 - - - +
215B ILE* 3.8 20.0 - - + -
220B GLU* 4.5 10.1 - - - +
224B LEU* 4.0 22.0 - - + -
244B PHE* 4.6 3.1 - - + -
253B SER 3.5 0.4 - - - -
254B LEU* 1.3 92.5 - - + +
256B ARG* 1.3 62.3 + - + +
258B TRP* 3.7 24.7 - - + -
259B ASN* 2.9 28.6 + - - +
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Residues in contact with ARG 256 (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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253B SER* 3.0 26.6 + - - +
255B LEU* 1.3 75.6 - - + +
257B ASN* 1.3 67.6 + - - +
259B ASN* 3.2 6.8 + - - +
260B SER* 3.0 29.9 + - - +
325B PHE* 5.4 0.4 - - - -
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Residues in contact with ASN 257 (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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248B PHE* 2.8 29.9 + - + +
249B GLN 4.1 1.6 - - - +
250B PRO* 2.9 33.4 + - - +
253B SER* 2.8 27.9 + - - -
254B LEU 3.3 4.3 - - - +
256B ARG* 1.3 78.8 - - - +
258B TRP* 1.3 56.8 + - - +
260B SER* 3.3 1.0 + - - -
261B LEU* 3.0 38.3 + - + +
325B PHE* 3.5 33.0 - - + -
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Residues in contact with TRP 258 (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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220B GLU* 3.4 50.9 - - + -
223B ALA* 3.5 8.3 - - + -
224B LEU* 3.2 37.9 - - + -
227B THR* 3.1 21.7 + - + -
244B PHE* 3.9 16.4 - + + -
248B PHE* 3.5 40.8 - + + -
254B LEU 3.1 11.9 + - - +
255B LEU* 3.7 29.6 - - + +
256B ARG 3.3 0.2 - - - -
257B ASN* 1.3 76.3 - - - +
259B ASN* 1.3 71.0 + - - +
262B ALA* 2.9 28.9 + - + +
263B VAL* 3.2 30.1 + - + +
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Residues in contact with ASN 259 (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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220B GLU* 3.7 20.1 + - - +
255B LEU 2.9 17.6 + - - +
256B ARG* 3.2 8.5 + - - +
258B TRP* 1.3 85.1 - - - +
260B SER* 1.3 59.8 + - - +
263B VAL* 3.3 26.1 + - - +
264B THR* 2.9 51.8 + - - +
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Residues in contact with SER 260 (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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256B ARG* 3.0 16.4 + - - +
257B ASN 3.9 2.9 - - - -
259B ASN* 1.3 77.9 - - - +
261B LEU* 1.3 59.1 + - - +
264B THR* 4.0 8.6 + - - -
265B HIS* 3.5 18.7 + - - +
325B PHE* 4.2 12.7 - - - -
347B PRO* 5.4 1.0 - - - +
349B LEU* 3.6 30.5 - - - +
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Residues in contact with LEU 261 (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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247B LEU 4.7 6.1 - - - +
248B PHE* 4.1 25.4 - - + -
249B GLN 5.9 0.9 - - - +
257B ASN* 3.0 23.5 + - + +
260B SER* 1.3 78.0 - - - +
262B ALA* 1.3 59.2 + - - +
265B HIS* 3.4 6.6 - - - +
268B TYR* 3.3 6.2 - - - +
293B PHE* 3.2 27.3 - - + -
324B LEU* 4.1 29.6 - - + -
325B PHE* 4.0 30.7 - - + +
328B LEU* 4.1 15.5 - - + -
349B LEU* 4.0 26.7 - - + -
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Residues in contact with ALA 262 (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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227B THR* 5.2 0.4 - - - +
248B PHE* 4.4 6.1 - - + -
258B TRP* 2.9 33.6 + - + +
260B SER 3.6 0.2 - - - -
261B LEU* 1.3 80.2 - - - +
263B VAL* 1.3 64.5 + - + +
264B THR 3.5 1.5 + - - -
265B HIS 3.9 10.5 + - - +
268B TYR* 3.6 44.0 - - + -
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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