Contacts of the helix formed by residues 241 - 255 (chain B) in PDB entry 1PUF
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 ASN 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B ASN 3.6 2.4 + - - -
240B PHE* 1.3 77.5 - - - +
242B LYS* 1.3 64.6 + - - +
243B GLN* 2.7 30.6 + - - +
244B ALA* 2.7 37.5 + - - +
245B THR* 3.2 16.5 + - - -
273B CYS 4.7 7.7 + - - -
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Residues in contact with LYS 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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240B PHE 3.8 0.2 + - - -
241B ASN* 1.3 73.8 - - - +
243B GLN* 1.3 71.5 + - - +
245B THR* 3.9 8.0 - - + -
246B GLU* 3.0 34.8 + - + +
305B TYR* 4.7 6.7 + - - -
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Residues in contact with GLN 243 (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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241B ASN* 2.7 40.4 + - - +
242B LYS* 1.3 80.2 - - - +
244B ALA* 1.3 60.2 + - - +
246B GLU* 3.2 7.6 + - - +
247B ILE* 3.2 27.6 + - + +
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Residues in contact with ALA 244 (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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240B PHE* 4.1 19.3 - - + -
241B ASN* 2.7 23.2 + - - +
243B GLN* 1.3 73.0 - - - +
245B THR* 1.3 62.4 + - - +
247B ILE* 3.2 4.3 + - - +
248B LEU* 3.0 31.4 + - + +
273B CYS* 3.7 40.8 - - + +
275B ILE* 5.2 2.2 - - + -
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Residues in contact with THR 245 (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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240B PHE* 3.8 19.2 + - - +
241B ASN 3.2 14.6 + - - -
242B LYS* 3.9 9.6 - - + -
244B ALA* 1.3 78.0 - - - +
246B GLU* 1.3 59.4 + - - +
248B LEU* 3.8 9.4 - - - +
249B ASN* 2.9 47.1 + - - +
283B TRP* 5.1 9.6 + - + +
305B TYR* 5.3 0.7 - - - +
8D G 4.8 3.6 + - - -
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Residues in contact with GLU 246 (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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242B LYS* 3.0 28.1 + - + +
243B GLN* 3.2 6.7 + - - +
245B THR* 1.3 77.2 - - - +
247B ILE* 1.3 58.1 + - + +
250B GLU* 2.8 31.1 + - - +
305B TYR* 3.3 25.1 - - + +
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Residues in contact with ILE 247 (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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243B GLN* 3.2 17.6 + - + +
244B ALA 3.5 6.3 - - - +
246B GLU* 1.3 77.9 - - + +
248B LEU* 1.3 62.7 + - - +
250B GLU* 3.3 8.7 + - + +
251B TYR* 3.1 21.8 + - - +
269B LEU* 3.7 23.3 - - + -
272B LYS* 3.9 41.5 - - + +
273B CYS* 3.9 16.4 - - - -
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Residues in contact with LEU 248 (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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240B PHE* 4.2 14.1 - - + -
244B ALA* 3.0 26.2 + - + +
245B THR* 3.9 2.9 - - - +
247B ILE* 1.3 76.8 - - - +
249B ASN* 1.3 57.3 + - - +
251B TYR* 3.3 5.9 + - - +
252B PHE* 2.9 29.6 + - - +
269B LEU* 4.6 10.5 - - + -
273B CYS* 4.0 15.0 - - - -
275B ILE* 4.4 9.6 - - + -
280B VAL* 4.5 15.9 - - + -
283B TRP* 3.5 52.2 - - + +
284B PHE* 4.0 22.5 - - + -
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Residues in contact with ASN 249 (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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245B THR* 2.9 35.1 + - - +
248B LEU* 1.3 74.8 - - - +
250B GLU* 1.3 66.3 + - - +
252B PHE* 4.2 1.1 - - - -
253B TYR* 2.9 40.0 + - + +
283B TRP* 3.1 20.3 - - - -
287B LYS* 2.8 35.9 + - - +
301B GLU* 4.0 10.2 - - - +
305B TYR* 3.5 28.9 + - + -
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Residues in contact with GLU 250 (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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246B GLU 2.8 20.2 + - - +
247B ILE* 3.4 9.9 - - + +
248B LEU 3.2 0.2 - - - -
249B ASN* 1.3 75.0 - - - +
251B TYR* 1.3 62.7 + - - +
253B TYR* 3.9 1.7 - - - +
254B SER* 3.0 26.8 + - - -
305B TYR* 3.7 16.3 - - + -
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Residues in contact with TYR 251 (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 ILE 3.1 10.0 + - - +
248B LEU 3.7 6.5 - - - +
250B GLU* 1.3 75.7 - - - +
252B PHE* 1.3 68.8 + - - +
254B SER* 2.9 10.5 + - - -
255B HIS* 2.9 65.2 + + + -
259B PRO* 5.3 0.2 - - + -
260B TYR 4.8 1.9 - - - -
261B PRO* 3.5 42.8 - - + +
265B ALA* 3.9 14.3 - - + +
269B LEU* 3.8 32.1 - - + -
284B PHE* 3.7 15.9 - + + -
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Residues in contact with PHE 252 (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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199A TRP* 3.9 21.3 - + - -
248B LEU 2.9 18.9 + - - +
249B ASN* 3.6 3.4 - - - +
251B TYR* 1.3 79.2 - - - +
253B TYR* 1.3 91.9 + + - +
255B HIS* 3.1 4.0 + - - +
256B LEU* 3.1 36.9 + - + -
259B PRO* 3.7 30.5 - - + +
283B TRP* 3.9 10.5 - + + -
284B PHE* 4.0 19.5 - + - -
287B LYS* 3.6 35.9 - - + -
288B ARG* 4.0 13.2 - - + -
291B TYR* 4.2 12.8 - + + -
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Residues in contact with TYR 253 (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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249B ASN* 2.9 45.4 + - + +
250B GLU 4.2 1.6 - - - +
252B PHE* 1.3 98.0 - + - +
254B SER* 1.3 61.9 + - - +
255B HIS 3.3 0.7 + - - -
256B LEU* 3.3 29.1 + - + +
287B LYS* 3.7 7.8 - - - -
291B TYR* 4.0 11.7 - + - -
298B PHE* 3.8 16.6 + - - +
301B GLU* 2.7 35.8 + - + -
302B ALA* 3.8 32.5 - - + +
305B TYR* 3.8 31.6 - + + -
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Residues in contact with SER 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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250B GLU 3.0 16.3 + - - -
251B TYR* 2.9 17.0 + - - -
253B TYR* 1.3 75.7 - - - +
255B HIS* 1.3 76.1 + - - +
256B LEU 3.5 0.4 + - - -
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Residues in contact with HIS 255 (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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251B TYR* 2.9 69.6 + + + +
252B PHE 3.3 5.2 - - - +
254B SER* 1.3 98.3 + - - +
256B LEU* 1.3 56.7 + - - +
257B SER* 3.2 4.0 - - - -
258B ASN 2.8 33.2 + - - +
259B PRO* 2.9 15.4 - - + -
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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