Contacts of the helix formed by residues 284 - 297 (chain B) in PDB entry 1PBW
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 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B ARG* 2.8 43.0 + - - -
282B ASN* 3.2 13.5 - - - +
283B THR* 1.3 80.3 + - - +
285B ASN* 1.3 64.0 + - - +
287B ILE* 3.5 12.0 + - - +
288B LYS* 3.2 22.9 + - + +
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Residues in contact with ASN 285 (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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210B ALA* 5.5 7.5 - - - +
219B TYR* 3.6 26.3 - - + +
282B ASN* 2.8 34.7 + - - +
283B THR 3.3 0.4 - - - -
284B GLU* 1.3 78.2 - - - +
286B LEU* 1.3 61.0 + - - +
288B LYS* 3.4 8.9 + - - +
289B VAL* 3.1 31.2 + - - +
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Residues in contact with LEU 286 (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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203B TYR* 3.2 38.4 - - + -
206B MET* 3.9 29.4 - - + -
207B ILE* 3.9 13.2 - - + -
219B TYR* 3.9 21.3 - - + +
269B SER* 4.7 0.7 - - - -
273B PHE* 4.0 31.5 - - + -
275B PHE* 4.3 10.8 - - + -
282B ASN 4.4 4.0 - - - +
283B THR* 3.5 13.7 - - - +
284B GLU 3.3 0.2 - - - -
285B ASN* 1.3 74.2 - - - +
287B ILE* 1.3 64.3 + - - +
289B VAL* 3.2 6.3 + - - +
290B ILE* 3.0 28.1 + - - +
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ARG* 3.5 32.1 - - - +
265B SER* 2.6 33.0 + - - +
266B GLU* 4.1 25.8 - - + +
269B SER* 3.9 19.7 - - - -
270B PRO* 5.4 2.2 - - + -
275B PHE* 4.4 14.8 - - + -
283B THR* 3.2 18.0 + - - +
284B GLU* 3.7 19.5 - - - +
286B LEU* 1.3 75.2 - - - +
288B LYS* 1.3 57.5 + - - +
291B GLU* 2.9 16.1 + - - +
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Residues in contact with LYS 288 (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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216B SER* 4.8 10.1 - - - -
262B ARG* 3.6 14.8 - - - +
284B GLU* 3.2 17.9 + - - +
285B ASN* 3.5 14.6 - - - +
286B LEU 3.2 0.4 - - - -
287B ILE* 1.3 79.2 - - - +
289B VAL* 1.3 57.4 + - + +
291B GLU* 3.3 32.2 + - - +
292B ILE* 2.9 48.1 + - + +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B MET* 4.7 5.4 - - + -
216B SER* 4.6 5.6 - - - +
219B TYR* 3.6 34.8 - - + -
220B ILE* 4.1 24.1 - - + +
223B LEU* 4.4 18.4 - - + -
273B PHE* 5.2 2.5 - - + -
285B ASN 3.1 15.2 + - - +
286B LEU* 3.2 10.9 + - - +
288B LYS* 1.3 76.5 - - + +
290B ILE* 1.4 68.9 + - + +
292B ILE* 3.3 5.2 + - - +
293B LEU* 3.0 42.8 + - + +
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Residues in contact with ILE 290 (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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198B ILE* 4.3 11.9 - - + -
223B LEU* 5.3 1.8 - - + -
240B LEU* 4.9 7.0 - - + -
244B LEU* 4.4 7.6 - - + -
247B PHE* 5.2 2.7 - - + -
265B SER* 3.4 9.9 - - - +
268B PHE* 6.0 0.2 - - + -
269B SER* 3.2 25.1 - - - +
272B LEU* 4.5 18.8 - - + -
273B PHE* 3.6 26.7 - - + -
286B LEU 3.0 12.0 + - - +
289B VAL* 1.4 76.9 - - + +
291B GLU* 1.3 64.7 + - - +
293B LEU* 3.1 17.8 + - + +
294B ILE* 3.0 42.3 + - + +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ALA* 3.6 14.0 - - + +
262B ARG* 3.0 59.5 + - - +
265B SER* 3.5 15.6 + - - -
287B ILE 2.9 16.1 + - - +
288B LYS* 3.3 26.3 + - + +
290B ILE* 1.3 78.1 - - - +
292B ILE* 1.4 64.5 + - + +
294B ILE* 3.4 1.4 + - - -
295B SER* 3.1 23.2 + - - +
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Residues in contact with ILE 292 (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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216B SER* 3.4 31.6 - - - +
220B ILE* 3.7 22.0 - - + -
288B LYS* 2.9 38.1 + - + +
289B VAL 3.3 3.3 + - - +
291B GLU* 1.4 75.4 - - + +
293B LEU* 1.3 54.8 + - - +
295B SER* 3.6 6.9 + - - +
296B THR* 2.5 57.0 + - + +
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Residues in contact with LEU 293 (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 ILE* 3.8 29.6 - - + -
223B LEU* 4.0 26.5 - - + -
224B LYS* 4.3 15.7 - - + -
237B TRP* 5.8 3.1 - - + -
240B LEU* 5.3 2.0 - - + -
244B LEU* 3.9 27.1 - - + -
289B VAL* 3.0 30.0 + - + +
290B ILE* 3.5 13.9 - - + +
292B ILE* 1.3 78.3 - - - +
294B ILE* 1.3 58.4 + - - +
296B THR* 3.5 8.9 + - - +
297B GLU* 2.9 39.5 + - - +
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Residues in contact with ILE 294 (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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244B LEU* 3.8 15.0 - - + -
247B PHE* 3.7 34.1 - - + +
248B PHE* 3.4 39.6 - - - +
251B SER* 4.5 4.5 - - - +
261B ALA* 3.9 34.5 - - + +
264B LEU* 4.0 10.1 - - + -
265B SER* 4.1 3.6 - - - +
290B ILE* 3.0 34.2 + - + +
291B GLU 3.7 5.8 - - - +
292B ILE 3.3 0.2 - - - -
293B LEU* 1.3 75.7 - - - +
295B SER* 1.4 62.6 + - - +
297B GLU* 3.4 13.4 + - - +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PHE* 4.2 7.9 - - - -
251B SER* 5.7 1.6 - - - -
261B ALA* 4.1 13.4 - - - +
291B GLU* 3.1 17.5 + - - +
292B ILE* 3.6 9.7 + - - +
294B ILE* 1.4 80.7 - - - +
296B THR* 1.3 59.8 + - - +
297B GLU 3.1 4.5 + - - -
298B TRP* 3.3 21.0 + - - +
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Residues in contact with THR 296 (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 ILE* 5.7 0.3 - - - +
292B ILE* 2.5 45.2 + - + +
293B LEU* 3.5 12.5 + - - +
294B ILE 3.3 0.2 - - - -
295B SER* 1.3 78.0 - - - +
297B GLU* 1.3 65.8 + - - +
298B TRP* 3.1 15.3 + - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLN* 4.0 21.6 + - - +
244B LEU* 4.0 32.1 - - + +
245B LYS* 5.0 3.6 + - - +
248B PHE* 3.8 23.9 - - + -
293B LEU* 2.9 34.6 - - - +
294B ILE 3.5 12.6 - - - +
295B SER 3.1 1.4 - - - -
296B THR* 1.3 84.2 + - - +
298B TRP* 1.3 64.1 + - - +
299B ASN* 3.1 5.9 + - - +
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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