Contacts of the helix formed by residues 276 - 294 (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 THR 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ARG* 5.8 5.6 - - - +
270B ALA* 3.9 2.7 - - - -
275B ILE* 1.3 80.6 - - - +
277B VAL* 1.3 63.7 + - - +
278B SER* 3.5 9.1 + - - -
279B GLN* 3.0 36.4 + - - +
280B VAL* 3.0 23.9 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLU* 5.3 2.9 - - + +
266B LYS* 4.0 23.1 - - + +
267B GLU* 3.6 42.8 - - + +
270B ALA* 3.9 10.7 - - + +
276B THR* 1.3 71.2 - - - +
278B SER* 1.3 67.5 + - - +
280B VAL* 3.1 5.2 + - - +
281B SER* 2.9 24.2 + - - +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 3.6 35.4 + - - +
276B THR* 3.2 8.8 + - - -
277B VAL* 1.3 78.4 - - - +
279B GLN* 1.3 58.6 + - - +
281B SER* 3.2 7.6 + - - -
282B ASN* 2.8 38.6 + - - +
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 5.4 8.1 + - - +
240B PHE* 4.0 26.8 - - + -
275B ILE* 3.1 19.5 - - + +
276B THR* 3.0 44.0 + - - +
278B SER* 1.3 77.2 - - - +
280B VAL* 1.3 59.8 + - - +
282B ASN* 3.8 2.7 - - - +
283B TRP* 2.9 29.1 + - - +
8D G 4.0 0.5 - - - +
9D A 2.9 39.0 + - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.5 3.8 - - + -
266B LYS* 3.9 26.9 - - + +
269B LEU* 4.4 9.6 - - + -
270B ALA* 3.7 33.7 - - + +
275B ILE* 3.8 13.2 - - + -
276B THR 3.0 19.1 + - - +
277B VAL* 3.1 8.5 + - - +
279B GLN* 1.3 75.9 - - - +
281B SER* 1.3 63.4 + - - +
283B TRP* 3.2 5.9 + - - +
284B PHE* 3.0 48.8 + - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 6.3 0.9 - - - -
266B LYS* 2.8 37.8 + - - +
277B VAL* 2.9 18.3 + - - +
278B SER* 3.2 11.0 + - - -
280B VAL* 1.3 78.0 - - - +
282B ASN* 1.3 58.6 + - - +
284B PHE* 3.5 3.5 + - - +
285B GLY* 3.0 26.3 + - - -
288B ARG* 5.0 1.9 + - - -
29E T 5.2 1.6 - - - -
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Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 5.0 11.2 + - - +
278B SER* 2.8 26.1 + - - +
279B GLN* 3.8 1.9 - - - +
281B SER* 1.3 79.0 - - - +
283B TRP* 1.3 58.1 + - - +
285B GLY* 3.4 1.0 + - - -
286B ASN* 2.9 44.4 + - - +
8D G 4.9 1.1 - - + -
9D A 3.1 51.9 + - + +
10D T 3.3 25.7 + - + +
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Residues in contact with TRP 283 (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 15.1 - + + -
245B THR* 4.6 11.4 + - + +
248B LEU* 3.5 60.7 - - + +
249B ASN* 3.1 34.3 - - - -
252B PHE* 3.9 12.8 - - + -
279B GLN 2.9 18.5 + - - +
280B VAL* 3.6 7.0 - - - +
282B ASN* 1.3 77.8 - - - +
284B PHE* 1.3 83.9 + + + +
286B ASN* 3.8 7.0 - - + +
287B LYS* 2.7 57.4 + - + +
8D G 3.6 26.1 + - - +
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.0 15.7 - - + -
251B TYR* 3.7 32.3 - + + -
252B PHE* 4.0 21.1 - + - -
259B PRO* 3.6 19.3 - - + -
261B PRO* 3.7 17.3 - - + -
266B LYS* 6.0 1.6 - - - -
269B LEU* 4.0 10.1 - - + -
280B VAL* 3.0 47.0 + - + +
281B SER* 4.0 5.2 - - - +
283B TRP* 1.3 101.3 - + - +
285B GLY* 1.3 67.4 + - - +
287B LYS* 4.3 1.1 - - - -
288B ARG* 2.9 44.8 + - - +
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER 3.0 14.9 + - - -
282B ASN 3.8 2.5 - - - -
284B PHE* 1.3 77.8 - - - +
286B ASN* 1.3 64.8 + - - +
288B ARG* 3.4 18.5 + - - +
289B ILE* 3.3 24.0 + - - +
29E T 6.1 0.4 - - - -
30E A 4.1 9.8 + - - -
31E A 5.6 3.8 - - - +
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Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASN* 2.9 28.0 + - - +
283B TRP* 3.8 5.7 - - + +
285B GLY* 1.3 75.6 - - - +
287B LYS* 1.3 61.5 + - - +
289B ILE* 3.3 8.7 - - - +
290B ARG* 3.1 49.9 + - - +
8D G 3.6 18.1 + - + +
9D A 2.9 48.7 + - - +
10D T 4.5 1.7 - - - +
32E A 4.4 5.0 + - - -
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 2.8 28.9 + - - +
252B PHE* 3.6 32.3 - - + -
253B TYR* 3.7 16.2 - - - -
283B TRP* 2.7 49.0 + - + +
284B PHE 3.8 2.9 - - - +
285B GLY 3.3 0.2 - - - -
286B ASN* 1.3 74.1 - - - +
288B ARG* 1.3 58.0 + - - +
290B ARG* 4.9 2.2 - - - -
291B TYR* 2.8 35.1 + - - +
298B PHE* 3.9 20.3 - - + -
301B GLU* 3.0 21.6 + - - -
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TRP* 3.4 27.2 - - + -
252B PHE* 4.0 7.4 - - + -
259B PRO* 2.9 39.1 + - + -
260B TYR* 3.4 39.3 - - - +
261B PRO* 4.7 1.2 - - - +
281B SER 5.0 1.8 + - - -
284B PHE* 2.9 42.1 + - - +
285B GLY* 3.4 16.4 + - - +
287B LYS* 1.3 74.3 - - - +
289B ILE* 1.3 59.1 + - - +
292B LYS* 2.8 34.9 + - - +
29E T 3.6 19.8 + - - +
30E A 2.8 36.8 + - - +
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Residues in contact with ILE 289 (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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285B GLY 3.3 12.8 + - - +
286B ASN* 3.3 18.2 - - - +
288B ARG* 1.3 78.8 - - - +
290B ARG* 1.3 68.9 + - + +
292B LYS* 3.6 8.0 - - + +
293B LYS* 2.8 57.7 + - + +
30E A 4.8 3.4 - - + -
31E A 3.5 68.6 - - + +
32E A 5.5 5.6 - - + +
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Residues in contact with ARG 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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286B ASN* 3.1 37.7 + - - +
287B LYS* 4.2 1.8 - - - +
289B ILE* 1.3 87.5 - - + +
291B TYR* 1.3 62.8 + - - +
293B LYS* 3.4 9.1 + - + +
294B ASN* 3.1 19.4 + - - +
298B PHE* 3.4 25.8 - - + -
7D T 3.7 34.5 + - - +
8D G 2.8 49.3 + - - -
9D A 3.6 5.3 - - - +
33E T 3.6 17.4 + - - +
34E C 4.5 1.0 - - - +
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Residues in contact with TYR 291 (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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195A PRO* 3.7 25.9 - - + +
196A ALA* 5.4 1.3 - - + -
199A TRP* 3.6 22.7 - + - -
252B PHE* 4.2 14.8 - + + -
253B TYR* 4.0 22.2 - + - -
256B LEU* 3.8 16.6 - - + +
287B LYS* 2.8 20.2 + - + +
288B ARG 3.9 1.8 - - - +
290B ARG* 1.3 73.8 - - - +
292B LYS* 1.3 69.5 + - - +
294B ASN 3.1 8.5 + - - -
295B ILE* 3.0 57.0 + - + +
298B PHE* 3.5 44.3 - + + -
299B GLN* 5.8 1.4 + - - -
302B ALA* 5.1 6.1 - - + +
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Residues in contact with LYS 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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196A ALA* 4.2 13.0 - - + -
199A TRP* 3.9 23.2 - - + -
200A LEU 3.2 14.6 + - - -
201A HIS* 3.0 36.8 + - + +
288B ARG* 2.8 20.6 + - - +
289B ILE* 3.6 9.0 - - + +
291B TYR* 1.3 79.5 - - - +
293B LYS* 1.3 61.9 + - + +
294B ASN 3.5 0.3 + - - -
295B ILE* 3.9 18.4 - - - +
30E A 4.3 4.2 + - - -
31E A 2.6 31.3 + - - +
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 2.8 44.0 + - + +
290B ARG* 3.8 10.1 - - + +
291B TYR 3.2 0.2 - - - -
292B LYS* 1.3 79.1 - - + +
294B ASN* 1.3 62.7 + - + +
295B ILE 4.1 0.2 - - - -
31E A 4.8 0.9 - - - -
32E A 2.9 33.6 + - - -
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ARG 3.1 12.2 + - - +
291B TYR 3.1 4.5 + - - -
293B LYS* 1.3 82.5 + - + +
295B ILE* 1.3 66.2 + - - +
296B GLY* 3.9 2.9 + - - -
297B LYS* 3.0 43.6 + - + +
298B PHE* 3.2 17.3 - - + -
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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
------------------------------------------------------------
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