Contacts of the helix formed by residues 248 - 266 (chain F) in PDB entry 5U07
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 ASP 248 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243F VAL* 4.5 2.7 - - - +
246F THR* 3.1 18.0 + - - +
247F GLY* 1.3 76.1 - - - +
249F ALA* 1.3 84.0 + - - +
250F GLN* 2.6 26.3 + - - +
251F THR* 3.1 34.6 + - + +
252F ALA* 3.4 3.6 + - - +
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Residues in contact with ALA 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F VAL* 4.4 17.4 - - + +
247F GLY 3.9 1.2 + - - -
248F ASP* 1.3 83.5 + - - +
250F GLN* 1.3 57.9 + - - +
252F ALA* 3.2 8.1 + - - +
253F ARG* 2.9 40.8 + - + +
368F PHE 6.2 1.3 - - - -
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Residues in contact with GLN 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F ASP* 2.6 23.8 + - - +
249F ALA* 1.3 70.2 - - - +
251F THR* 1.3 76.3 + - - +
253F ARG* 3.0 19.3 + - + +
254F THR* 3.0 35.3 + - - +
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Residues in contact with THR 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F THR* 3.5 20.3 + - - +
248F ASP* 3.1 30.6 + - + +
250F GLN* 1.3 86.4 + - - +
252F ALA* 1.3 63.5 + - - +
254F THR* 2.8 21.8 + - - +
255F ALA* 2.9 13.2 + - - +
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Residues in contact with ALA 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F LEU* 4.3 15.9 - - + -
243F VAL* 3.9 13.5 - - + -
246F THR* 3.7 12.3 - - - +
248F ASP 3.4 11.2 + - - +
249F ALA 3.2 6.2 + - - +
250F GLN 3.2 0.4 - - - -
251F THR* 1.3 83.9 + - - +
253F ARG* 1.3 75.8 + - - +
255F ALA* 3.3 6.9 + - - +
256F VAL* 2.8 34.7 + - - +
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Residues in contact with ARG 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F LEU* 3.9 34.4 - - - +
243F VAL* 4.1 14.7 - - - +
249F ALA* 2.9 21.6 + - + +
250F GLN* 3.0 12.3 + - + +
252F ALA* 1.3 100.5 + - - +
254F THR* 1.3 66.7 + - + +
256F VAL* 3.2 4.9 + - - +
257F ALA* 2.9 26.2 + - - +
364F VAL* 3.9 27.4 + - + +
367F ALA* 4.4 0.4 + - - +
368F PHE* 2.2 47.0 + - - +
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Residues in contact with THR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 4.9 13.5 - - - +
250F GLN* 3.0 35.1 + - - +
251F THR* 2.8 24.8 + - - +
253F ARG* 1.3 75.2 - - + +
255F ALA* 1.3 62.7 + - - +
257F ALA* 3.5 3.9 + - - +
258F GLU* 3.0 35.1 + - - +
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Residues in contact with ALA 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 5.5 0.7 - - + -
165F VAL* 4.1 22.9 - - + -
168F ASN* 6.5 0.2 - - + -
169F LEU* 4.5 8.3 - - + +
242F LEU* 4.6 11.4 - - + -
246F THR* 5.3 6.5 - - + -
251F THR 2.9 14.8 + - - +
252F ALA* 3.5 7.9 - - - +
254F THR* 1.3 82.6 + - - +
256F VAL* 1.3 57.0 + - - +
258F GLU* 3.4 13.8 - - - +
259F PHE* 2.9 31.1 + - - +
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 4.9 7.4 - - + -
169F LEU* 5.3 0.9 - - + -
237F VAL* 4.0 10.3 - - + -
239F LEU* 3.8 26.0 - - + -
242F LEU* 3.6 23.6 - - + -
252F ALA 2.8 24.1 + - - +
253F ARG* 3.9 6.3 - - - +
255F ALA* 1.3 70.6 - - - +
257F ALA* 1.3 67.5 + - - +
259F PHE* 3.1 5.6 + - - -
260F LEU* 2.8 40.3 + - + +
364F VAL* 3.9 22.4 - - + -
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Residues in contact with ALA 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F ARG 2.9 16.5 + - - +
254F THR* 4.0 3.6 - - - +
256F VAL* 1.3 78.0 - - - +
258F GLU* 1.3 63.6 + - - +
260F LEU* 3.2 2.9 + - - +
261F ARG* 3.0 24.5 + - - +
360F ILE* 4.3 20.5 - - + +
361F ASP* 4.6 6.3 - - - +
364F VAL* 4.3 21.0 - - + +
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Residues in contact with GLU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F VAL* 3.6 25.8 - - + +
54F ARG* 4.7 23.3 - - + +
55F LEU* 3.0 60.5 + - - +
165F VAL* 3.9 6.1 - - - +
254F THR* 3.0 22.8 + - - +
255F ALA* 3.4 7.6 - - - +
257F ALA* 1.3 77.1 - - - +
259F PHE* 1.3 60.9 + - - +
261F ARG* 3.9 5.2 - - - +
262F ALA* 2.9 30.5 + - - +
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Residues in contact with PHE 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 5.4 1.6 - - + -
47F VAL* 3.7 26.7 - - + -
51F VAL* 4.0 9.0 - - + -
169F LEU* 3.7 26.7 - - + -
170F PHE* 4.0 17.3 - + - -
186F VAL* 3.8 18.6 - - + -
188F PHE* 5.1 4.9 - + - -
235F ALA* 4.7 11.0 - - + -
237F VAL* 3.6 25.8 - - + -
255F ALA 2.9 20.5 + - - +
256F VAL* 3.1 5.3 + - - +
258F GLU* 1.3 78.5 - - - +
260F LEU* 1.3 77.5 + - + +
262F ALA* 3.2 1.9 + - - +
263F PHE* 2.8 44.5 + + + +
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Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 4.0 22.4 - - + -
6F ILE* 4.3 17.5 - - + -
237F VAL* 4.3 7.0 - - + -
256F VAL* 2.8 31.5 + - + +
257F ALA* 3.8 3.6 - - - +
259F PHE* 1.3 97.5 - - + +
261F ARG* 1.3 65.6 + - - +
263F PHE* 2.9 17.4 + - - +
264F LEU* 3.1 17.9 + - - +
286F ILE* 3.7 26.9 - - + -
360F ILE* 4.1 15.7 - - + -
363F MET* 5.9 0.4 - - + -
364F VAL* 4.5 15.5 - - + -
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Residues in contact with ARG 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E ASP* 4.7 13.9 + - - +
329E TRP* 3.8 36.6 - - + -
50F GLU* 4.4 14.1 + - - -
54F ARG* 3.1 54.0 - - - +
257F ALA 3.0 16.3 + - - +
258F GLU* 3.9 4.9 - - - +
260F LEU* 1.3 76.4 - - - +
262F ALA* 1.3 64.2 + - - +
264F LEU* 3.2 8.5 + - - +
265F SER* 2.9 25.2 + - - -
357F PRO* 5.2 13.4 - - + +
360F ILE* 4.7 20.7 - - + +
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 4.1 14.6 - - + +
50F GLU* 4.1 17.3 - - + -
51F VAL* 3.8 20.2 - - + +
54F ARG* 6.4 1.6 - - - -
258F GLU 2.9 20.0 + - - +
259F PHE 3.5 4.9 - - - +
261F ARG* 1.3 77.6 - - - +
263F PHE* 1.3 62.5 + - - +
265F SER* 4.4 5.2 - - - +
266F THR* 3.0 32.6 + - + +
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Residues in contact with PHE 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 3.6 39.5 - - + -
8F ALA* 4.4 6.5 - - + -
43F TRP* 3.7 8.8 - - - -
47F VAL* 3.8 12.3 - - + +
188F PHE* 3.1 38.1 - + - -
233F ARG* 2.6 65.4 + - + -
234F TYR 4.5 7.2 - - - -
235F ALA* 3.8 22.4 - - + -
259F PHE* 2.8 24.2 + + + +
260F LEU* 2.9 13.4 + - - +
262F ALA* 1.3 77.4 - - - +
264F LEU* 1.3 64.2 + - + +
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Residues in contact with LEU 264 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292E ARG* 3.9 4.3 + - - -
329E TRP* 4.8 11.2 - - + -
6F ILE* 4.0 9.6 - - + -
8F ALA* 4.5 2.7 - - + -
10F GLN* 4.7 1.2 - - - +
233F ARG* 4.7 2.0 + - - +
260F LEU 3.1 12.5 + - - +
261F ARG* 3.7 7.4 - - - +
263F PHE* 1.3 102.1 - - + +
265F SER* 1.3 63.9 + - - +
266F THR 3.7 3.8 + - - +
279F THR 4.9 0.7 - - - +
280F LEU* 5.1 0.8 - - + +
281F PRO* 3.7 34.9 - - + +
284F VAL* 3.7 40.6 - - + -
356F TYR* 4.0 25.8 - - + -
360F ILE* 4.8 11.4 - - + -
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Residues in contact with SER 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E ASP* 6.2 0.2 - - - +
292E ARG* 2.4 49.9 + - - +
329E TRP* 4.0 22.6 - - - -
50F GLU* 3.7 24.2 + - - -
261F ARG* 2.9 22.0 + - - -
262F ALA* 4.0 3.1 - - - -
264F LEU* 1.3 78.0 - - - +
266F THR* 1.3 60.1 + - - +
278F MET* 5.1 0.7 - - - +
280F LEU* 5.9 0.2 - - - -
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Residues in contact with THR 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F TRP* 2.9 29.8 + - - -
46F ALA* 3.7 21.8 - - - +
47F VAL* 3.3 21.2 + - - +
50F GLU* 2.9 42.8 - - + +
262F ALA 3.0 17.3 + - - +
264F LEU 3.5 2.6 - - - +
265F SER* 1.3 78.9 - - - +
267F VAL* 1.3 64.7 + - - +
278F MET* 5.9 0.7 - - - -
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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