Contacts of the helix formed by residues 248 - 266 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243G VAL* 4.5 2.7 - - - +
246G THR* 3.2 17.7 + - - +
247G GLY* 1.3 76.4 - - - +
249G ALA* 1.3 84.6 + - - +
250G GLN* 2.6 28.5 + - - +
251G THR* 3.1 33.4 + - + +
252G ALA* 3.4 4.2 + - - +
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Residues in contact with ALA 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G VAL* 4.5 15.6 - - + +
247G GLY 4.0 1.2 + - - -
248G ASP* 1.3 82.4 + - - +
250G GLN* 1.3 58.1 + - - +
252G ALA* 3.2 9.0 + - - +
253G ARG* 2.9 39.2 + - + +
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Residues in contact with GLN 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248G ASP* 2.6 24.0 + - - +
249G ALA* 1.3 70.4 - - - +
251G THR* 1.3 76.4 + - - +
253G ARG* 3.0 19.2 + - + +
254G THR* 3.0 36.3 + - - +
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Residues in contact with THR 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G THR* 3.3 22.4 + - - +
248G ASP* 3.1 29.4 + - + +
250G GLN* 1.3 85.7 + - - +
252G ALA* 1.3 60.3 + - - +
254G THR* 3.0 7.9 + - - -
255G ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G LEU* 5.8 1.6 - - + -
242G LEU* 4.5 13.9 - - + -
243G VAL* 3.8 25.4 - - + -
246G THR* 4.0 9.2 - - - +
248G ASP 3.4 10.2 + - - +
249G ALA 3.2 9.8 + - - +
250G GLN 3.1 0.6 - - - -
251G THR* 1.3 82.6 + - - +
253G ARG* 1.3 63.4 + - - +
255G ALA* 3.7 5.1 - - - +
256G VAL* 2.8 37.1 + - + +
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Residues in contact with ARG 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G LEU* 4.8 18.2 - - - +
243G VAL* 4.8 7.9 - - - +
249G ALA* 2.9 31.3 + - - +
250G GLN* 3.0 11.6 + - + +
252G ALA* 1.3 85.8 - - - +
254G THR* 1.3 63.8 + - + +
256G VAL* 4.8 2.2 - - - +
257G ALA* 2.9 28.4 + - - +
364G VAL* 3.5 35.9 + - + +
365G ALA* 5.4 1.3 - - - +
367G ALA* 2.9 36.0 + - - +
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Residues in contact with THR 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 5.1 16.4 - - - +
250G GLN* 3.0 33.6 + - - +
251G THR* 3.0 16.5 + - - +
253G ARG* 1.3 76.8 - - + +
255G ALA* 1.3 65.0 + - - +
257G ALA* 4.2 3.1 - - - +
258G GLU* 3.0 30.2 + - - +
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Residues in contact with ALA 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G VAL* 5.6 0.6 - - - +
55G LEU* 4.7 5.6 - - + -
165G VAL* 3.9 27.6 - - + -
168G ASN* 6.6 0.2 - - + -
169G LEU* 4.5 8.7 - - + +
242G LEU* 4.6 11.2 - - + -
246G THR* 5.3 6.5 - - + -
251G THR 2.9 14.9 + - - +
252G ALA* 3.7 6.1 - - - +
254G THR* 1.3 83.7 + - - +
256G VAL* 1.3 57.6 + - - +
258G GLU* 3.9 3.2 - - - +
259G PHE* 2.9 30.8 + - - +
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 4.9 9.0 - - + -
169G LEU* 5.2 0.9 - - + -
237G VAL* 4.1 11.7 - - + -
239G LEU* 3.9 24.9 - - + -
242G LEU* 3.5 25.1 - - + -
252G ALA* 2.8 25.9 + - + +
253G ARG* 4.0 4.0 - - - +
255G ALA* 1.3 69.1 - - - +
257G ALA* 1.3 68.3 + - - +
259G PHE* 3.0 5.9 + - - +
260G LEU* 2.9 41.1 + - + +
364G VAL* 4.0 17.5 - - + -
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Residues in contact with ALA 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ARG 2.9 16.8 + - - +
254G THR* 4.2 3.4 - - - +
256G VAL* 1.3 78.0 - - - +
258G GLU* 1.3 64.8 + - - +
260G LEU* 3.2 2.3 + - - +
261G ARG* 3.0 23.3 + - - +
360G ILE* 3.7 11.6 - - + +
361G ASP* 4.8 9.2 - - - +
364G VAL* 3.8 28.4 - - + +
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Residues in contact with GLU 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G GLU* 3.8 1.0 - - - +
51G VAL* 3.0 50.8 + - - +
54G ARG* 3.3 38.9 - - + +
55G LEU* 4.6 19.0 - - + +
254G THR 3.0 20.4 + - - +
255G ALA* 4.2 2.6 - - - +
257G ALA* 1.3 76.8 - - - +
259G PHE* 1.3 57.2 + - - +
261G ARG* 3.4 7.1 + - + +
262G ALA* 2.9 28.1 + - - +
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Residues in contact with PHE 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ILE* 5.4 2.9 - - + -
47G VAL* 3.5 29.2 - - + -
51G VAL* 3.9 9.0 - - + -
169G LEU* 3.8 25.8 - - + -
170G PHE* 3.9 15.5 - + - -
186G VAL* 4.0 17.9 - - + -
188G PHE* 5.3 3.8 - + - -
235G ALA* 4.8 9.4 - - + -
237G VAL* 3.7 24.2 - - + -
255G ALA 2.9 22.5 + - - +
256G VAL* 3.0 4.5 + - - +
258G GLU* 1.3 74.9 + - - +
260G LEU* 1.3 79.9 + - + +
262G ALA* 3.1 1.7 + - - +
263G PHE* 2.8 47.6 + + + +
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Residues in contact with LEU 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 4.2 20.9 - - + -
6G ILE* 4.4 17.5 - - + -
237G VAL* 4.6 6.1 - - + -
256G VAL* 2.9 33.8 + - + +
257G ALA 3.7 4.0 - - - +
259G PHE* 1.3 94.1 - - + +
261G ARG* 1.3 64.5 + - - +
263G PHE* 2.9 17.1 + - - +
264G LEU* 3.0 15.9 + - - +
286G ILE* 3.6 27.4 - - + -
360G ILE* 3.8 16.6 - - + -
363G MET* 5.7 0.4 - - + -
364G VAL* 4.2 18.8 - - + -
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Residues in contact with ARG 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ASP* 4.5 15.4 + - - +
329F TRP* 3.7 37.1 - - + -
50G GLU* 4.6 10.7 + - - -
54G ARG* 3.1 54.1 - - - +
257G ALA 3.0 15.2 + - - +
258G GLU* 3.8 7.4 - - + +
260G LEU* 1.3 77.6 - - - +
262G ALA* 1.3 63.2 + - - +
264G LEU* 3.2 4.6 + - - +
265G SER* 3.0 26.1 + - - -
357G PRO* 5.3 13.1 - - + +
360G ILE* 3.6 18.7 - - + +
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Residues in contact with ALA 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G VAL* 4.3 7.9 - - + +
50G GLU* 4.2 20.4 - - + -
51G VAL* 3.6 22.9 - - + -
54G ARG* 6.4 0.2 - - - +
258G GLU* 2.9 24.9 + - - +
259G PHE 3.1 4.5 + - - +
261G ARG* 1.3 78.1 - - - +
263G PHE* 1.3 64.7 + - - +
265G SER* 4.4 5.2 - - - +
266G THR* 2.9 30.5 + - - +
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Residues in contact with PHE 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ILE* 3.4 48.2 - - + -
8G ALA* 4.4 6.1 - - + -
43G TRP* 3.7 9.1 - - - -
47G VAL* 3.9 10.9 - - + +
188G PHE* 3.2 33.7 - + - -
233G ARG* 2.7 66.4 + - + -
234G TYR 4.5 5.4 - - - -
235G ALA* 3.7 16.8 - - + -
259G PHE* 2.8 26.8 + + + +
260G LEU* 2.9 13.4 + - - +
262G ALA* 1.3 76.7 - - - +
264G LEU* 1.3 65.2 + - + +
266G THR 4.4 0.2 - - - +
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Residues in contact with LEU 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F ARG* 3.8 4.0 + - - -
329F TRP* 4.8 10.8 - - + -
6G ILE* 4.0 8.3 - - + -
8G ALA* 4.7 2.2 - - + -
10G GLN* 4.8 1.6 + - - +
233G ARG* 4.6 2.0 + - - +
260G LEU 3.0 11.1 + - - +
261G ARG 3.8 5.2 - - - +
263G PHE* 1.3 101.3 - - + +
265G SER* 1.3 63.7 + - - +
266G THR 4.1 3.6 - - - +
279G THR 5.0 1.0 - - - +
280G LEU* 5.2 0.8 - - - +
281G PRO* 3.8 33.9 - - + +
284G VAL* 3.7 41.1 - - + -
356G TYR* 3.9 28.9 - - + -
359G LEU* 6.2 0.2 - - + -
360G ILE* 4.2 16.2 - - + -
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Residues in contact with SER 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F ARG* 2.3 54.4 + - - +
329F TRP* 3.9 21.7 - - - -
50G GLU* 3.8 20.5 + - - -
261G ARG* 3.0 21.8 + - - -
262G ALA* 4.0 4.0 - - - -
264G LEU* 1.3 80.0 - - - +
266G THR* 1.3 61.7 + - - +
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Residues in contact with THR 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLN* 5.2 0.2 + - - -
43G TRP* 3.2 29.0 - - + +
46G ALA* 3.4 25.4 + - + +
47G VAL* 3.5 33.0 - - + +
50G GLU* 3.8 18.8 + - - +
262G ALA 2.9 19.7 + - - +
264G LEU 3.5 2.8 - - - +
265G SER* 1.3 80.5 - - - +
267G VAL* 1.3 70.3 + - - +
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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
------------------------------------------------------------
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