Contacts of the helix formed by residues 248 - 266 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243E VAL* 4.3 2.7 - - - +
246E THR* 3.1 24.3 + - - +
247E GLY* 1.3 76.2 - - - +
249E ALA* 1.3 84.0 + - - +
250E GLN* 2.6 26.8 + - - +
251E THR* 3.2 27.0 + - + +
252E ALA* 3.4 2.9 + - - +
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Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E VAL* 4.2 23.0 - - + +
247E GLY 3.9 1.2 + - - -
248E ASP* 1.3 83.3 + - - +
250E GLN* 1.3 58.2 + - - +
252E ALA* 3.3 2.8 + - - +
253E ARG* 2.9 41.3 + - + +
368E PHE* 5.9 4.5 - - + -
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Residues in contact with GLN 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ASP* 2.6 24.6 + - - +
249E ALA* 1.3 69.7 - - - +
251E THR* 1.3 78.3 + - - +
253E ARG* 3.0 10.2 + - + +
254E THR* 3.0 42.9 + - - +
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Residues in contact with THR 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E VAL* 6.0 0.5 - - - +
246E THR* 3.4 20.8 + - - +
248E ASP* 3.2 29.5 + - + +
250E GLN* 1.3 87.4 + - - +
252E ALA* 1.3 60.1 + - - +
254E THR* 2.8 22.2 + - - +
255E ALA* 2.9 16.2 + - - +
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Residues in contact with ALA 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E LEU* 4.5 11.2 - - + -
243E VAL* 3.7 25.1 - - + +
246E THR* 3.6 20.4 - - - +
248E ASP 3.4 5.1 + - - +
249E ALA 3.3 9.6 + - - +
250E GLN 3.2 0.6 - - - -
251E THR* 1.3 83.2 + - - +
253E ARG* 1.3 63.5 + - - +
255E ALA* 3.3 6.5 + - - +
256E VAL* 2.9 34.5 + - - +
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Residues in contact with ARG 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E LEU* 4.0 34.8 - - - +
243E VAL* 3.9 15.4 - - - +
249E ALA* 2.9 27.0 + - + +
250E GLN* 3.0 11.4 + - + +
252E ALA* 1.3 96.1 - - - +
254E THR* 1.3 68.3 + - + +
256E VAL* 3.2 4.7 + - - +
257E ALA* 2.9 24.8 + - - +
364E VAL* 3.9 19.7 + - + +
367E ALA* 4.0 3.6 + - - +
368E PHE* 3.0 71.1 - - + +
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Residues in contact with THR 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU* 5.0 15.8 - - - +
250E GLN* 3.0 34.6 + - - +
251E THR* 2.8 23.9 + - - -
253E ARG* 1.3 76.2 - - + +
255E ALA* 1.3 63.2 + - - +
257E ALA* 4.7 1.8 - - - -
258E GLU* 2.4 43.2 + - - +
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Residues in contact with ALA 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 5.5 1.6 - - - +
55E LEU* 4.9 4.9 - - - -
165E VAL* 4.1 30.0 - - + +
168E ASN* 6.2 0.7 - - + -
169E LEU* 4.5 16.5 - - + +
242E LEU* 5.0 3.6 - - + -
246E THR* 5.2 7.0 - - + -
251E THR 2.9 13.7 + - - +
252E ALA* 3.5 8.7 - - - +
253E ARG 3.2 0.2 - - - -
254E THR* 1.3 83.1 + - - +
256E VAL* 1.3 57.2 + - - +
258E GLU* 3.9 1.8 - - - +
259E PHE* 2.9 30.4 + - - +
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 5.1 5.8 - - + -
169E LEU* 5.3 0.9 - - + -
237E VAL* 4.0 9.2 - - + -
239E LEU* 3.7 24.7 - - + -
242E LEU* 3.6 24.7 - - + -
252E ALA 2.9 22.0 + - - +
253E ARG* 3.2 4.9 + - - +
255E ALA* 1.3 74.6 - - - +
257E ALA* 1.3 67.9 + - - +
259E PHE* 3.1 5.1 + - - -
260E LEU* 2.8 39.0 + - + +
364E VAL* 3.7 28.3 - - + -
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E ARG 2.9 14.4 + - - +
254E THR* 4.7 1.3 - - - -
256E VAL* 1.3 78.6 - - - +
258E GLU* 1.3 74.5 + - - +
260E LEU* 3.3 1.4 + - - +
261E ARG* 3.0 25.4 + - - +
360E ILE* 4.0 17.8 - - + +
361E ASP* 5.7 5.6 - - + -
364E VAL* 4.6 10.9 - - + +
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Residues in contact with GLU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 4.0 11.1 - - + +
54E ARG* 3.8 40.1 + - + +
55E LEU* 4.8 22.8 - - + +
254E THR* 2.4 46.4 + - - +
255E ALA* 4.5 2.0 - - - +
257E ALA* 1.3 82.4 - - - +
259E PHE* 1.3 58.1 + - - +
261E ARG* 3.9 6.1 - - - +
262E ALA* 2.9 31.2 + - - +
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Residues in contact with PHE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 5.3 2.5 - - + -
47E VAL* 3.7 26.0 - - + -
51E VAL* 3.9 9.3 - - + +
169E LEU* 3.5 28.0 - - + -
170E PHE* 4.0 14.1 - + - -
186E VAL* 3.6 22.9 - - + -
188E PHE* 5.7 2.5 - + - -
235E ALA* 4.6 10.8 - - + -
237E VAL* 3.6 25.1 - - + -
255E ALA 2.9 22.1 + - - +
256E VAL* 3.1 4.7 + - - +
258E GLU* 1.3 77.1 - - - +
260E LEU* 1.3 78.1 + - + +
262E ALA* 3.3 2.1 + - - +
263E PHE* 2.8 44.4 + + + +
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.1 19.7 - - + -
6E ILE* 4.4 23.5 - - + +
237E VAL* 4.4 7.2 - - + -
256E VAL* 2.8 32.4 + - + +
259E PHE* 1.3 98.8 - - + +
261E ARG* 1.3 65.3 + - - +
263E PHE* 2.9 17.3 + - - +
264E LEU* 3.0 16.1 + - - +
286E ILE* 4.9 10.1 - - + -
360E ILE* 3.7 35.9 - - + -
364E VAL* 4.1 16.2 - - + -
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Residues in contact with ARG 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 4.7 11.1 + - - -
54E ARG* 3.0 54.4 - - - +
257E ALA 3.0 16.4 + - - +
258E GLU* 4.0 5.8 - - - +
260E LEU* 1.3 76.6 - - - +
262E ALA* 1.3 59.6 + - - +
264E LEU* 3.2 4.9 + - - +
265E SER* 2.9 29.1 + - - -
357E PRO* 5.2 12.8 - - + +
360E ILE* 3.7 18.1 - - + +
291I ASP* 4.8 11.5 + - - +
329I TRP* 3.4 41.9 - - + -
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 4.3 7.9 - - + +
50E GLU* 4.1 24.5 - - + -
51E VAL* 3.8 19.7 - - + -
54E ARG* 6.2 3.3 - - - +
258E GLU 2.9 19.4 + - - +
259E PHE 3.6 4.3 - - - +
261E ARG* 1.3 78.7 - - - +
263E PHE* 1.3 58.1 + - - +
265E SER* 4.3 5.4 - - - +
266E THR* 2.8 36.9 + - - +
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Residues in contact with PHE 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 3.7 39.7 - - + -
8E ALA* 4.5 6.7 - - + -
43E TRP* 3.7 9.7 - - - -
47E VAL* 3.9 13.9 - - + +
188E PHE* 3.1 39.3 - + - -
233E ARG* 2.4 71.4 + - + -
234E TYR 4.4 5.6 - - - -
235E ALA* 3.7 19.5 - - + -
259E PHE* 2.8 26.0 + + + +
260E LEU* 3.1 12.8 - - - +
262E ALA* 1.3 77.2 - - - +
264E LEU* 1.3 62.8 + - + +
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Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 4.0 8.7 - - + -
8E ALA* 4.8 2.0 - - + -
10E GLN* 4.7 1.0 + - - +
233E ARG* 4.4 3.0 + - - +
260E LEU 3.0 11.2 + - - +
261E ARG* 3.7 6.1 - - - +
262E ALA 3.1 0.2 - - - -
263E PHE* 1.3 98.0 - - + +
265E SER* 1.3 63.9 + - - +
266E THR 4.1 3.8 - - - +
279E THR 4.9 0.9 - - - +
280E LEU* 4.3 2.0 - - + +
281E PRO* 3.8 31.5 - - + +
284E VAL* 3.6 30.7 - - + -
356E TYR* 3.7 36.8 - - + -
359E LEU* 6.2 0.2 - - + -
360E ILE* 3.7 24.5 - - + -
292I ARG* 3.9 4.0 + - - -
329I TRP* 5.1 6.3 - - + -
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Residues in contact with SER 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 3.3 23.6 + - - -
261E ARG* 2.9 21.9 + - - -
262E ALA* 3.9 3.1 - - - -
264E LEU* 1.3 78.5 - - - +
266E THR* 1.3 61.3 + - - +
278E MET* 5.3 0.7 - - - +
280E LEU* 4.9 2.9 - - - -
292I ARG* 2.3 54.3 + - - +
329I TRP* 4.3 18.6 - - - -
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Residues in contact with THR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLN* 5.2 0.2 + - - -
43E TRP* 3.1 42.8 - - + +
46E ALA* 3.3 27.3 + - + +
47E VAL* 3.5 20.4 - - + +
50E GLU* 3.6 18.5 + - - -
262E ALA 2.8 23.2 + - - +
264E LEU 3.5 3.0 - - - +
265E SER* 1.3 76.2 - - - +
267E VAL* 1.3 70.5 + - - +
278E MET* 6.3 0.2 - - - -
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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