Contacts of the helix formed by residues 245 - 258 (chain E) in PDB entry 1XFB
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 245 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244E TYR* 1.3 73.4 - - - +
246E PRO* 1.3 67.1 - - + +
247E GLU* 2.7 39.7 - - + +
248E GLU* 2.6 51.5 + - - +
249E ILE* 2.9 11.9 + - - +
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Residues in contact with PRO 246 (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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244E TYR 3.8 4.2 - - - +
245E THR* 1.3 88.8 - - + +
247E GLU* 1.3 69.4 + - - +
249E ILE* 3.8 5.2 - - + +
250E ALA* 2.9 21.3 + - - +
282E PHE* 4.5 18.6 - - + +
283E ASN* 3.1 32.8 + - - +
286E ALA* 3.2 24.5 - - + +
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Residues in contact with GLU 247 (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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245E THR* 2.7 34.4 - - + +
246E PRO* 1.3 90.1 - - - +
248E GLU* 1.3 54.2 + - + +
250E ALA* 3.1 7.0 + - - +
251E MET* 2.8 37.3 + - - +
286E ALA* 4.1 15.3 - - - +
289E ARG* 5.0 10.4 + - - -
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Residues in contact with GLU 248 (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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199E LEU* 3.6 12.9 - - + +
243E LYS 4.0 3.1 - - - +
244E TYR* 3.0 31.1 - - + +
245E THR* 2.6 45.6 + - - +
247E GLU* 1.3 77.8 - - + +
249E ILE* 1.3 60.6 + - - +
251E MET* 3.3 8.9 + - - +
252E ALA* 3.1 18.4 + - - +
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Residues in contact with ILE 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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199E LEU* 4.4 10.5 - - + -
233E MET* 4.7 5.8 - - + -
234E VAL 3.5 20.3 - - - +
235E THR* 3.9 21.5 - - + -
236E PRO* 4.8 4.3 - - + -
244E TYR* 4.3 20.6 - - + +
245E THR 2.9 13.5 + - - +
246E PRO* 3.8 8.5 - - + +
248E GLU* 1.3 72.7 - - - +
250E ALA* 1.3 63.5 + - - +
252E ALA* 3.3 2.1 + - - +
253E THR* 2.9 38.6 + - - +
279E GLU* 5.9 2.0 - - - +
283E ASN* 3.8 37.2 - - + +
287E ILE* 5.5 1.6 - - + -
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Residues in contact with ALA 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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246E PRO 2.9 19.4 + - - +
247E GLU* 3.4 5.6 - - - +
249E ILE* 1.3 76.4 - - - +
251E MET* 1.3 57.5 + - - +
253E THR* 4.4 0.2 - - - -
254E VAL* 2.9 36.9 + - - +
286E ALA* 3.5 8.7 - - + +
287E ILE* 3.4 46.0 - - + +
290E CYS* 4.5 6.3 - - + -
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Residues in contact with MET 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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247E GLU 2.8 18.3 + - - +
248E GLU* 3.5 10.3 - - - +
250E ALA* 1.3 77.5 - - - +
252E ALA* 1.3 54.0 + - - +
254E VAL* 4.0 0.9 - - - +
255E THR* 2.7 40.2 + - - +
290E CYS* 3.9 5.1 - - - -
291E PRO* 3.8 33.7 - - + -
292E LEU* 3.6 29.2 - - + -
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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
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199E LEU* 3.9 14.4 - - + -
203E GLN* 3.4 24.5 - - - +
234E VAL* 3.3 25.6 - - + -
248E GLU 3.1 15.8 + - - +
249E ILE 3.8 1.6 - - - +
251E MET* 1.3 73.8 - - - +
253E THR* 1.3 61.8 + - - +
255E THR* 3.3 1.8 + - - -
256E ALA* 2.9 31.5 + - - +
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Residues in contact with THR 253 (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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232E ASN 5.2 0.4 - - - +
233E MET* 3.7 11.1 - - - +
234E VAL* 2.9 34.1 + - + +
249E ILE* 2.9 21.9 + - - +
250E ALA 3.8 2.5 - - - -
252E ALA* 1.3 78.4 - - - +
254E VAL* 1.3 64.8 + - + +
256E ALA* 3.4 1.6 + - - +
257E LEU* 3.1 25.7 + - + +
270E PHE* 3.3 39.7 - - + -
287E ILE* 3.8 14.6 - - + -
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Residues in contact with VAL 254 (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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250E ALA 2.9 21.2 + - - +
253E THR* 1.3 72.9 - - + +
255E THR* 1.3 66.2 + - - +
257E LEU* 3.3 7.1 + - + +
258E ARG* 2.9 44.2 + - + +
287E ILE* 3.8 28.9 - - + +
290E CYS* 4.0 21.1 - - + -
292E LEU* 3.8 14.6 - - + -
294E ARG* 3.8 22.2 - - + -
296E TRP* 6.0 1.1 - - + +
298E LEU* 4.3 7.6 - - + -
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Residues in contact with THR 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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203E GLN* 3.7 7.6 - - - +
251E MET* 2.7 28.6 + - - +
252E ALA* 3.6 5.1 - - - -
254E VAL* 1.3 80.4 - - - +
256E ALA* 1.3 65.4 + - - +
258E ARG* 3.2 11.0 + - + +
259E ARG* 3.2 60.6 + - + +
292E LEU* 3.6 13.7 - - + +
225H GLU* 4.1 3.6 - - - +
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Residues in contact with ALA 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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203E GLN* 3.9 10.0 - - + +
206E THR* 4.1 13.7 - - + -
207E GLU* 3.7 28.7 - - + -
210E LEU* 5.2 1.1 - - - -
234E VAL* 4.0 11.4 - - + -
252E ALA 2.9 17.7 + - - +
253E THR 3.6 4.5 - - - +
255E THR* 1.3 76.2 - - - +
257E LEU* 1.3 64.1 + - + +
259E ARG* 3.1 14.7 + - - +
260E THR* 3.2 17.0 + - - +
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Residues in contact with LEU 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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206E THR* 5.9 1.1 - - + -
210E LEU* 3.8 18.2 - - + -
229E LEU* 4.0 11.0 - - + -
231E PRO* 4.3 5.8 - - + -
253E THR* 3.1 19.6 + - + +
254E VAL* 3.8 6.7 - - + +
256E ALA* 1.3 79.2 - - + +
258E ARG* 1.3 58.4 + - - +
259E ARG 3.2 0.5 + - - -
260E THR* 4.0 2.9 - - - -
261E VAL* 2.8 49.3 + - + +
268E VAL* 3.8 16.2 - - + -
270E PHE* 3.5 35.7 - - + -
296E TRP* 3.4 17.5 - - + +
298E LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 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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254E VAL* 2.9 43.5 + - + +
255E THR* 3.2 13.2 + - + +
257E LEU* 1.3 75.2 - - - +
259E ARG* 1.3 51.5 + - + +
260E THR 3.4 0.4 - - - -
292E LEU* 4.0 19.5 - - - +
293E PRO* 3.0 48.4 + - - +
295E PRO* 5.7 0.2 - - - +
296E TRP* 3.8 14.1 - - + -
225H GLU* 5.5 5.5 + - - +
263H PRO* 3.5 35.1 + - + +
264H ALA* 2.5 55.6 + - + +
295H PRO* 5.1 6.1 + - - +
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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