Contacts of the helix formed by residues 247 - 261 (chain P) in PDB entry 1SXG
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 247 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72P ASN* 5.6 4.3 + - - +
73P ILE* 5.3 5.8 - - + -
196P LYS* 4.6 2.4 + - - -
221P TYR* 3.8 26.0 - - + +
245P VAL* 3.2 8.7 + - - +
246P GLY* 1.3 81.7 + - - +
248P ASP* 1.3 68.9 + - - +
249P GLU* 3.6 11.7 - - + +
250P MET* 3.1 37.1 + - + +
251P ALA* 3.0 15.0 + - - +
274P PHE 3.7 9.2 - - - -
275P ASP* 4.1 10.3 + - - +
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Residues in contact with ASP 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P ILE* 4.7 3.3 - - + +
247P THR* 1.3 69.7 - - - +
249P GLU* 1.3 57.3 + - - +
251P ALA* 2.6 27.8 + - - +
252P LEU* 3.0 17.6 + - + +
274P PHE 3.2 22.2 + - - +
275P ASP* 4.9 1.0 + - + -
277P THR* 2.6 54.4 + - + +
279P LEU* 4.8 0.2 - - + -
280P SER* 2.8 17.1 + - - -
287P LEU* 3.6 12.7 - - + +
289P SER* 2.9 26.0 + - - -
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Residues in contact with GLU 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278F ARG* 2.9 43.6 + - - -
282F MET* 3.7 24.0 - - + +
73P ILE* 4.0 18.5 - - + +
221P TYR 3.7 17.0 - - - +
222P THR* 4.1 3.3 - - - +
223P TYR* 3.4 28.2 + - + +
247P THR* 3.3 7.6 + - + +
248P ASP* 1.3 77.8 - - - +
250P MET* 1.3 63.1 + - - +
252P LEU* 3.3 14.8 + - - +
253P GLY 3.5 6.4 + - - -
279P LEU* 3.9 17.0 - - + +
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Residues in contact with MET 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P VAL* 4.1 10.3 - - + +
184P SER 3.8 15.0 - - - +
185P GLY* 3.8 25.4 - - - +
219P GLY* 4.0 3.1 - - - -
221P TYR* 3.5 34.1 - - + +
222P THR 3.5 22.7 - - - +
225P SER* 3.7 8.3 - - - +
226P GLY* 3.5 7.3 - - - -
245P VAL* 3.6 14.6 - - + -
246P GLY 4.6 1.1 - - - -
247P THR* 3.1 34.4 + - + +
249P GLU* 1.3 74.8 - - - +
251P ALA* 1.3 60.8 + - - +
253P GLY* 2.8 17.7 + - - -
254P VAL* 2.8 16.5 + - - +
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Residues in contact with ALA 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245P VAL* 3.3 25.9 - - + +
247P THR 3.0 11.6 + - - +
248P ASP 2.6 18.3 + - - +
250P MET* 1.3 72.9 - - - +
252P LEU* 1.3 55.3 + - - +
254P VAL* 3.1 2.9 + - - +
255P ILE* 2.8 33.1 + - - +
271P ILE* 4.4 2.8 - - + +
273P GLY* 4.0 5.8 - - - -
287P LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282F MET* 4.1 26.5 - - + +
223P TYR* 3.7 12.3 - - + -
248P ASP 3.0 23.9 + - - +
249P GLU 3.6 8.5 - - - +
250P MET 3.1 0.4 - - - -
251P ALA* 1.3 75.9 - - - +
253P GLY* 1.3 57.7 + - - +
255P ILE* 3.6 6.4 + - - +
256P HIS* 3.1 34.8 + - + -
279P LEU* 3.7 31.6 - - + +
282P MET* 5.1 4.9 - - + +
283P VAL* 3.5 39.9 - - + -
287P LEU* 3.8 17.0 - - + -
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Residues in contact with GLY 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223P TYR* 3.6 32.9 - - - -
226P GLY 3.5 6.5 - - - -
227P ILE* 3.4 18.0 - - - +
249P GLU 3.5 4.0 + - - -
250P MET 2.8 8.9 + - - -
252P LEU* 1.3 77.1 - - - +
254P VAL* 1.3 59.1 + - - +
256P HIS 4.6 0.2 - - - -
257P GLY* 2.9 22.5 + - - -
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Residues in contact with VAL 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P VAL* 4.0 17.0 - - + -
226P GLY* 3.6 14.6 - - - +
230P VAL* 3.5 24.2 - - + +
243P ILE* 3.8 9.9 - - + -
245P VAL* 3.5 21.1 - - + -
250P MET 2.8 16.4 + - - +
251P ALA 3.1 7.2 + - - +
253P GLY* 1.3 74.7 - - - +
255P ILE* 1.3 67.7 + - - +
257P GLY 3.2 0.2 + - - -
258P ALA* 2.9 23.4 + - - +
271P ILE* 3.7 32.1 - - + -
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Residues in contact with ILE 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P ALA 2.8 23.7 + - - +
252P LEU* 3.7 8.5 - - + +
254P VAL* 1.3 80.1 - - - +
256P HIS* 1.3 63.8 + - + +
258P ALA* 3.1 3.7 + - - +
259P GLN* 3.0 55.9 + - - +
265P VAL* 3.9 20.9 - - + -
271P ILE* 3.5 35.7 - - + -
283P VAL* 4.7 10.8 - - + -
284P ARG 4.0 8.3 - - - +
285P PRO* 4.2 7.6 - - + +
287P LEU* 4.4 7.6 - - + -
330P SER* 4.4 11.0 - - - +
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Residues in contact with HIS 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F HIS* 6.2 1.6 - - - -
282F MET* 3.5 32.3 - - + -
283F VAL* 3.7 8.5 - - - -
284F ARG* 3.4 34.2 + - + +
223P TYR* 2.6 27.9 + + + +
227P ILE* 5.0 0.4 - - + -
252P LEU* 3.1 14.1 + - + +
253P GLY 4.2 2.5 - - - +
255P ILE* 1.3 83.6 - - + +
257P GLY* 1.3 59.3 + - - +
259P GLN* 3.6 21.5 - - - +
260P ASP* 2.8 37.5 + - - +
283P VAL* 3.7 20.6 - - + +
284P ARG 4.9 3.2 + - - -
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Residues in contact with GLY 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P ILE* 4.4 12.5 - - - +
230P VAL* 3.8 13.2 - - - -
253P GLY 2.9 19.8 + - - -
254P VAL 3.7 0.9 - - - -
256P HIS* 1.3 78.4 - - - +
258P ALA* 1.3 62.0 + - - +
260P ASP* 3.6 5.1 - - - +
261P ARG* 2.8 39.4 + - - -
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Residues in contact with ALA 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230P VAL* 4.2 3.3 - - + +
234P LEU* 4.4 12.8 - - - -
254P VAL* 2.9 12.5 + - + +
255P ILE 3.3 9.6 - - - +
257P GLY* 1.3 74.7 - - - +
259P GLN* 1.3 65.5 + - - +
261P ARG* 2.9 16.1 + - - +
262P GLY 3.4 0.3 + - - -
263P LEU* 3.3 24.9 + - + +
265P VAL* 4.3 13.0 - - + -
269P LEU* 3.8 28.0 - - + -
271P ILE* 5.8 0.2 - - + -
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Residues in contact with GLN 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F ARG* 4.7 8.4 - - + +
255P ILE* 3.0 38.5 + - + +
256P HIS* 3.6 20.4 - - - +
258P ALA* 1.3 75.5 - - - +
260P ASP* 1.3 64.4 + - - +
262P GLY* 2.9 14.7 + - - -
263P LEU 3.4 18.8 - - - +
264P ASN* 5.4 0.4 - - - -
265P VAL* 4.5 11.0 - - + +
284P ARG 3.0 18.4 + - - +
285P PRO* 3.5 9.9 - - - +
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Residues in contact with ASP 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F ARG* 2.8 48.4 + - - +
227P ILE* 4.7 5.9 - - - +
256P HIS 2.8 27.9 + - - +
257P GLY* 3.6 7.7 + - - +
258P ALA 3.2 0.2 + - - -
259P GLN* 1.3 73.4 - - - +
261P ARG* 1.3 67.6 + - - +
262P GLY 3.3 1.1 + - - -
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Residues in contact with ARG 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P ILE* 4.1 18.7 - - - +
231P GLU* 2.9 64.2 + - - +
234P LEU* 4.3 20.7 - - + +
257P GLY* 2.8 29.4 + - - -
258P ALA 2.9 8.8 + - - +
260P ASP* 1.3 84.9 - - - +
262P GLY* 1.3 60.2 + - - +
263P LEU* 3.6 4.8 - - + +
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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