Contacts of the helix formed by residues 247 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D PHE* 6.5 0.4 - - + -
196D LYS* 4.8 3.6 - - - +
221D TYR* 3.4 38.9 + - + -
245D VAL* 3.3 9.6 - - - +
246D GLY* 1.3 81.5 - - - +
248D ASP* 1.3 64.5 + - - +
249D GLU* 3.7 7.3 + - - +
250D MET* 3.1 31.3 + - - +
251D ALA* 3.1 17.8 + - - +
274D PHE 3.4 9.9 - - - -
275D ASP* 3.8 10.5 - - - +
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Residues in contact with ASP 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D THR* 1.3 72.5 - - - +
249D GLU* 1.3 67.6 + - - +
251D ALA* 2.8 8.2 + - - +
252D LEU* 2.8 28.7 + - + +
274D PHE 3.3 10.9 + - - -
275D ASP* 3.7 3.9 + - - +
276D ASN* 3.1 7.8 + - - -
277D THR* 2.7 49.0 + - + +
279D LEU* 4.4 8.7 - - + -
280D SER* 3.8 4.8 - - - -
287D LEU* 3.0 20.8 - - + +
289D SER* 2.7 23.4 + - - -
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Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ARG* 2.7 37.3 + - - -
282A MET* 4.3 7.3 - - + +
72D ASN* 3.6 16.4 + - - +
221D TYR 3.7 17.1 - - - +
222D THR* 4.1 3.5 - - - -
223D TYR* 3.2 43.4 + - + +
247D THR* 3.3 5.4 + - - +
248D ASP* 1.3 80.3 - - - +
250D MET* 1.3 60.9 + - - +
252D LEU* 3.5 6.4 + - - +
253D GLY 3.4 13.5 + - - -
279D LEU* 4.0 17.1 - - + +
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Residues in contact with MET 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D VAL* 3.6 21.1 - - + +
184D SER 3.4 22.4 - - - +
185D GLY* 4.5 2.0 - - - -
219D GLY* 3.3 25.1 - - - -
220D ASP 3.9 0.4 - - - +
221D TYR* 3.8 28.5 - - - -
222D THR 4.0 8.3 - - - +
223D TYR* 4.6 0.2 - - - +
225D SER* 3.1 23.8 - - - +
226D GLY* 3.7 9.8 - - - +
245D VAL* 3.4 15.0 - - + -
246D GLY* 5.3 0.2 - - - -
247D THR* 3.1 20.7 + - - +
248D ASP 3.2 0.4 - - - -
249D GLU* 1.3 74.5 - - - +
251D ALA* 1.3 67.3 + - - +
253D GLY* 3.0 3.7 + - - +
254D VAL* 2.9 24.4 + - - +
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D VAL* 3.3 22.6 - - + +
247D THR 3.1 15.0 + - - +
248D ASP 2.8 8.9 + - - +
250D MET* 1.3 77.1 - - - +
252D LEU* 1.3 63.8 + - - +
254D VAL* 2.9 12.2 + - - +
255D ILE* 3.0 18.7 + - - +
271D ILE* 4.6 1.7 - - + +
273D GLY* 4.1 3.6 - - - -
287D LEU* 3.5 34.1 - - + -
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A MET* 3.8 20.2 - - + +
223D TYR* 3.6 11.0 - - + -
248D ASP 2.8 20.5 + - - +
249D GLU 3.7 8.3 - - - +
250D MET 3.2 0.2 - - - -
251D ALA* 1.3 78.0 - - - +
253D GLY* 1.3 63.5 + - - +
255D ILE* 3.3 3.8 + - - +
256D HIS* 3.1 29.6 + - - +
279D LEU* 3.6 45.8 - - + +
282D MET 4.6 5.6 - - - +
283D VAL* 3.4 42.6 - - + -
287D LEU* 4.3 13.7 - - + -
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Residues in contact with GLY 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D TYR* 3.3 38.7 - - - -
226D GLY 3.7 6.5 - - - -
227D ILE* 2.9 27.9 - - - +
249D GLU 3.4 1.4 + - - -
250D MET 3.0 8.3 + - - -
252D LEU* 1.3 80.5 - - - +
254D VAL* 1.3 55.9 + - - +
257D GLY 2.9 11.4 + - - -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D VAL* 4.3 11.0 - - + -
226D GLY* 3.4 16.4 - - - +
230D VAL* 3.2 20.4 - - + +
243D ILE* 3.9 22.0 - - + -
245D VAL* 3.6 24.7 - - + -
250D MET 2.9 20.3 + - - +
251D ALA 2.9 6.5 + - - +
253D GLY* 1.3 74.3 - - - +
255D ILE* 1.3 66.4 + - - +
258D ALA* 3.1 23.1 + - + +
269D LEU* 5.5 0.2 - - + -
271D ILE* 3.7 22.7 - - + -
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Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ALA 3.0 15.9 + - - +
252D LEU* 3.7 6.1 - - - +
254D VAL* 1.3 76.3 - - - +
256D HIS* 1.3 62.5 + - - +
258D ALA* 3.3 2.1 + - - +
259D GLN* 2.9 55.4 + - + +
265D VAL* 4.0 10.8 - - + -
271D ILE* 3.4 26.9 - - + -
283D VAL* 4.4 13.5 - - + -
284D ARG 4.3 3.1 - - - +
285D PRO* 4.0 30.5 - - + +
287D LEU* 4.1 26.7 - - + -
330D SER* 4.2 9.2 - - - +
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Residues in contact with HIS 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A HIS* 6.1 2.2 - - - -
282A MET 3.5 19.2 + - - -
283A VAL* 3.6 6.8 - - + -
284A ARG* 3.0 49.6 - - + +
223D TYR* 2.7 36.5 - + - +
227D ILE* 3.8 3.1 - - + -
252D LEU* 3.1 12.4 + - - +
255D ILE* 1.3 75.0 - - + +
257D GLY* 1.3 56.7 + - - +
259D GLN* 3.1 17.0 + - - +
260D ASP* 2.6 41.2 + - - +
283D VAL* 3.8 27.6 - - + +
284D ARG 5.0 3.8 - - - -
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Residues in contact with GLY 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ILE* 3.3 25.0 - - - +
230D VAL* 4.4 10.3 - - - -
231D GLU* 5.9 2.0 - - - -
253D GLY 2.9 17.1 + - - -
254D VAL 4.0 0.7 - - - -
256D HIS* 1.3 74.0 - - - +
258D ALA* 1.3 62.9 + - - +
260D ASP* 3.1 7.6 + - - +
261D ARG* 3.1 28.7 + - - +
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D VAL* 3.9 17.0 - - + +
234D LEU* 4.8 0.4 - - - -
254D VAL 3.1 18.6 + - - +
255D ILE* 3.4 6.5 - - - +
257D GLY* 1.3 71.5 - - - +
259D GLN* 1.3 68.6 + - - +
261D ARG* 2.9 13.1 + - - -
262D GLY 3.3 0.2 + - - -
263D LEU* 3.0 34.5 + - + +
265D VAL* 4.7 9.2 - - + -
269D LEU* 4.2 18.6 - - + -
271D ILE* 5.1 1.1 - - + -
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Residues in contact with GLN 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG* 4.8 8.3 - - + +
255D ILE* 2.9 33.4 + - + +
256D HIS* 3.6 22.6 + - - +
258D ALA* 1.3 71.3 - - - +
260D ASP* 1.3 55.1 + - - +
262D GLY* 2.7 26.7 + - - -
263D LEU 3.2 18.8 + - - +
264D ASN* 5.6 0.4 - - - +
265D VAL* 4.2 12.0 + - + +
284D ARG 3.5 23.8 + - - +
285D PRO* 3.6 14.1 - - - +
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Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG* 2.9 43.4 + - - +
227D ILE* 4.5 2.4 - - - +
256D HIS 2.6 30.4 + - - +
257D GLY* 3.4 9.4 + - - +
258D ALA 3.1 0.2 - - - -
259D GLN* 1.3 73.8 - - - +
261D ARG* 1.3 64.5 + - - +
262D GLY 3.1 1.3 + - - -
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Residues in contact with ARG 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D GLU* 3.3 49.1 + - + +
234D LEU* 3.8 22.2 - - + +
235D GLU* 4.4 16.0 + - - -
257D GLY* 3.1 17.5 - - - +
258D ALA 2.9 7.7 + - - +
260D ASP* 1.3 84.3 - - - +
262D GLY* 1.3 59.5 + - - +
263D LEU* 3.5 16.0 - - + +
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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