Contacts of the helix formed by residues 247 - 261 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ASN* 6.0 3.1 - - - +
196I LYS* 5.2 0.9 + - - -
221I TYR* 3.8 21.6 - - + +
245I VAL* 3.1 4.9 + - - +
246I GLY* 1.3 83.2 + - - +
248I ASP* 1.3 53.3 + - - +
249I GLU* 3.2 25.4 - - + +
250I MET* 3.1 31.5 + - + +
251I ALA* 2.7 34.7 + - - +
274I PHE 3.7 9.9 - - - -
275I ASP* 4.1 10.5 + - - +
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Residues in contact with ASP 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I THR* 1.3 71.5 - - - +
249I GLU* 1.3 64.0 + - - +
251I ALA* 3.1 6.7 + - - +
252I LEU* 2.9 30.9 + - - +
274I PHE 2.9 21.3 + - - +
275I ASP* 4.6 1.8 + - - +
277I THR* 2.7 50.6 + - + +
279I LEU* 4.4 7.4 - - + -
280I SER* 2.7 17.6 + - - -
287I LEU* 3.4 7.1 - - + +
289I SER* 2.8 25.0 + - - -
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Residues in contact with GLU 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.1 38.5 + - - -
282B MET* 3.9 12.8 - - + -
72I ASN* 3.8 10.8 + - - +
73I ILE* 3.4 30.8 + - - +
221I TYR 3.9 16.7 - - - +
222I THR* 4.7 1.6 - - - -
223I TYR* 3.4 31.2 + - - +
247I THR* 3.2 11.2 - - + +
248I ASP* 1.3 79.3 - - - +
250I MET* 1.3 62.5 + - - +
252I LEU* 3.7 2.8 + - - +
253I GLY 3.5 7.8 + - - -
279I LEU* 3.8 18.3 - - + +
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Residues in contact with MET 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I VAL* 4.3 12.3 - - + +
184I SER 3.7 14.6 - - - +
185I GLY* 3.6 19.5 - - - +
219I GLY* 3.9 5.6 - - - -
221I TYR* 3.5 57.9 - - + -
222I THR 3.6 16.6 - - - +
225I SER* 3.7 9.2 - - - +
226I GLY* 3.8 6.1 - - - -
245I VAL* 3.5 14.1 - - + -
246I GLY 4.7 0.7 - - - -
247I THR* 3.1 21.8 + - + +
249I GLU* 1.3 74.1 - - - +
251I ALA* 1.3 60.3 + - - +
253I GLY* 2.8 18.9 + - - -
254I VAL* 2.8 15.8 + - - +
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Residues in contact with ALA 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I VAL* 3.2 27.7 - - + +
247I THR 2.7 20.0 + - - +
248I ASP* 3.1 6.0 + - - +
250I MET* 1.3 73.7 - - - +
252I LEU* 1.3 56.5 + - - +
254I VAL* 3.0 4.0 + - - +
255I ILE* 2.9 32.1 + - - +
271I ILE* 4.5 0.8 - - + +
273I GLY* 4.0 4.0 - - - -
287I LEU* 3.7 32.1 - - + -
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Residues in contact with LEU 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 6.2 0.4 - - + -
282B MET* 4.4 26.9 - - + +
223I TYR* 3.6 10.3 - - + -
248I ASP 2.9 32.2 + - - +
249I GLU 4.0 5.8 - - - +
250I MET 3.2 0.2 - - - -
251I ALA* 1.3 77.6 - - - +
253I GLY* 1.3 58.0 + - - +
255I ILE* 3.1 6.8 + - + +
256I HIS* 2.8 36.7 + - - +
279I LEU* 4.0 32.1 - - + +
282I MET* 4.3 7.4 - - + +
283I VAL* 3.1 42.0 - - + -
287I LEU* 4.4 12.1 - - + -
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Residues in contact with GLY 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I TYR* 3.3 39.9 - - - -
226I GLY 3.5 6.3 - - - -
227I ILE* 3.2 17.7 - - - +
249I GLU 3.5 1.4 + - - -
250I MET 2.8 8.6 + - - -
252I LEU* 1.3 78.5 - - - +
254I VAL* 1.3 57.3 + - - +
257I GLY* 3.1 21.2 + - - -
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Residues in contact with VAL 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I VAL* 3.9 16.8 - - + -
226I GLY* 3.8 8.7 - - - +
230I VAL* 3.1 25.9 - - + +
243I ILE* 4.1 13.5 - - + -
245I VAL* 3.7 20.4 - - + -
250I MET 2.8 14.9 + - - +
251I ALA 3.0 8.7 + - - +
253I GLY* 1.3 79.7 - - - +
255I ILE* 1.3 58.7 + - - +
258I ALA* 3.0 28.2 + - - +
271I ILE* 3.4 32.5 - - + -
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Residues in contact with ILE 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ALA 2.9 17.7 + - - +
252I LEU* 3.1 6.3 + - - +
254I VAL* 1.3 77.4 - - - +
256I HIS* 1.3 65.4 + - + +
258I ALA* 3.6 4.0 + - - +
259I GLN* 3.0 49.0 + - - +
265I VAL* 4.5 9.1 - - + +
271I ILE* 4.0 19.7 - - + -
283I VAL* 4.9 10.1 - - + -
284I ARG 4.2 4.5 - - - +
285I PRO* 4.1 27.6 - - + +
287I LEU* 3.8 27.6 - - + -
330I SER* 4.1 17.0 - - - -
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Residues in contact with HIS 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 6.0 1.2 + - - -
282B MET 3.1 25.4 + - - -
283B VAL* 3.5 10.4 - - - -
284B ARG* 3.1 51.7 + - + +
223I TYR* 3.0 24.0 + + + +
227I ILE* 4.9 0.2 - - + -
252I LEU* 2.8 26.7 + - + +
253I GLY 4.5 0.4 - - - +
255I ILE* 1.3 76.9 - - + +
257I GLY* 1.3 56.7 + - - +
259I GLN* 3.2 10.8 + - - +
260I ASP* 2.7 40.9 + - - -
283I VAL* 3.5 28.4 - - + +
284I ARG 5.8 1.8 - - - -
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Residues in contact with GLY 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I ILE* 3.8 27.2 - - - +
230I VAL* 4.6 4.9 - - - -
231I GLU* 3.3 17.3 - - - +
253I GLY 3.1 19.7 + - - -
254I VAL 4.3 0.2 - - - -
256I HIS* 1.3 76.7 - - - +
258I ALA* 1.3 61.2 + - - +
260I ASP* 3.4 10.1 + - - +
261I ARG* 3.4 11.6 - - - +
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Residues in contact with ALA 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230I VAL* 3.8 19.8 - - + +
234I LEU* 4.0 4.9 - - - +
254I VAL 3.0 22.0 + - - +
255I ILE* 3.8 4.7 - - - +
257I GLY* 1.3 77.0 - - - +
259I GLN* 1.3 61.7 + - - +
261I ARG* 3.3 12.5 + - - +
263I LEU* 3.1 28.2 - - + +
265I VAL* 4.7 6.3 - - + -
269I LEU* 3.8 21.3 - - + -
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Residues in contact with GLN 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ARG* 4.0 27.4 - - + +
255I ILE* 3.0 44.6 + - - +
256I HIS* 3.4 17.2 + - - +
258I ALA* 1.3 72.5 - - - +
260I ASP* 1.3 61.1 + - - +
261I ARG 3.0 2.2 - - - -
262I GLY* 2.9 19.0 + - - -
263I LEU 3.1 18.6 - - - +
264I ASN* 5.4 2.5 - - - -
265I VAL* 5.0 7.8 - - + +
284I ARG 3.8 15.5 + - - +
285I PRO* 4.3 5.7 - - - +
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Residues in contact with ASP 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ARG* 3.1 43.1 + - - +
227I ILE* 4.8 5.7 - - - +
231I GLU* 4.9 4.7 - - - +
256I HIS 2.7 25.5 + - - +
257I GLY* 3.5 11.9 - - - +
258I ALA 3.2 0.2 - - - -
259I GLN* 1.3 73.9 - - - +
261I ARG* 1.3 60.0 + - - +
262I GLY 3.1 3.7 + - - -
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Residues in contact with ARG 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231I GLU* 3.5 36.2 + - - +
234I LEU* 3.1 53.1 + - + +
235I GLU* 4.4 14.4 + - - +
239I LYS* 4.0 10.1 - - - +
257I GLY 3.4 16.6 - - - +
258I ALA 3.3 8.9 + - - +
259I GLN 3.0 0.4 - - - -
260I ASP* 1.3 80.1 - - - +
262I GLY* 1.3 54.0 + - - -
263I LEU* 3.2 8.6 + - + +
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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