Contacts of the helix formed by residues 247 - 262 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN* 4.3 12.8 + - - +
196A LYS* 4.6 5.2 - - - +
221A TYR* 3.9 34.2 + - + -
245A VAL* 3.3 3.2 + - - +
246A GLY* 1.3 83.9 - - - +
248A ASP* 1.3 65.9 + - - +
249A GLU* 3.9 5.8 + - - +
250A MET* 3.4 24.8 + - + +
251A ALA* 3.1 20.1 + - - +
274A PHE 3.2 12.6 - - - +
275A ASP* 3.6 19.5 - - - +
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Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 5.5 0.2 - - + -
247A THR* 1.3 73.0 - - - +
249A GLU* 1.3 59.4 + - - +
251A ALA* 2.9 10.0 + - - +
252A LEU* 2.7 32.0 + - - +
274A PHE 2.9 23.1 + - - +
275A ASP* 4.8 0.4 - - - +
276A ASN 3.0 2.4 + - - -
277A THR* 2.5 49.3 + - + +
279A LEU* 4.4 9.2 - - + -
280A SER* 2.7 13.7 + - - -
287A LEU* 3.4 14.9 - - + +
289A SER* 2.9 19.7 + - - -
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER 4.5 4.2 - - - +
72A ASN* 5.4 1.2 - - - -
73A ILE* 4.0 17.0 + - + +
221A TYR 4.2 13.7 - - - +
222A THR* 4.1 2.4 - - - -
223A TYR* 3.3 40.2 + - + +
247A THR* 3.4 4.9 + - - +
248A ASP* 1.3 77.8 - - - +
250A MET* 1.3 62.6 + - - +
252A LEU* 3.3 6.7 + - + +
253A GLY 3.2 14.7 + - - -
279A LEU* 3.8 21.8 - - + +
278D ARG* 2.6 41.3 + - - -
282D MET* 4.1 8.0 - - - +
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Residues in contact with MET 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 4.3 7.6 - - + +
184A SER 3.6 34.3 - - - +
185A GLY 4.1 0.9 - - - +
219A GLY* 4.1 4.3 - - - -
221A TYR* 3.4 38.8 - - + -
222A THR 3.3 11.4 - - - +
225A SER* 3.3 22.7 - - - +
226A GLY* 3.6 11.3 - - - +
245A VAL* 3.6 15.0 - - + -
246A GLY* 4.3 1.6 - - - +
247A THR* 3.4 33.5 + - - +
248A ASP 3.3 0.6 - - - -
249A GLU* 1.3 77.5 - - - +
251A ALA* 1.3 57.4 + - - +
253A GLY* 2.7 22.2 + - - -
254A VAL* 2.8 15.0 + - - +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 3.4 27.1 - - + +
247A THR 3.1 14.2 + - - +
248A ASP* 2.9 14.6 + - - +
250A MET* 1.3 77.0 - - - +
252A LEU* 1.3 60.6 + - - +
254A VAL* 2.8 14.2 + - - +
255A ILE* 2.9 17.8 + - - +
271A ILE* 4.8 1.5 - - + +
273A GLY* 4.0 4.5 - - - -
287A LEU* 3.7 27.6 - - + -
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TYR* 3.6 10.5 - - + -
248A ASP 2.7 23.0 + - - +
249A GLU* 3.6 9.2 - - - +
250A MET 3.2 0.2 - - - -
251A ALA* 1.3 71.7 - - - +
253A GLY* 1.3 61.0 + - - +
255A ILE* 3.5 8.5 + - + +
256A HIS* 3.1 29.9 + - - +
279A LEU* 3.7 51.8 - - + +
282A MET* 4.5 2.7 - - + +
283A VAL* 3.1 41.3 - - + -
287A LEU* 3.8 16.6 - - + -
279D LEU* 6.1 0.2 - - + -
282D MET* 5.0 14.8 - - + +
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TYR* 3.4 33.1 - - - -
227A ILE* 3.4 23.9 - - - +
249A GLU 3.2 6.5 + - - -
250A MET 2.7 15.9 + - - -
252A LEU* 1.3 70.9 - - - +
254A VAL* 1.3 62.6 + - - -
256A HIS* 4.0 0.4 - - - -
257A GLY 3.0 18.4 + - - -
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 4.5 11.4 - - + -
226A GLY* 3.8 14.8 - - - +
230A VAL* 3.2 27.7 - - + +
243A ILE* 3.9 14.4 - - + -
245A VAL* 3.5 24.9 - - + -
250A MET 2.8 18.9 + - - +
251A ALA* 2.8 9.0 + - - +
253A GLY* 1.3 73.9 - - - +
255A ILE* 1.3 65.8 + - - +
258A ALA* 3.0 23.7 + - - +
271A ILE* 3.6 25.4 - - + -
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ALA 2.9 19.7 + - - +
252A LEU* 3.6 13.7 - - + +
254A VAL* 1.3 77.5 - - - +
256A HIS* 1.3 56.5 + - + +
258A ALA* 3.2 2.8 + - - +
259A GLN* 2.7 67.5 + - + +
265A VAL* 3.8 20.2 - - + -
271A ILE* 3.4 34.5 - - + -
283A VAL* 5.5 7.2 - - + -
284A ARG 4.1 9.4 - - - +
285A PRO* 4.1 11.4 - - + +
287A LEU* 4.7 7.2 - - + -
330A SER* 4.4 10.5 - - - -
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TYR* 2.5 38.3 + + + +
227A ILE* 5.1 1.3 - - + -
252A LEU* 3.1 12.5 + - + +
253A GLY 4.0 2.2 - - - +
255A ILE* 1.3 81.9 - - + +
257A GLY* 1.3 61.4 + - - +
259A GLN* 3.0 24.9 + - - +
260A ASP* 2.8 36.0 + - - +
283A VAL* 4.4 17.9 - - + +
284A ARG 5.0 4.0 + - - -
256D HIS* 6.1 2.2 - - - -
282D MET 3.1 33.4 - - - -
283D VAL* 3.7 5.3 - - - -
284D ARG* 3.5 31.8 + - + +
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 4.2 21.2 - - - +
230A VAL* 4.3 8.5 - - - -
231A GLU* 5.6 3.6 - - - -
253A GLY 3.0 16.8 + - - -
254A VAL 4.0 0.7 - - - -
256A HIS* 1.3 74.4 - - - +
258A ALA* 1.3 62.7 + - - +
260A ASP* 3.2 9.2 + - - +
261A ARG* 3.1 30.4 + - - +
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 4.1 9.0 - - + +
234A LEU* 4.5 8.7 - - + -
254A VAL 3.0 17.3 + - - +
255A ILE* 3.5 4.9 - - - +
257A GLY* 1.3 77.6 - - - +
259A GLN* 1.3 59.1 + - - +
261A ARG* 3.4 2.4 + - - +
262A GLY 3.4 4.9 + - - -
263A LEU* 3.0 35.9 + - + +
265A VAL* 4.7 5.6 - - + -
269A LEU* 3.4 32.3 - - + -
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ILE* 2.7 30.1 + - + +
256A HIS* 3.0 30.8 + - - +
258A ALA* 1.3 76.1 - - - +
260A ASP* 1.3 64.3 + - - +
262A GLY* 3.6 9.6 + - - -
263A LEU 3.5 14.9 - - - +
264A ASN* 5.6 0.2 - - - -
265A VAL* 4.6 11.5 + - + +
284A ARG 3.1 22.7 + - - +
285A PRO* 3.5 15.2 - - - +
284D ARG* 4.3 8.8 - - + +
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Residues in contact with ASP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 5.8 2.3 - - - +
256A HIS 2.8 22.6 + - - +
257A GLY* 3.2 8.1 + - - +
259A GLN* 1.3 71.9 - - - +
261A ARG* 1.3 66.2 + - + +
262A GLY 3.2 2.0 + - - -
284D ARG* 2.6 45.4 + - - +
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLU* 3.8 54.0 + - + +
234A LEU* 4.0 35.1 + - + +
235A GLU* 4.1 12.7 + - - +
257A GLY 3.1 18.9 + - - +
258A ALA 3.8 5.6 - - - +
260A ASP* 1.3 78.8 - - - +
262A GLY* 1.3 57.8 + - - +
263A LEU* 4.7 4.0 - - + +
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ALA 3.4 1.2 + - - -
259A GLN 3.6 7.3 + - - -
260A ASP 3.2 4.0 - - - -
261A ARG* 1.3 81.3 - - - +
263A LEU* 1.3 66.9 + - - +
264A ASN* 4.0 1.2 + - - +
268A ASP* 4.7 2.8 - - - +
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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