Contacts of the helix formed by residues 222 - 235 (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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A SER* 5.8 6.1 - - - +
220A ASP* 2.8 31.8 + - - +
221A TYR* 1.3 80.5 - - - +
223A TYR* 1.3 65.8 + - - +
224A ASP* 3.5 12.1 + - - +
225A SER* 2.8 33.3 + - - -
249A GLU* 4.3 4.0 - - - -
250A MET* 3.3 9.0 - - - +
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Residues in contact with TYR 223 (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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222A THR* 1.3 72.4 - - - +
224A ASP* 1.3 72.8 + - - +
226A GLY* 3.1 11.8 + - - -
227A ILE* 3.4 26.9 + - + +
249A GLU* 3.3 38.4 + - + +
252A LEU* 3.6 7.6 - - + -
253A GLY* 3.4 37.3 - - - -
256A HIS* 2.5 36.3 + - - +
278D ARG* 6.0 0.7 - - - -
281D THR* 3.3 23.7 + - - -
282D MET* 3.7 29.8 - - + -
284D ARG* 3.2 17.0 + - - -
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Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 3.1 10.1 + - - +
223A TYR* 1.3 93.1 - - - +
225A SER* 1.3 63.0 + - - +
227A ILE* 3.1 15.4 + - + +
228A GLU* 3.1 23.0 + - - +
281D THR* 5.5 2.3 + - - -
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Residues in contact with SER 225 (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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219A GLY* 3.8 9.0 - - - -
220A ASP* 3.2 39.9 + - - -
222A THR* 2.8 32.5 + - - -
224A ASP* 1.3 76.7 - - - +
226A GLY* 1.3 57.4 + - - +
228A GLU* 3.1 19.5 - - - +
229A ALA* 2.9 29.0 + - - +
250A MET* 3.3 12.0 - - - +
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Residues in contact with GLY 226 (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* 4.9 1.1 - - - -
222A THR 3.5 1.4 + - - -
223A TYR 3.1 8.3 + - - -
224A ASP 3.0 1.0 - - - -
225A SER* 1.3 80.9 + - - +
227A ILE* 1.3 66.2 + - - +
229A ALA* 3.1 8.8 + - - +
230A VAL* 3.0 23.9 + - - +
250A MET* 3.6 27.1 - - - -
253A GLY 3.8 6.3 - - - -
254A VAL* 3.8 4.8 - - - +
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Residues in contact with ILE 227 (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 38.0 + - + +
224A ASP* 3.1 16.9 + - - +
226A GLY* 1.3 74.8 - - - +
228A GLU* 1.3 66.7 + - - +
230A VAL* 2.9 17.8 + - - +
231A GLU* 3.1 27.7 + - - +
253A GLY* 3.4 23.3 + - - +
257A GLY* 4.2 17.5 - - - +
260A ASP* 5.8 1.6 - - - +
284D ARG* 5.2 9.4 - - - +
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Residues in contact with GLU 228 (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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218A GLU 5.3 2.5 - - - +
219A GLY* 5.4 0.3 - - - -
220A ASP* 4.5 6.2 - - - +
224A ASP 3.1 7.0 + - - +
225A SER* 3.1 35.5 - - - +
227A ILE* 1.3 81.5 - - - +
229A ALA* 1.3 61.1 + - + +
231A GLU* 3.3 10.2 + - - +
232A LYS* 3.0 56.9 + - - +
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Residues in contact with ALA 229 (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* 3.6 20.6 - - + -
217A VAL* 3.4 27.4 - - + +
218A GLU 5.9 1.6 - - - +
219A GLY* 5.9 0.4 - - - -
225A SER 2.9 15.7 + - - +
226A GLY 3.2 10.3 - - - +
227A ILE 3.0 0.2 - - - -
228A GLU* 1.3 81.4 - - + +
230A VAL* 1.3 61.3 + - - +
232A LYS* 3.4 8.5 + - - +
233A LEU* 3.0 29.5 + - - +
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Residues in contact with VAL 230 (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* 5.2 0.4 - - - +
226A GLY 3.0 18.5 + - - +
227A ILE* 3.1 9.0 - - - +
229A ALA* 1.3 71.8 - - - +
231A GLU* 1.3 59.5 + - - +
233A LEU* 3.4 6.1 + - - +
234A LEU* 2.8 42.6 + - + +
243A ILE* 3.7 15.9 - - + -
253A GLY 3.7 4.5 - - - +
254A VAL* 3.2 51.1 - - + +
257A GLY* 4.3 6.7 - - - -
258A ALA* 4.1 18.8 - - + +
269A LEU* 4.2 2.7 - - + -
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Residues in contact with GLU 231 (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* 3.1 29.0 + - + +
228A GLU* 3.6 10.1 - - - +
230A VAL* 1.3 75.8 - - + +
232A LYS* 1.3 68.8 + - + +
234A LEU* 3.0 4.0 + - - +
235A GLU* 3.0 36.3 + - - +
257A GLY* 5.6 3.8 - - - -
261A ARG* 3.8 35.9 + - + +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.7 19.3 - - + +
218A GLU 4.0 18.2 + - - +
228A GLU* 3.0 50.0 + - + +
229A ALA* 3.7 9.9 - - - +
231A GLU* 1.3 74.2 - - + +
233A LEU* 1.3 64.1 + - - +
235A GLU* 3.0 31.4 + - - +
236A GLU* 3.4 13.5 - - - +
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Residues in contact with LEU 233 (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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181A ALA* 3.6 33.4 - - + -
182A PHE 5.2 0.4 - - - +
183A VAL* 3.7 26.7 - - + -
214A SER 3.6 23.6 - - - +
215A TYR* 4.2 6.5 - - + -
217A VAL* 3.9 14.4 - - + -
229A ALA 3.0 19.4 + - - +
230A VAL* 3.7 4.9 - - - +
232A LYS* 1.3 81.4 - - - +
234A LEU* 1.3 58.3 + - + +
235A GLU 3.1 0.2 - - - -
236A GLU* 2.9 29.8 + - - +
239A LYS* 4.4 1.2 - - - -
240A PRO* 3.8 24.1 - - + +
243A ILE* 4.0 16.4 - - + -
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Residues in contact with LEU 234 (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* 2.8 41.7 + - + +
231A GLU 3.0 4.4 + - - +
233A LEU* 1.3 72.0 - - + +
235A GLU* 1.3 56.6 + - - +
236A GLU 3.1 6.0 + - - -
239A LYS* 3.0 51.2 - - + -
240A PRO* 4.5 8.5 - - + +
258A ALA* 4.5 4.7 - - - -
261A ARG* 4.0 44.8 + - + +
263A LEU* 3.9 33.0 - - + -
269A LEU* 5.4 3.4 - - + -
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Residues in contact with GLU 235 (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* 3.0 39.9 + - - +
232A LYS* 3.0 19.3 + - - +
234A LEU* 1.3 76.8 - - - +
236A GLU* 1.3 62.5 + - - +
237A ASP 4.0 0.5 + - - -
261A ARG* 4.1 11.6 + - - +
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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