Contacts of the helix formed by residues 222 - 235 (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 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D ASP* 2.6 40.4 + - - +
221D TYR* 1.3 81.7 - - - +
223D TYR* 1.3 65.0 + - - +
224D ASP* 2.9 11.9 + - - +
225D SER* 3.0 25.1 + - - -
226D GLY 3.5 2.8 + - - -
249D GLU* 3.9 5.6 - - - -
250D MET* 4.0 4.7 - - - +
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Residues in contact with TYR 223 (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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281A THR* 3.0 26.5 - - - -
282A MET* 3.4 29.2 - - + -
284A ARG* 2.6 31.0 + - - -
286A GLN* 5.2 1.1 - - - -
222D THR* 1.3 71.7 - - - +
224D ASP* 1.3 75.2 + - - +
226D GLY 3.4 3.8 + - - -
227D ILE* 3.6 11.4 + - + +
249D GLU* 3.2 40.9 + - + +
250D MET* 4.6 0.2 - - - +
252D LEU* 3.6 7.2 - - + -
253D GLY* 3.3 54.9 - - - -
256D HIS* 2.7 26.5 - + - +
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Residues in contact with ASP 224 (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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281A THR* 5.8 0.2 + - - -
222D THR* 2.9 11.5 + - - +
223D TYR* 1.3 89.3 - - - +
225D SER* 1.3 55.7 + - - +
226D GLY 3.0 5.2 - - - -
227D ILE* 2.9 28.1 + - - +
228D GLU* 3.0 26.4 + - + +
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Residues in contact with SER 225 (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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219D GLY* 3.6 8.8 - - - -
220D ASP* 3.0 45.3 + - - -
222D THR* 3.0 12.7 + - - -
224D ASP* 1.3 76.7 - - - +
226D GLY* 1.3 57.1 + - - +
228D GLU* 3.6 11.9 - - - +
229D ALA* 2.8 30.1 + - - +
250D MET* 3.1 12.5 - - - +
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Residues in contact with GLY 226 (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* 4.5 2.2 - - - -
222D THR 3.5 2.4 + - - -
223D TYR 3.4 6.1 + - - -
224D ASP 3.0 1.0 - - - -
225D SER* 1.3 79.2 + - - +
227D ILE* 1.3 54.9 + - - +
229D ALA* 3.9 4.6 - - - +
230D VAL* 2.8 36.2 + - - +
250D MET* 3.7 26.9 - - - -
253D GLY 3.7 7.2 - - - -
254D VAL* 3.4 10.4 - - - +
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Residues in contact with ILE 227 (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* 4.2 5.8 - - - +
223D TYR* 3.6 28.6 + - + +
224D ASP* 2.9 16.4 + - - +
226D GLY* 1.3 74.6 - - - +
228D GLU* 1.3 74.0 + - - +
230D VAL* 3.0 16.2 + - - +
231D GLU* 3.2 24.5 + - + +
253D GLY* 2.9 28.7 - - - +
256D HIS* 3.8 11.4 - - + -
257D GLY* 3.3 24.2 - - - +
260D ASP* 4.5 1.3 - - - +
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Residues in contact with GLU 228 (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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224D ASP* 3.0 28.8 - - + +
225D SER* 3.6 13.2 - - - +
227D ILE* 1.3 82.0 - - - +
229D ALA* 1.3 65.8 + - - +
230D VAL 3.1 0.5 + - - -
231D GLU* 3.1 23.4 + - - +
232D LYS* 2.9 22.3 + - - +
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Residues in contact with ALA 229 (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* 3.7 30.5 - - + -
217D VAL* 3.6 30.6 - - + +
219D GLY* 5.7 0.9 - - - -
225D SER 2.8 21.9 + - - +
226D GLY 3.9 2.5 - - - +
227D ILE 3.3 0.4 - - - -
228D GLU* 1.3 72.7 - - - +
230D VAL* 1.3 57.6 + - - +
232D LYS* 3.5 4.8 + - - +
233D LEU* 2.9 33.9 + - - +
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Residues in contact with VAL 230 (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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226D GLY 2.8 28.3 - - - +
227D ILE* 3.0 8.7 + - - +
229D ALA* 1.3 71.3 - - - +
231D GLU* 1.3 58.0 + - - +
233D LEU* 2.8 11.1 + - + +
234D LEU* 2.7 57.4 + - + +
243D ILE* 4.6 10.3 - - + -
253D GLY 4.1 0.4 - - - +
254D VAL* 3.2 39.7 - - + +
257D GLY* 4.4 2.0 - - - -
258D ALA* 3.9 23.8 - - + +
269D LEU* 4.6 2.7 - - + -
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Residues in contact with GLU 231 (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* 3.2 17.5 + - + +
228D GLU* 3.1 30.5 + - - +
230D VAL* 1.3 77.9 - - + +
232D LYS* 1.3 64.0 + - - +
234D LEU* 3.0 6.5 + - - +
235D GLU* 3.0 32.1 + - + +
257D GLY* 5.8 2.2 - - - +
261D ARG* 3.3 44.8 + - + +
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Residues in contact with LYS 232 (chain D).
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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214D SER 5.7 0.9 - - - +
217D VAL* 3.9 32.3 - - + -
228D GLU 2.9 12.4 + - - +
229D ALA* 3.6 9.2 - - - +
231D GLU* 1.3 77.5 - - - +
233D LEU* 1.3 58.6 + - - +
235D GLU* 2.9 29.9 + - + +
236D GLU* 3.4 14.3 + - - +
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Residues in contact with LEU 233 (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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181D ALA* 3.5 30.7 - - + -
183D VAL* 3.9 20.4 - - + -
214D SER 3.9 20.6 - - - +
215D TYR* 4.1 8.1 - - + +
217D VAL* 4.1 11.0 - - + -
229D ALA 2.9 18.9 + - - +
230D VAL* 2.8 11.6 + - + +
232D LYS* 1.3 73.9 - - - +
234D LEU* 1.3 59.7 + - + +
236D GLU* 3.0 28.1 - - - +
239D LYS* 4.6 0.7 - - - +
240D PRO* 3.7 26.6 - - + +
243D ILE* 3.7 28.9 - - + -
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Residues in contact with LEU 234 (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* 2.7 38.6 + - + +
231D GLU* 3.0 8.0 + - - +
233D LEU* 1.3 70.9 - - + +
235D GLU* 1.3 61.1 + - + +
236D GLU 3.1 5.6 - - - -
239D LYS* 3.1 51.5 + - + +
240D PRO* 5.7 3.1 - - + +
258D ALA* 4.8 1.8 - - - -
261D ARG* 3.8 42.6 - - + +
263D LEU* 4.0 30.3 - - + -
269D LEU* 5.0 5.8 - - + -
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Residues in contact with GLU 235 (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* 3.0 28.0 + - + +
232D LYS* 2.9 13.7 + - - +
234D LEU* 1.3 79.0 - - - +
236D GLU* 1.3 64.7 + - - +
237D ASP* 3.7 2.6 + - - -
261D ARG* 4.4 18.4 + - - -
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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