Contacts of the helix formed by residues 222 - 234 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278F ARG* 6.6 0.4 - - - -
220P ASP* 2.8 34.6 + - - +
221P TYR* 1.3 81.6 - - - +
223P TYR* 1.3 69.9 + - + +
224P ASP* 3.5 24.9 - - + +
225P SER* 2.6 24.4 + - - -
226P GLY 3.2 3.1 + - - -
249P GLU* 4.2 4.0 - - - +
250P MET* 3.5 4.2 - - - +
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Residues in contact with TYR 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278F ARG* 6.3 0.9 - - - -
281F THR* 3.2 24.7 + - - -
282F MET* 3.4 37.0 - - + -
284F ARG* 3.0 23.3 + - - -
286F GLN* 5.2 1.8 - - - -
222P THR* 1.3 73.1 - - + +
224P ASP* 1.3 68.9 + - - +
226P GLY* 2.7 24.0 + - - +
227P ILE* 3.2 28.6 + - + -
249P GLU* 3.4 34.7 + - + +
252P LEU* 3.6 15.0 - - + -
253P GLY* 3.6 18.2 - - - -
256P HIS* 2.6 33.5 + - - -
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Residues in contact with ASP 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F THR* 5.3 2.9 + - - -
222P THR* 3.1 16.2 - - + +
223P TYR* 1.3 94.2 - - - +
225P SER* 1.3 57.6 + - - +
227P ILE* 3.2 12.6 + - - +
228P GLU* 3.0 30.4 + - + +
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Residues in contact with SER 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P GLU 5.3 1.2 - - - +
219P GLY* 3.7 12.1 - - - -
220P ASP* 2.9 42.0 + - - -
222P THR* 2.6 21.3 + - - -
224P ASP* 1.3 76.7 - - - +
226P GLY* 1.3 59.0 + - - +
228P GLU* 3.6 15.8 - - - +
229P ALA* 2.8 31.1 + - - +
250P MET* 3.7 5.8 - - - -
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Residues in contact with GLY 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P VAL* 5.1 1.3 - - - -
222P THR 3.2 2.6 + - - -
223P TYR 2.7 11.0 + - - -
225P SER* 1.3 83.6 + - - +
227P ILE* 1.3 60.8 + - - +
229P ALA* 3.2 11.3 + - - +
230P VAL* 2.9 19.9 + - - +
250P MET* 3.5 26.2 - - - -
253P GLY 3.5 7.1 - - - +
254P VAL* 3.6 6.9 - - - +
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Residues in contact with ILE 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F ARG* 3.9 19.1 - - - +
286F GLN* 5.9 1.3 - - - +
223P TYR* 3.2 34.9 + - + +
224P ASP* 3.2 14.3 + - - +
226P GLY* 1.3 74.4 - - - +
228P GLU* 1.3 65.3 + - + +
229P ALA 3.1 1.4 + - - -
230P VAL* 3.1 7.6 - - - +
231P GLU* 3.1 19.4 + - - +
253P GLY* 3.4 22.7 - - - +
257P GLY* 4.4 11.2 - - - +
260P ASP* 4.7 4.0 - - - +
261P ARG* 4.1 19.4 + - - +
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Residues in contact with GLU 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217P VAL* 5.2 0.4 - - - +
224P ASP* 3.0 15.8 + - + +
225P SER* 3.8 19.7 + - - +
227P ILE* 1.3 78.3 - - + +
229P ALA* 1.3 61.2 + - - +
231P GLU* 3.3 23.9 - - - +
232P LYS* 3.2 24.4 + - - +
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Residues in contact with ALA 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P VAL* 3.4 36.6 - - + -
217P VAL* 3.9 20.7 - - + +
218P GLU 5.7 2.2 - - - +
225P SER 2.8 17.3 + - - +
226P GLY 3.5 6.1 - - - +
227P ILE 3.1 0.4 - - - -
228P GLU* 1.3 75.6 - - - +
230P VAL* 1.3 60.6 + - - +
232P LYS* 3.4 4.0 + - - +
233P LEU* 3.0 33.2 + - - +
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Residues in contact with VAL 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226P GLY 2.9 20.2 - - - +
227P ILE 3.1 10.3 - - - +
229P ALA* 1.3 72.1 - - - +
231P GLU* 1.3 58.0 + - - +
233P LEU* 4.2 5.2 - - - -
234P LEU* 2.7 47.7 + - + +
243P ILE* 3.7 26.9 - - + -
253P GLY 3.7 4.3 - - - +
254P VAL* 3.5 36.1 - - + +
257P GLY* 3.8 9.4 - - - -
258P ALA* 4.2 10.1 - - + +
261P ARG* 5.8 0.2 - - - -
269P LEU* 4.3 10.5 - - + -
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Residues in contact with GLU 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P ILE* 3.1 12.4 + - - +
228P GLU* 3.3 30.8 - - - +
230P VAL* 1.3 79.1 - - - +
232P LYS* 1.3 66.1 + - - +
234P LEU* 3.3 7.1 + - - +
235P GLU* 3.2 27.5 + - - +
261P ARG* 2.9 44.3 + - - +
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Residues in contact with LYS 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217P VAL* 4.5 18.6 - - + -
228P GLU 3.2 12.2 + - - +
229P ALA 3.5 7.6 - - - +
231P GLU* 1.3 79.8 - - - +
233P LEU* 1.3 59.1 + - + +
235P GLU* 2.8 44.3 + - - +
236P GLU* 3.5 36.3 + - - +
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Residues in contact with LEU 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181P ALA* 3.4 29.6 - - + -
183P VAL* 4.1 10.8 - - + -
214P SER 4.0 17.7 - - - +
215P TYR* 4.2 6.7 - - + +
217P VAL* 3.7 25.8 - - + -
229P ALA 3.0 20.7 + - - +
230P VAL* 3.7 3.8 - - - +
232P LYS* 1.3 78.0 - - - +
234P LEU* 1.3 60.3 + - + +
235P GLU 3.0 4.7 + - - -
236P GLU* 3.2 23.1 + - - +
239P LYS* 4.4 0.9 - - - +
240P PRO* 3.8 20.9 - - + +
243P ILE* 3.3 33.0 - - + -
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Residues in contact with LEU 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230P VAL* 2.7 32.1 + - + +
231P GLU* 3.8 4.7 - - - +
232P LYS 3.1 0.2 + - - -
233P LEU* 1.3 75.2 - - + +
235P GLU* 1.3 59.2 + - + +
236P GLU 3.6 0.2 - - - -
239P LYS* 3.2 36.5 - - + -
240P PRO* 5.4 6.3 - - + +
243P ILE* 5.9 0.4 - - + -
258P ALA* 4.4 10.3 - - - -
261P ARG* 4.3 32.3 - - + +
263P LEU* 3.5 34.8 - - + -
269P LEU* 4.6 13.7 - - + -
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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