Contacts of the helix formed by residues 224 - 243 (chain A) in PDB entry 6TOS
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 TYR 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.0 35.3 + + + +
222A VAL 3.6 0.8 - - - -
223A THR* 1.3 85.6 + - - +
225A LEU* 1.3 76.6 + - + +
226A ALA 3.7 1.1 - - - -
227A PRO* 3.6 2.6 - - - +
228A LEU* 3.2 56.8 + - + +
307A PHE* 5.3 1.1 - + - -
308A ALA* 2.7 36.4 + - - +
311A TYR* 3.7 26.7 - + + -
312A LEU* 3.5 28.3 - - + +
315A SER* 3.6 24.0 - - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 3.0 43.5 + - + +
221A ILE* 4.1 11.9 - - + -
224A TYR* 1.3 83.3 - - + +
226A ALA* 1.3 62.1 + - - +
228A LEU* 4.4 0.6 - - - +
229A GLY* 2.9 28.9 + - - -
214B ILE* 3.7 28.5 - - + -
218B CYS* 3.8 13.5 - - - -
405B PGW 4.5 11.9 - - + +
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 2.9 29.2 + - + +
225A LEU* 1.3 72.6 - - - +
227A PRO* 1.4 62.6 - - + +
230A LEU* 3.1 31.8 + - + +
218B CYS* 4.4 4.2 - - + -
222B VAL* 3.8 26.2 - - + -
405B PGW 3.9 28.1 - - + +
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Residues in contact with PRO 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.7 27.8 - - + -
135A LEU* 6.2 1.1 - - + -
138A SER* 3.6 21.8 - - - +
221A ILE 3.5 4.0 - - - +
222A VAL 3.2 27.8 - - - +
223A THR 4.2 0.9 - - - -
224A TYR 3.6 10.5 - - - +
226A ALA* 1.4 90.6 - - + +
228A LEU* 1.4 55.0 + - - +
230A LEU* 3.5 1.7 + - - +
231A MET* 2.9 36.4 + - + +
405B PGW 4.4 24.5 - - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.8 3.6 - - + -
137A LEU* 5.2 0.9 - - + -
224A TYR* 3.2 63.4 + - + +
225A LEU* 4.4 1.8 - - - +
227A PRO* 1.4 72.8 - - - +
229A GLY* 1.3 59.3 + - - +
231A MET* 3.7 22.0 - - + +
232A ALA* 3.0 30.1 + - - +
304A VAL* 3.9 28.0 - - + +
307A PHE* 4.0 25.4 - - + -
308A ALA* 3.9 15.5 - - + -
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 2.9 18.2 + - - -
226A ALA 4.0 0.9 - - - -
228A LEU* 1.3 74.8 - - - +
230A LEU* 1.4 62.5 + - - +
232A ALA* 3.4 5.1 + - - +
233A MET* 3.2 34.5 + - - +
405B PGW 4.1 20.4 - - - -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 3.1 27.1 + - + +
227A PRO 3.8 2.0 - - - +
229A GLY* 1.4 72.5 - - - +
231A MET* 1.4 58.5 + - - +
233A MET* 3.4 21.6 + - + +
234A ALA* 2.9 27.9 + - - +
175B ILE* 3.9 50.7 - - + +
178B PRO* 4.1 9.0 - - + -
222B VAL* 6.3 0.2 - - + -
405B PGW 3.7 69.6 - - + +
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Residues in contact with MET 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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134A VAL* 4.0 6.1 - - + -
137A LEU* 3.6 38.6 - - + +
138A SER* 3.8 22.0 - - - +
141A ALA* 3.7 20.2 - - + -
227A PRO* 2.9 42.0 + - + +
228A LEU* 3.7 21.3 - - + +
229A GLY 3.5 0.2 - - - -
230A LEU* 1.4 71.0 - - - +
232A ALA* 1.4 56.2 + - - +
234A ALA* 3.2 7.0 + - - +
235A TYR* 2.8 40.3 + - + -
304A VAL* 4.1 26.2 - - + -
405B PGW 4.6 3.1 - - + -
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Residues in contact with ALA 232 (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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228A LEU 3.0 20.0 + - - +
229A GLY* 3.7 6.7 - - - +
230A LEU 3.3 0.2 - - - -
231A MET* 1.4 75.4 - - - +
233A MET* 1.3 59.3 + - + +
235A TYR* 3.4 5.0 + - - +
236A PHE* 2.9 29.8 + - - +
304A VAL* 5.3 4.8 - - + +
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Residues in contact with MET 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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229A GLY* 3.2 27.6 + - - +
230A LEU* 3.7 13.2 - - + +
232A ALA* 1.3 75.6 - - + +
234A ALA* 1.4 60.5 + - - +
236A PHE* 3.6 8.3 + - - +
237A GLN* 3.3 27.7 + - - +
178B PRO* 3.8 25.8 - - + -
405B PGW 3.5 89.8 - - + +
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Residues in contact with ALA 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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141A ALA* 4.7 8.1 - - + +
145A TRP* 3.9 21.1 - - + -
230A LEU 2.9 11.9 + - - +
231A MET* 3.2 6.9 + - - +
233A MET* 1.4 76.0 - - - +
235A TYR* 1.4 58.1 + - - +
237A GLN* 3.2 5.2 + - - +
238A ILE* 3.0 32.8 + - + +
405B PGW 3.4 39.0 - - + +
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Residues in contact with TYR 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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137A LEU 4.8 0.9 + - - -
140A ILE* 3.6 21.8 - - - +
141A ALA* 3.7 26.6 + - + -
144A ARG* 4.5 4.6 - - + +
231A MET* 2.8 31.5 + - + +
232A ALA* 4.0 4.7 - - - +
234A ALA* 1.4 70.0 - - + +
236A PHE* 1.3 59.6 + - - +
237A GLN 3.2 0.2 - - - -
238A ILE* 4.0 20.6 - - + -
239A PHE* 2.9 29.1 + - - +
297A ALA* 4.7 5.4 - - - -
300A LEU* 3.6 35.2 + - + +
301A MET* 3.4 41.3 - - + +
304A VAL* 3.8 29.7 - - + +
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Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA 2.9 18.3 + - - +
233A MET* 3.8 11.0 - - - +
234A ALA 3.3 0.2 - - - -
235A TYR* 1.3 75.7 - - - +
237A GLN* 1.3 67.3 + - + +
239A PHE* 3.5 14.8 + + - +
240A ARG* 3.2 65.8 + - + +
417A SOG 4.1 19.7 - - + -
405B PGW 5.7 3.8 - - + -
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Residues in contact with GLN 237 (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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145A TRP* 2.8 22.4 + - - +
149A CYS* 3.9 13.2 - - - -
233A MET 3.3 12.2 + - - +
234A ALA 3.2 9.0 + - - +
236A PHE* 1.3 75.9 - - + +
238A ILE* 1.3 58.5 + - - +
240A ARG* 3.3 4.3 + - - +
241A LYS* 3.0 27.2 + - - +
414A SOG 2.7 54.4 + - - -
417A SOG 3.5 35.5 - - + +
405B PGW 3.5 24.9 + - + +
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Residues in contact with ILE 238 (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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141A ALA 4.2 2.9 - - - +
144A ARG* 3.7 21.8 - - + +
145A TRP* 3.6 28.7 - - + +
148A ILE* 3.7 25.6 - - + -
149A CYS* 3.9 18.6 - - - -
234A ALA* 3.0 24.0 + - + +
235A TYR* 3.8 20.6 - - + +
237A GLN* 1.3 71.7 - - - +
239A PHE* 1.4 56.2 + - - +
241A LYS* 3.3 1.0 + - - +
242A LEU* 2.9 46.9 + - + +
297A ALA* 4.0 14.6 - - + -
301A MET* 4.3 3.6 - - + -
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Residues in contact with PHE 239 (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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235A TYR 2.9 19.1 + - - +
236A PHE* 3.5 19.5 - + - +
238A ILE* 1.4 76.3 - - - +
240A ARG* 1.4 69.5 + - + +
243A TRP* 2.9 78.5 + + + +
301A MET* 4.1 12.1 - - + -
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Residues in contact with ARG 240 (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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236A PHE* 3.2 45.8 + - + +
237A GLN 3.3 9.1 + - - +
239A PHE* 1.4 84.7 - - + +
241A LYS* 1.3 62.9 + - - +
244A GLY* 3.3 23.7 - - - +
417A SOG 3.5 40.2 - - + +
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Residues in contact with LYS 241 (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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148A ILE* 3.2 48.0 + - + +
149A CYS* 3.5 25.6 + - + -
151A PRO* 4.8 4.6 - - - +
237A GLN 3.0 15.9 + - - +
238A ILE 3.3 0.6 + - - +
240A ARG* 1.3 79.9 - - - +
242A LEU* 1.4 62.4 + - + +
244A GLY* 3.9 4.3 + - - -
290A MET* 5.0 4.5 - - - +
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Residues in contact with LEU 242 (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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148A ILE* 4.0 22.9 - - + -
238A ILE* 2.9 28.8 + - + +
241A LYS* 1.4 74.6 - - + +
243A TRP* 1.4 67.4 + - + +
244A GLY 3.4 1.2 + - - -
290A MET* 3.5 31.1 - - + +
293A ARG* 3.5 49.6 - - + +
294A ARG* 2.8 34.6 + - + +
297A ALA* 3.7 19.1 - - + -
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Residues in contact with TRP 243 (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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239A PHE* 2.9 72.8 + + + +
240A ARG* 5.3 0.2 - - - -
242A LEU* 1.4 88.1 - - + +
244A GLY* 1.3 61.7 + - - +
294A ARG* 3.4 72.4 + - + +
297A ALA* 4.1 7.0 - - + -
298A LYS* 4.2 19.5 - - + +
301A MET* 4.1 16.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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