Contacts of the helix formed by residues 223 - 239 (chain A) in PDB entry 2XT6
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 ARG 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TYR* 3.8 6.1 - - - -
221A THR 5.4 2.1 + - - +
222A MET* 1.3 76.0 - - - +
224A PHE* 1.4 66.9 + - - +
225A GLY 3.3 0.9 - - - +
226A GLN* 2.9 42.9 + - + +
227A PHE* 3.0 19.6 + - - +
341A GLU* 4.2 4.9 - - - +
345A GLU* 3.7 30.7 - - - +
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Residues in contact with PHE 224 (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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155A ILE* 3.8 24.0 - - + -
159A HIS* 3.7 28.5 - - + -
160A LEU* 4.2 12.3 - - + -
163A TYR* 3.4 40.9 + + + -
223A ARG* 1.4 72.1 - - - +
225A GLY* 1.3 58.4 + - - +
227A PHE* 3.1 5.3 + + - +
228A ILE* 3.0 49.9 + - + +
341A GLU* 3.3 13.1 + - - +
342A ILE* 4.0 39.5 - - + -
345A GLU* 3.6 12.7 - - + +
346A LEU* 4.2 17.5 - - + -
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Residues in contact with GLY 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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224A PHE* 1.3 73.7 - - - +
226A GLN* 1.4 55.8 + - - +
228A ILE* 3.4 13.7 - - - +
229A ALA* 3.1 28.3 + - - +
345A GLU* 3.0 30.6 - - - +
346A LEU* 5.5 0.4 - - - -
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Residues in contact with GLN 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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221A THR 3.9 15.2 + - - +
222A MET* 4.0 16.9 - - + +
223A ARG* 2.9 61.4 + - + +
225A GLY* 1.4 71.2 - - - +
227A PHE* 1.4 60.6 + - - +
229A ALA* 3.3 7.6 + - - +
230A ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 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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159A HIS* 3.3 30.7 - - - -
162A GLY* 3.7 7.2 - - - -
163A TYR* 3.5 42.2 - + + -
166A VAL* 4.4 7.0 - - + -
196A LEU* 3.8 24.0 - - + -
216A ILE* 3.9 18.3 - - + +
219A CYS* 4.2 22.9 - - + -
222A MET* 3.8 15.4 - - + -
223A ARG 3.0 13.4 + - - +
224A PHE* 3.1 8.7 + + - +
226A GLN* 1.4 77.8 - - - +
228A ILE* 1.4 60.6 + - + +
230A ALA* 3.4 2.8 + - - +
231A TYR* 2.8 44.2 + + - +
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Residues in contact with ILE 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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155A ILE* 3.7 20.0 - - + -
159A HIS* 3.5 38.8 - - + +
224A PHE* 3.0 43.0 + - + +
225A GLY* 3.4 14.1 - - - +
227A PHE* 1.4 75.1 - - + +
229A ALA* 1.4 54.9 + - - +
231A TYR* 3.5 4.4 - - - +
232A GLU* 2.8 41.1 + - + +
346A LEU* 3.7 22.7 - - + -
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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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225A GLY 3.1 18.6 + - - +
226A GLN* 3.4 9.0 - - - +
227A PHE 3.3 0.2 - - - -
228A ILE* 1.4 77.2 - - - +
230A ALA* 1.3 54.6 + - - +
232A GLU* 3.5 4.8 + - - +
233A ASP* 2.9 29.4 + - - +
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Residues in contact with ALA 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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216A ILE* 3.6 25.8 - - + -
222A MET* 3.8 16.4 - - + -
226A GLN 2.9 17.6 + - - +
227A PHE 3.6 2.5 - - - +
229A ALA* 1.3 72.2 - - - +
231A TYR* 1.4 63.5 + - - +
233A ASP* 3.2 16.8 + - - +
234A ILE* 3.3 26.0 + - + +
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Residues in contact with TYR 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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156A SER* 4.2 2.9 + - - -
158A THR* 3.4 35.2 + - + +
159A HIS* 3.2 37.7 - + - -
162A GLY* 6.2 0.2 - - - -
196A LEU* 5.9 0.2 - - + -
198A LEU* 3.6 38.6 - - + +
216A ILE* 3.8 17.6 - - + +
227A PHE* 2.8 32.3 + + + +
228A ILE* 3.5 9.6 - - - +
230A ALA* 1.4 73.7 - - - +
232A GLU* 1.3 67.9 + - - +
234A ILE* 3.6 3.6 + - - +
235A VAL* 3.2 41.7 + - + +
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Residues in contact with GLU 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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154A LYS 6.0 0.4 - - - -
159A HIS* 2.9 32.8 + - + +
228A ILE* 2.8 25.0 + - + +
229A ALA* 4.1 4.5 - - - +
231A TYR* 1.3 81.3 - - - +
233A ASP* 1.4 55.8 + - - +
235A VAL* 3.7 19.0 - - - +
236A ARG* 2.8 37.3 + - + +
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Residues in contact with ASP 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 ALA 2.9 17.9 + - - +
230A ALA* 3.2 9.6 + - - +
232A GLU* 1.4 77.3 - - - +
234A ILE* 1.4 72.4 + - - +
236A ARG* 3.6 4.0 + - - +
237A ARG* 3.2 54.0 + - - +
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Residues in contact with ILE 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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198A LEU* 6.0 4.3 - - + -
200A ILE* 5.7 5.2 - - + -
214A ALA* 3.7 29.8 - - + -
215A ALA 3.8 23.6 - - - +
216A ILE* 4.6 14.6 - - + -
217A LYS 5.6 0.4 - - - +
230A ALA* 3.3 25.4 + - + +
231A TYR* 4.0 5.4 - - - +
233A ASP* 1.4 94.2 - - - +
235A VAL* 1.4 66.3 + - + +
237A ARG* 3.1 21.6 + - - +
238A ALA* 3.0 27.1 + - + +
243A LEU* 5.9 0.9 - - - +
247A ASP* 4.3 11.9 - - - +
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Residues in contact with VAL 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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198A LEU* 6.5 0.2 - - + -
200A ILE* 5.8 7.0 - - + -
231A TYR* 3.2 40.8 + - + +
232A GLU* 3.7 22.4 - - - +
234A ILE* 1.4 75.8 - - + +
236A ARG* 1.4 56.6 + - + +
237A ARG 2.9 10.8 + - - -
238A ALA* 3.2 15.3 + - - +
239A ARG* 3.3 16.9 + - + +
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Residues in contact with ARG 236 (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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232A GLU* 2.8 24.9 + - + +
233A ASP* 4.2 4.3 - - - +
234A ILE 3.5 0.4 - - - -
235A VAL* 1.4 70.9 - - + +
237A ARG* 1.3 62.1 + - - +
239A ARG* 5.0 2.7 - - - -
240A ASP* 3.0 31.2 - - - +
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Residues in contact with ARG 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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233A ASP* 3.2 45.9 + - - +
234A ILE* 3.4 16.4 - - - +
235A VAL 3.0 0.6 - - - -
236A ARG* 1.3 80.5 - - - +
238A ALA* 1.3 57.6 + - - +
239A ARG 3.4 1.1 - - - -
240A ASP* 4.2 4.5 - - + +
241A GLY* 2.8 13.0 + - - -
242A LYS* 2.7 62.9 + - + +
243A LEU* 3.8 7.3 + - + +
244A THR* 5.4 4.6 + - - +
247A ASP* 3.5 34.8 + - - -
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Residues in contact with ALA 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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200A ILE* 4.4 25.1 - - + -
234A ILE* 3.0 15.3 + - + +
235A VAL* 3.2 7.8 + - - +
237A ARG* 1.3 76.3 - - - +
239A ARG* 1.4 60.3 + - - +
241A GLY* 3.6 9.4 + - - -
243A LEU* 5.1 8.9 - - + +
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Residues in contact with ARG 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 VAL* 3.3 14.3 + - + +
236A ARG* 5.0 1.6 - - - -
238A ALA* 1.4 79.9 - - - +
240A ASP* 1.4 64.0 + - - +
241A GLY 3.3 1.2 + - - -
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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