Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 2XXA
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 ASP 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.4 7.3 - - - +
196A HIS* 4.5 2.4 - - - -
225A THR* 6.0 0.9 - - - -
226A GLY 3.1 1.0 + - - +
227A GLN* 1.4 72.4 - - - +
229A ALA* 1.4 55.0 + - - +
230A ALA 3.0 5.2 - - - -
231A ASN* 2.9 30.6 + - - +
232A THR* 3.2 23.1 + - - -
42B ILE 5.1 1.0 + - - -
44B ASP* 3.8 3.4 + - - +
227B SER* 3.9 32.3 - - - +
256B THR* 2.7 31.8 + - - +
257B ALA* 3.2 26.3 + - - +
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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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44A ALA* 5.9 0.4 - - + -
221A VAL* 5.6 0.4 - - + -
225A THR* 4.6 9.2 - - - +
226A GLY 3.1 17.0 + - - +
227A GLN 4.8 0.2 - - - -
228A ASP* 1.4 76.3 - - - +
230A ALA* 1.4 52.1 + - - +
232A THR* 3.7 10.9 - - - -
233A ALA* 2.8 37.1 + - - +
258A ALA* 4.1 17.0 - - + -
261A SER* 4.4 12.3 - - - -
262A ILE* 3.9 19.6 - - + +
265A ILE* 5.2 0.7 - - - -
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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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44A ALA* 3.8 19.8 - - + +
46A PRO* 4.9 9.0 - - + -
227A GLN 3.3 15.0 + - - +
228A ASP 2.9 0.6 + - - -
229A ALA* 1.4 77.0 - - - +
231A ASN* 1.4 63.8 + - - +
234A LYS* 3.3 42.0 + - - +
265A ILE* 3.8 19.2 - - + +
42B ILE* 5.8 5.2 - - + -
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Residues in contact with ASN 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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196A HIS* 4.2 8.1 - - + +
227A GLN 4.5 3.2 + - - -
228A ASP* 2.9 27.9 + - - +
230A ALA* 1.4 77.2 - - - +
232A THR* 1.3 61.3 + - - +
234A LYS* 3.7 11.4 + - - +
235A ALA* 3.4 25.3 + - - +
42B ILE* 5.9 4.4 - - - +
256B THR* 3.7 35.5 + - + +
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Residues in contact with THR 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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108A LEU* 3.7 27.4 - - + +
196A HIS* 4.1 11.6 - - - +
219A PHE* 3.5 27.6 - - + -
221A VAL* 5.1 8.1 - - + -
228A ASP* 3.2 27.6 + - - -
229A ALA* 3.7 11.8 - - - -
231A ASN* 1.3 74.6 - - - +
233A ALA* 1.4 59.7 + - - +
235A ALA* 4.2 0.2 - - - +
236A PHE* 3.1 41.2 + - + +
262A ILE* 5.4 0.7 - - + -
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Residues in contact with ALA 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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219A PHE* 4.9 5.2 - - - -
229A ALA 2.8 21.5 + - - +
230A ALA 4.2 0.9 - - - +
232A THR* 1.4 69.7 - - - +
234A LYS* 1.4 67.1 + - - +
236A PHE* 4.6 1.1 - - - +
237A ASN* 3.3 24.6 + - - +
261A SER 4.6 0.2 - - - +
262A ILE* 4.0 20.2 - - + +
265A ILE* 3.8 26.2 - - + +
266A THR* 3.6 19.7 - - + +
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Residues in contact with LYS 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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46A PRO* 4.9 14.1 - - - +
230A ALA* 3.3 29.9 + - - +
231A ASN* 3.9 11.5 + - - +
232A THR 3.3 0.4 - - - -
233A ALA* 1.4 78.8 - - - +
235A ALA* 1.3 57.4 + - - +
237A ASN* 3.8 1.7 - - - +
238A GLU* 2.9 49.3 + - - +
265A ILE* 3.8 27.1 - - + -
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Residues in contact with ALA 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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196A HIS* 3.8 32.3 - - + +
202A MET* 4.4 2.6 - - + +
231A ASN 3.4 15.0 + - - +
232A THR 4.2 0.2 - - - +
234A LYS* 1.3 77.9 - - - +
236A PHE* 1.4 58.4 + - - +
238A GLU* 3.9 6.2 - - - +
239A ALA* 3.1 33.6 + - - +
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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
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106A ALA* 4.2 11.2 - - + -
107A GLY* 3.8 31.4 - - - -
108A LEU* 4.5 9.0 - - + -
194A ARG* 3.8 29.8 - - + -
196A HIS* 3.9 23.8 - - + -
202A MET* 3.7 26.2 - - + -
219A PHE* 3.5 34.8 - + + -
232A THR* 3.1 27.9 + - + +
233A ALA 4.6 1.1 - - - +
235A ALA* 1.4 75.2 - - - +
237A ASN* 1.3 56.5 + - - +
240A LEU* 3.3 33.8 + - + +
242A LEU* 3.5 17.3 - - + +
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Residues in contact with ASN 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 ALA 3.3 16.7 + - - +
234A LYS 3.3 3.7 + - - +
236A PHE* 1.3 74.9 - - - +
238A GLU* 1.4 64.9 + - + +
239A ALA 3.3 1.6 - - - -
240A LEU 3.0 24.3 - - - +
241A PRO* 4.7 2.1 - - - +
242A LEU* 3.8 14.9 + - + +
265A ILE* 4.6 3.0 + - + -
266A THR* 3.2 36.2 + - + +
268A LYS* 3.4 24.4 + - - +
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Residues in contact with GLU 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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234A LYS* 2.9 42.6 + - - +
235A ALA* 4.1 5.7 + - - +
237A ASN* 1.4 79.0 - - + +
239A ALA* 1.3 56.6 + - - +
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Residues in contact with ALA 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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202A MET* 4.2 20.9 - - + -
206A LYS* 3.7 45.9 - - + +
235A ALA 3.1 17.9 + - - +
238A GLU* 1.3 79.2 - - - +
240A LEU* 1.3 59.0 + - + +
241A PRO* 4.5 3.0 - - - +
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Residues in contact with LEU 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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104A LEU* 4.7 2.2 - - + -
106A ALA* 4.7 5.4 - - + -
202A MET* 4.0 17.3 - - + -
205A ILE* 3.8 47.1 - - + +
206A LYS* 4.2 7.0 - - + -
209A HIS* 3.7 38.1 - - + -
217A THR* 4.7 2.2 - - + -
236A PHE* 3.3 31.0 + - + +
237A ASN 3.0 17.1 - - - +
239A ALA* 1.3 82.4 - - + +
241A PRO* 1.4 63.5 - - + +
242A LEU* 2.9 19.6 + - + +
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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