Contacts of the helix formed by residues 224 - 236 (chain A) in PDB entry 2XTJ
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A THR* 3.9 0.7 - - - -
188A SER* 3.3 38.1 - - - +
189A ILE* 4.1 4.4 - - - +
190A GLN* 3.5 27.1 + - - +
222A LYS* 3.8 16.7 + - - +
223A CYS* 1.3 75.6 + - - +
225A SER* 1.3 59.3 + - - +
226A HIS 3.5 2.2 - - - -
228A THR* 2.6 31.9 + - - -
373A SER* 2.8 24.9 + - - -
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Residues in contact with SER 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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221A SER* 3.3 22.1 + - - -
222A LYS* 2.9 29.2 + - - -
223A CYS 3.6 0.6 - - - -
224A ASP* 1.3 78.1 + - - +
226A HIS* 1.3 68.8 + - - +
228A THR* 4.3 0.5 - - - -
229A HIS* 3.3 24.1 + - - +
371A ALA 5.0 0.5 - - - +
372A SER* 5.9 0.2 - - - -
373A SER* 3.4 18.6 + - - +
374A ASP* 5.8 2.5 - - - -
380A VAL* 5.7 2.2 - - - +
382A GLN* 5.4 7.0 + - - +
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Residues in contact with HIS 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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186A ASP* 2.8 36.6 + - - +
187A THR* 3.9 12.7 - - + +
222A LYS 4.9 0.2 + - - -
224A ASP 3.5 0.6 - - - -
225A SER* 1.3 83.7 + - - +
227A GLY* 1.3 59.9 + - - +
229A HIS* 3.7 4.1 + - - +
230A LEU* 3.3 36.9 + - + +
253A LEU* 4.7 0.2 - - + -
257A GLY* 6.0 0.4 - - - -
288A PRO 3.6 7.4 - - - -
382A GLN* 6.0 3.8 - - - -
386A SER* 3.3 11.5 + - - -
387A GLN* 5.3 4.2 + - - -
151P ALA* 3.5 29.7 - - + +
152P GLN* 2.9 25.5 + - - -
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Residues in contact with GLY 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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184A LEU* 3.7 6.4 - - - +
186A ASP* 3.2 22.4 + - - -
187A THR* 3.1 16.7 + - - -
189A ILE* 3.9 14.1 - - - -
224A ASP 4.1 0.2 + - - -
226A HIS* 1.3 74.3 - - - +
228A THR* 1.3 61.0 + - - +
229A HIS 3.2 1.6 - - - -
230A LEU* 3.2 1.2 + - - -
231A ALA* 2.8 32.4 + - - +
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Residues in contact with THR 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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189A ILE* 3.4 7.6 - - - +
190A GLN* 2.8 41.8 + - + +
193A HIS* 4.4 4.3 - - + -
196A ILE* 4.4 6.5 - - + +
224A ASP 2.6 25.2 + - - -
225A SER 4.3 1.6 - - - -
227A GLY* 1.3 75.1 - - - +
229A HIS* 1.3 63.3 + - - +
231A ALA* 3.5 4.7 + - - +
232A GLY 3.1 16.6 + - - -
371A ALA* 3.8 25.4 - - + +
372A SER 4.4 0.9 - - - -
373A SER* 3.7 21.3 - - - +
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Residues in contact with HIS 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 SER 3.3 16.5 + - - +
226A HIS* 3.8 5.8 - - - +
227A GLY 3.2 0.4 - - - -
228A THR* 1.3 80.2 - - - +
230A LEU* 1.3 56.8 + - - +
232A GLY* 3.1 3.6 + - - -
233A VAL* 3.0 43.5 + - + +
368A ILE 2.8 28.5 + - - -
370A GLY* 3.4 19.6 + - - -
371A ALA 3.2 12.7 + - - +
380A VAL* 3.1 32.6 + - + -
382A GLN* 3.4 19.8 - - + +
387A GLN* 2.8 36.0 + - + -
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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
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184A LEU* 4.5 11.4 - - + -
186A ASP* 3.2 26.0 - - - +
226A HIS* 3.3 24.3 + - + +
227A GLY 3.2 5.3 + - - +
229A HIS* 1.3 74.2 - - - +
231A ALA* 1.3 57.0 + - - +
232A GLY 3.0 1.3 - - - -
233A VAL* 2.3 31.4 - - + +
234A VAL* 3.3 11.1 - - - +
247A MET* 5.4 0.4 - - - -
286A LEU* 4.9 1.6 - - + -
288A PRO* 3.4 23.6 - - + -
386A SER* 3.6 26.0 - - - +
387A GLN* 3.3 28.3 - - + +
390A ALA* 3.8 15.0 - - + -
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Residues in contact with ALA 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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184A LEU* 4.2 10.4 - - + +
189A ILE* 4.7 9.4 - - + -
196A ILE* 4.0 24.2 - - + +
200A VAL* 4.9 3.1 - - + -
227A GLY 2.8 17.4 + - - +
228A THR* 3.8 5.8 - - - +
230A LEU* 1.3 75.7 - - - +
232A GLY* 1.3 54.2 + - - +
233A VAL 2.7 11.1 - - - +
235A SER* 3.0 26.9 + - - -
236A GLY 3.7 0.5 + - - -
247A MET* 3.8 22.0 - - + +
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Residues in contact with GLY 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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195A GLU* 5.2 1.6 - - - -
196A ILE* 4.2 6.7 - - - +
228A THR 3.1 13.4 + - - -
229A HIS 3.3 5.2 - - - -
230A LEU 3.0 1.2 - - - -
231A ALA* 1.3 71.3 - - - +
233A VAL* 1.3 62.1 + - - -
236A GLY* 2.6 37.5 + - - -
239A ALA 5.2 0.9 - - - -
240A GLY* 3.3 7.4 - - - -
370A GLY* 4.9 4.3 - - - -
371A ALA* 4.3 15.0 - - - -
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Residues in contact with VAL 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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157A ASN* 5.4 2.0 - - - +
229A HIS* 3.0 42.1 + - + +
230A LEU* 2.3 32.3 - - + +
231A ALA 2.7 2.1 - - - +
232A GLY* 1.3 74.0 - - - -
234A VAL* 1.3 65.0 + - - +
239A ALA 4.9 4.0 - - - +
240A GLY* 4.5 5.8 - - - -
241A VAL* 4.2 15.7 - - + -
368A ILE* 3.9 23.8 - - + -
369A ILE 4.7 4.7 - - - +
370A GLY* 4.6 3.6 - - - -
387A GLN* 4.3 12.8 - - + +
390A ALA* 3.9 18.4 - - + -
391A HIS* 4.3 4.7 - - + +
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Residues in contact with VAL 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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182A VAL* 4.3 20.6 - - + -
230A LEU 3.3 11.9 - - - +
231A ALA 3.9 1.3 - - - +
232A GLY 3.5 0.2 + - - -
233A VAL* 1.3 85.6 - - - +
235A SER* 1.3 59.3 + - - +
241A VAL* 3.7 16.6 - - - +
242A ALA* 2.5 40.4 + - + +
245A ALA* 5.5 0.2 - - + -
247A MET* 3.7 22.7 - - + -
286A LEU* 3.9 12.6 - - + -
390A ALA* 3.2 37.5 - - + +
393A ALA* 4.7 1.3 - - + -
394A GLY* 4.5 12.6 - - - +
397A ALA* 6.1 0.2 - - + -
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Residues in contact with SER 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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195A GLU 4.1 3.3 - - - +
196A ILE* 4.3 2.3 - - - +
199A ARG* 5.7 2.8 - - - +
200A VAL* 4.2 12.8 - - - +
231A ALA 3.0 14.1 + - - -
233A VAL 3.1 3.2 + - - -
234A VAL* 1.3 80.3 - - - +
236A GLY* 1.3 68.1 + - - +
237A ARG 3.5 0.9 + - - -
242A ALA 3.3 7.4 - - - -
243A LYS 3.2 14.0 - - - +
244A GLY 3.9 3.5 - - - +
245A ALA* 3.8 27.3 + - - -
247A MET* 3.3 24.5 - - - +
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Residues in contact with GLY 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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195A GLU* 3.4 26.7 - - - -
196A ILE* 4.5 1.1 - - - -
231A ALA 3.7 0.4 + - - -
232A GLY* 2.6 29.6 + - - -
235A SER* 1.3 73.6 + - - +
237A ARG* 1.3 66.0 + - - -
238A ASP 3.3 2.7 - - - -
240A GLY* 3.0 18.3 + - - -
243A LYS* 3.5 8.7 - - - +
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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