Contacts of the helix formed by residues 229 - 242 (chain A) in PDB entry 2AX1
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ARG* 3.8 23.3 - - + +
58A GLN* 2.7 35.0 + - + +
227A THR 3.6 13.2 - - - +
228A VAL* 1.3 75.4 - - - +
230A GLU* 1.3 71.4 + - - +
231A ASN* 3.4 4.2 + - - -
232A ASP* 2.8 36.4 + - - +
233A ILE* 3.1 17.6 + - - +
278A ARG 4.5 0.7 - - - -
347A SER* 3.6 13.2 - - - +
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Residues in contact with GLU 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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1A SER* 2.6 34.6 + - - -
56A ARG* 3.6 5.4 + - - -
229A THR* 1.3 78.9 - - - +
231A ASN* 1.3 58.3 + - - +
233A ILE* 3.3 11.7 + - - +
234A ARG* 2.9 38.3 + - - +
262A ILE* 3.9 27.0 - - + +
278A ARG* 3.5 28.7 + - + +
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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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58A GLN* 3.9 7.5 + - - +
60A LEU* 3.6 28.3 - - - +
64A TYR* 4.9 1.6 + - - -
229A THR* 3.1 9.0 + - - +
230A GLU* 1.3 77.2 + - - +
232A ASP* 1.3 59.4 + - - +
234A ARG* 3.2 16.9 + - - +
235A VAL* 2.8 47.8 + - - +
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Residues in contact with ASP 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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58A GLN* 2.9 21.7 + - - +
64A TYR* 4.1 10.0 + - - -
227A THR 3.7 0.5 - - - +
228A VAL* 3.4 14.5 - - + -
229A THR* 2.8 42.4 + - - +
231A ASN* 1.3 75.9 + - - +
233A ILE* 1.3 57.7 + - - +
235A VAL* 3.3 9.8 + - - +
236A GLU* 2.9 31.6 + - - +
294A THR* 4.1 11.8 + - + +
298A LYS* 2.7 34.5 + - - -
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Residues in contact with ILE 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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228A VAL* 3.7 20.4 - - + -
229A THR 3.1 18.0 + - - +
230A GLU 3.6 6.1 - - - +
232A ASP* 1.3 75.4 - - - +
234A ARG* 1.3 58.5 + - - +
236A GLU* 3.3 12.1 - - - +
237A GLU* 3.2 22.7 + - - +
257A THR* 4.0 4.4 + - + +
261A TYR* 3.1 57.2 - - + +
262A ILE* 3.8 17.7 - - + -
279A CYS* 4.0 18.8 - - - -
280A ARG* 3.8 18.8 - - - +
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Residues in contact with ARG 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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230A GLU* 2.9 26.9 + - - +
231A ASN* 3.2 15.8 + - - +
233A ILE* 1.3 75.1 - - - +
235A VAL* 1.3 65.6 + - + +
236A GLU 3.2 0.4 - - - -
237A GLU* 3.3 13.7 + - - +
238A SER* 3.0 21.5 + - - -
257A THR* 4.5 2.2 - - + -
258A GLU* 2.9 35.8 + - - +
262A ILE* 4.0 16.2 - - + -
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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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64A TYR* 3.7 24.2 - - + +
68A LEU* 3.7 40.6 - - + -
231A ASN* 2.8 34.1 + - - +
232A ASP* 3.5 6.3 - - - +
234A ARG* 1.3 73.6 - - - +
236A GLU* 1.3 66.7 + - - +
238A SER* 2.6 25.1 + - - +
239A ILE* 3.1 12.5 + - + +
297A LEU* 4.1 8.7 - - + -
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Residues in contact with GLU 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 ASP 2.9 15.8 + - - +
233A ILE* 3.3 17.5 - - - +
235A VAL* 1.3 79.2 - - - +
237A GLU* 1.3 62.4 + - - +
239A ILE* 3.0 22.2 + - + +
240A TYR* 3.1 36.3 + - + +
261A TYR* 6.0 1.4 - - - -
280A ARG* 2.5 43.7 + - - -
286A THR* 4.5 4.2 + - - +
290A GLY* 3.2 26.9 - - - +
293A LEU* 4.7 9.4 - - + -
294A THR* 3.1 13.7 + - - +
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Residues in contact with GLU 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 ILE 3.2 8.9 + - - +
234A ARG* 3.5 12.5 + - - +
235A VAL 3.2 0.4 - - - -
236A GLU* 1.3 81.4 - - - +
238A SER* 1.3 57.7 + - - +
240A TYR* 3.0 11.1 + - - +
241A GLN* 2.8 56.8 + - + +
253A ILE* 3.9 14.1 - - + -
254A LYS* 3.3 23.8 - - - +
257A THR* 3.3 39.6 - - + +
258A GLU* 4.2 8.3 - - - +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.3 29.4 + - - -
234A ARG 3.0 12.5 + - - -
235A VAL* 2.6 25.3 + - - +
237A GLU* 1.3 76.3 - - - +
239A ILE* 1.3 59.9 + - - +
241A GLN* 3.6 9.9 + - - +
242A CYS* 3.3 27.7 + - - -
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Residues in contact with ILE 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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68A LEU* 4.0 23.3 - - + -
71A MET* 4.0 30.7 - - + +
72A LYS* 4.4 6.3 - - + -
75A ALA* 3.6 22.3 - - + +
182A LEU* 4.1 13.8 - - + +
186A VAL* 4.6 9.2 - - + -
235A VAL* 3.3 17.3 - - + +
236A GLU* 3.0 16.9 + - + +
238A SER* 1.3 77.3 + - - +
240A TYR* 1.3 65.4 + - + +
242A CYS* 3.2 22.5 + - - +
243A CYS 4.1 0.5 + - - -
293A LEU* 4.4 20.2 - - + -
297A LEU* 5.3 2.0 - - + -
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Residues in contact with TYR 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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175A LEU* 4.1 11.0 - - + -
178A VAL* 3.6 27.3 - - + +
179A VAL* 5.1 0.9 - - + -
182A LEU* 3.6 12.3 - - + -
236A GLU* 3.1 44.7 + - + +
237A GLU* 3.0 14.2 + - + +
239A ILE* 1.3 77.5 - - - +
241A GLN* 1.3 56.1 + - - +
243A CYS* 3.1 28.6 + - - +
245A LEU* 3.3 9.3 - - - +
253A ILE* 4.3 21.5 - - + -
257A THR* 5.4 2.0 - - - -
261A TYR* 5.6 4.3 - + - -
286A THR* 3.9 26.4 - - + -
289A CYS* 3.8 22.0 - - - -
290A GLY* 3.6 18.5 + - - -
293A LEU* 4.0 12.7 - - + +
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Residues in contact with GLN 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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237A GLU* 2.8 45.8 + - - +
238A SER* 3.9 9.4 - - - +
239A ILE 3.3 0.4 - - - -
240A TYR* 1.3 71.1 - - - +
242A CYS* 1.3 61.0 + - - +
243A CYS 3.0 6.7 - - - +
245A LEU* 3.8 5.0 - - - +
250A ARG* 2.8 83.8 + - - +
253A ILE* 3.7 14.4 - - - +
254A LYS* 4.4 1.8 - - - +
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Residues in contact with CYS 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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72A LYS* 3.6 42.6 - - - +
75A ALA* 3.8 14.6 - - + -
76A SER* 3.3 26.4 + - - +
238A SER 3.3 22.8 + - - -
239A ILE 3.2 12.2 + - - +
240A TYR 3.1 1.6 - - - -
241A GLN* 1.3 76.5 - - - +
243A CYS* 1.3 61.5 + - - +
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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