Contacts of the helix formed by residues 226 - 242 (chain A) in PDB entry 2AVD
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 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A TRP* 4.4 2.4 + - - -
218A LYS* 3.2 37.3 + - - +
223A PRO* 3.0 34.7 + - + +
224A LYS 3.1 1.2 - - - +
225A GLY* 1.3 73.8 - - - +
227A VAL* 1.3 64.0 + - - +
228A ALA* 3.6 6.8 + - - +
229A ALA* 3.2 24.2 + - + -
230A GLU* 3.1 29.0 + - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 4.7 16.8 - - + +
225A GLY* 3.1 15.0 + - - +
226A ASP* 1.3 69.5 + - - +
228A ALA* 1.3 61.2 + - - +
230A GLU* 3.4 15.8 + - - +
231A CYS* 2.9 40.5 + - - -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS* 4.0 15.2 - - + +
189A GLU* 4.2 16.6 + - - +
215A TRP* 3.9 26.9 - - + +
226A ASP* 3.4 5.2 + - - +
227A VAL* 1.3 77.7 - - - +
229A ALA* 1.3 57.7 + - - +
231A CYS* 3.0 7.1 + - - +
232A VAL* 2.9 33.9 + - - +
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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
----------------------------------------------------------
215A TRP* 3.6 24.7 - - + +
218A LYS* 3.9 13.7 - - + +
219A VAL* 4.7 2.9 - - - +
222A PRO* 3.8 18.9 - - + +
226A ASP* 3.2 32.5 + - + +
228A ALA* 1.3 79.5 - - - +
230A GLU* 1.3 54.9 + - - +
232A VAL* 3.4 3.4 + - - +
233A ARG* 3.0 29.1 + - - +
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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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222A PRO* 3.9 14.6 - - + +
223A PRO 4.3 8.3 - - - +
224A LYS* 5.1 1.4 - - - -
225A GLY* 4.5 7.9 + - - -
226A ASP 3.1 20.3 + - - +
227A VAL* 3.6 21.5 + - + +
229A ALA* 1.3 71.7 - - - +
231A CYS* 1.3 61.0 + - - +
233A ARG* 3.4 29.2 + - - +
234A ASN* 2.9 40.6 + - - +
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Residues in contact with CYS 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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188A LYS 3.3 28.7 - - - +
189A GLU* 3.8 20.4 - - - -
191A CYS* 3.8 7.4 - - - -
192A SER* 4.7 2.3 + - - -
227A VAL* 2.9 30.1 + - - +
228A ALA 3.0 8.7 + - - +
230A GLU* 1.3 77.5 - - - +
232A VAL* 1.3 61.9 + - - +
234A ASN* 3.8 8.5 - - - +
235A LEU* 3.1 24.3 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS* 3.6 38.6 - - + +
191A CYS* 4.7 4.9 - - - -
212A ARG 4.0 1.6 - - - +
213A VAL* 3.1 41.7 - - + +
215A TRP* 4.0 17.5 - - + -
219A VAL* 3.5 12.8 - - + -
228A ALA 2.9 17.9 + - - +
229A ALA 3.7 5.6 - - - +
231A CYS* 1.3 73.5 - - - +
233A ARG* 1.3 64.1 + - - +
235A LEU* 3.3 4.7 + - - +
236A ASN* 3.1 23.8 + - - +
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Residues in contact with ARG 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 VAL* 3.9 21.2 - - - +
222A PRO* 3.2 39.6 - - + +
229A ALA 3.0 17.2 + - - +
230A GLU* 3.5 28.5 + - - +
232A VAL* 1.3 76.7 - - - +
234A ASN* 1.3 88.7 + - - +
236A ASN* 3.3 4.7 + - - +
237A GLU* 3.2 32.3 + - + +
57B TYR* 4.3 14.1 - - + +
61B ARG* 6.2 0.4 - - - +
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 5.0 4.9 - - - +
230A GLU* 2.9 26.2 + - - +
231A CYS* 3.8 7.8 - - - +
233A ARG* 1.3 104.6 + - - +
235A LEU* 1.3 63.2 + - - +
237A GLU* 3.2 9.5 + - - +
238A ARG* 3.1 19.8 + - - +
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Residues in contact with LEU 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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184A VAL* 5.8 0.4 - - + -
191A CYS* 3.7 38.6 - - + +
192A SER* 3.8 20.3 + - - +
195A TYR* 3.8 35.7 - - + -
210A VAL* 4.3 19.1 - - + -
213A VAL* 6.2 0.2 - - + -
231A CYS 3.1 16.8 + - - +
232A VAL* 3.9 4.0 - - - +
234A ASN* 1.3 76.5 - - - +
236A ASN* 1.3 60.2 + - - +
238A ARG* 3.1 12.6 + - + -
239A ILE* 2.9 47.8 + - + +
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Residues in contact with ASN 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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213A VAL* 2.8 50.2 + - - +
219A VAL* 4.0 2.8 - - - +
232A VAL* 3.1 18.6 + - - +
233A ARG 3.3 5.1 + - - +
235A LEU* 1.3 76.6 - - - +
237A GLU* 1.3 58.2 + - - +
239A ILE* 3.5 8.8 + - - +
240A ARG* 2.9 31.6 + - - +
249A LEU* 5.1 5.5 - - - +
257A THR* 4.6 3.6 + - - -
57B TYR* 2.9 35.5 + - - +
61B ARG* 4.4 11.1 - - + +
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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 ARG* 3.2 21.6 + - + +
234A ASN* 3.2 9.6 + - - +
236A ASN* 1.3 75.5 - - - +
238A ARG* 1.3 62.2 + - - +
240A ARG* 3.0 18.6 + - - +
241A ARG* 2.8 65.1 + - - +
57B TYR* 4.2 5.5 + - - -
61B ARG* 2.6 42.7 + - - +
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 4.7 17.8 + - - -
195A TYR* 4.4 15.0 - - + -
196A GLU* 2.8 53.2 + - - +
234A ASN 3.1 10.4 + - - +
235A LEU* 3.1 16.4 + - - +
237A GLU* 1.3 73.8 - - - +
239A ILE* 1.3 67.2 + - - +
241A ARG* 3.2 8.2 + - - +
242A ASP* 3.1 21.9 + - + +
244A ARG* 4.7 5.2 - - - +
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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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195A TYR* 3.5 40.8 - - + +
210A VAL* 4.1 17.0 - - + -
213A VAL* 5.9 0.4 - - + -
235A LEU* 2.9 45.1 + - + +
236A ASN* 4.0 9.6 - - - +
238A ARG* 1.3 71.9 - - - +
240A ARG* 1.3 64.5 + - - +
242A ASP* 3.0 19.4 + - - +
247A ILE* 3.8 29.5 - - + +
257A THR* 4.1 21.8 - - + -
259A ALA* 4.9 1.1 - - + -
61B ARG 5.6 0.4 - - - +
64B ARG* 3.0 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 ASN 2.9 18.6 + - - +
237A GLU* 3.0 31.2 + - - +
238A ARG 3.3 0.2 - - - -
239A ILE* 1.3 75.8 - - - +
241A ARG* 1.3 76.8 + - + +
247A ILE* 4.0 4.9 - - - +
60B SER* 3.1 34.4 + - - +
61B ARG* 3.5 49.4 + - - +
62B SER 6.1 0.4 - - - -
63B MET 6.2 0.4 - - - +
64B ARG* 3.1 24.8 + - - +
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Residues in contact with ARG 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 58.2 + - - +
238A ARG* 3.2 7.0 + - - +
239A ILE 3.1 0.6 - - - -
240A ARG* 1.3 92.6 - - + +
242A ASP* 1.3 63.3 + - - +
243A VAL* 3.2 14.2 + - - +
64B ARG* 4.2 0.9 - - - -
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Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A TYR* 2.7 26.6 + - - +
199A LEU* 3.8 2.9 - - - +
238A ARG* 3.1 16.9 + - + +
239A ILE* 3.0 13.6 + - - +
240A ARG 3.4 0.4 - - - -
241A ARG* 1.3 74.2 - - - +
243A VAL* 1.3 63.8 + - - +
244A ARG* 2.9 56.7 + - - +
245A VAL* 3.3 16.9 - - + +
64B ARG* 2.8 21.7 + - - -
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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
------------------------------------------------------------
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