Contacts of the helix formed by residues 212 - 228 (chain A) in PDB entry 2WXH
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 MET 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A LYS 3.8 11.7 - - - +
211A ASP* 1.3 78.0 - - - +
213A PRO* 1.4 72.5 - - + +
214A LEU* 3.2 11.9 - - + +
215A ALA* 3.2 20.6 + - + +
216A LEU* 3.5 9.7 + - - +
252A GLY 5.2 0.7 - - - +
253A ASN* 3.9 15.9 - - - +
254A TYR* 3.6 21.3 - - - -
255A PRO* 3.4 38.1 - - + -
256A LEU* 4.2 2.1 - - - +
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Residues in contact with PRO 213 (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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212A MET* 1.4 85.9 - - + +
214A LEU* 1.3 56.7 + - - +
216A LEU* 3.2 4.8 + - + +
217A MET* 2.9 40.1 + - + +
241A LEU* 4.1 16.3 - - + +
250A LEU* 4.4 11.2 - - + +
251A TYR* 4.4 8.3 - - - +
252A GLY 3.5 20.9 - - - +
254A TYR 3.0 17.5 - - - +
256A LEU* 4.0 16.2 - - + -
259A PHE* 3.8 24.0 - - + -
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Residues in contact with LEU 214 (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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212A MET* 3.2 9.5 - - + -
213A PRO* 1.3 79.9 - - - +
215A ALA* 1.3 56.7 + - - +
217A MET* 3.3 17.0 + - + +
218A ALA* 2.8 28.8 + - - +
236A PRO* 3.7 28.6 - - + +
237A GLU* 3.8 38.1 - - + +
252A GLY 5.5 0.2 + - - -
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Residues in contact with ALA 215 (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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207A VAL* 5.8 1.1 - - + -
211A ASP* 4.5 19.3 - - + +
212A MET* 3.2 19.0 + - + +
214A LEU* 1.3 75.5 - - - +
216A LEU* 1.3 65.5 + - - +
218A ALA* 3.2 9.2 - - - +
219A CYS* 3.1 29.8 + - - -
222A ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 216 (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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192A VAL* 4.1 13.9 - - + -
194A VAL* 3.3 33.7 - - + -
205A PHE* 4.9 4.9 - - + -
207A VAL* 4.5 16.6 - - + +
211A ASP* 5.5 0.8 - - + +
212A MET 3.5 7.2 + - - +
213A PRO 3.2 9.8 + - - +
215A ALA* 1.3 80.6 - - - +
217A MET* 1.3 56.4 + - - +
219A CYS* 3.4 9.7 + - - +
220A ALA* 3.1 23.0 + - - +
241A LEU* 4.2 15.0 - - + -
256A LEU* 3.7 33.4 - - + -
262A ILE* 6.3 0.2 - - + -
274A LEU* 4.0 21.1 - - + -
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Residues in contact with MET 217 (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 PRO* 2.9 22.0 + - + +
214A LEU* 3.6 32.1 - - + +
216A LEU* 1.3 72.6 - - - +
218A ALA* 1.3 60.7 + - - +
220A ALA* 3.5 2.0 + - - +
221A LEU* 3.0 35.9 + - - +
236A PRO* 3.6 17.5 - - + +
237A GLU* 5.4 0.4 - - - -
239A TYR* 3.4 44.6 - - - +
240A ALA* 4.1 7.9 - - - -
241A LEU* 3.9 15.9 - - + -
250A LEU 5.6 1.1 - - - +
251A TYR* 5.9 3.1 - - + -
276A MET* 3.6 26.4 - - + +
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Residues in contact with ALA 218 (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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214A LEU 2.8 14.5 + - - +
215A ALA* 3.2 14.6 - - - +
217A MET* 1.3 74.4 - - - +
219A CYS* 1.3 65.3 + - - +
221A LEU* 3.2 3.8 + - - +
222A ARG* 3.0 42.5 + - + +
236A PRO* 4.3 17.9 - - + +
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Residues in contact with CYS 219 (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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205A PHE* 3.6 26.2 - - + -
206A GLN 5.8 0.7 - - - -
207A VAL* 4.6 14.8 - - - -
215A ALA* 3.1 24.0 + - - -
216A LEU* 3.7 9.2 - - - +
218A ALA* 1.3 74.1 - - - +
220A ALA* 1.3 64.0 + - - +
222A ARG* 3.3 30.8 + - - +
223A LYS* 2.9 28.6 + - - +
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Residues in contact with ALA 220 (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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194A VAL* 4.0 27.4 - - + -
196A PHE* 3.7 9.6 - - + -
203A PHE* 4.5 2.2 - - + -
205A PHE* 3.6 14.5 - - + -
216A LEU 3.1 14.3 + - - +
217A MET 3.5 9.4 - - - +
218A ALA 3.3 0.2 - - - -
219A CYS* 1.3 76.1 - - - +
221A LEU* 1.3 57.5 + - - +
223A LYS* 3.3 3.6 + - - +
224A LYS* 3.0 28.6 + - - +
276A MET* 4.0 15.3 - - + -
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Residues in contact with LEU 221 (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 PHE* 3.9 15.7 - - + -
217A MET 3.0 21.2 + - - +
218A ALA* 3.9 3.4 - - - +
220A ALA* 1.3 73.6 - - - +
222A ARG* 1.3 65.5 + - + +
224A LYS* 4.0 13.1 - - - +
225A ALA* 3.1 24.1 + - - +
235A GLN 3.8 14.4 - - - +
236A PRO* 3.5 39.0 - - + -
239A TYR* 3.7 27.4 - - + +
276A MET* 3.7 13.5 - - + -
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Residues in contact with ARG 222 (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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218A ALA* 3.0 39.5 + - - +
219A CYS* 3.6 33.1 + - - +
221A LEU* 1.3 75.8 - - + +
223A LYS* 1.3 68.2 + - + +
225A ALA* 3.3 8.0 + - - +
226A THR* 3.3 27.8 + - + +
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Residues in contact with LYS 223 (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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203A PHE* 4.1 20.9 - - + -
205A PHE* 3.2 40.6 - - + -
219A CYS* 2.9 12.5 + - - +
220A ALA 3.6 4.3 - - - +
222A ARG* 1.3 76.8 - - + +
224A LYS* 1.3 64.7 + - - +
226A THR* 2.9 26.7 + - + +
227A VAL* 3.2 13.7 + - + +
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Residues in contact with LYS 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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196A PHE* 3.6 47.3 - - + -
203A PHE* 4.1 12.7 - - + -
220A ALA 3.0 17.0 + - - +
221A LEU* 4.0 16.1 + - - +
223A LYS* 1.3 74.8 - - - +
225A ALA* 1.3 58.2 + - - +
227A VAL* 4.2 2.0 - - - +
228A PHE* 2.7 56.7 + - + +
239A TYR* 5.1 3.4 - - - -
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Residues in contact with ALA 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 LEU 3.1 18.8 + - - +
222A ARG* 3.4 9.0 - - - +
223A LYS 3.2 0.2 - - - -
224A LYS* 1.3 83.8 - - - +
226A THR* 1.3 57.2 + - + +
228A PHE 4.6 1.3 - - - -
229A ARG 3.0 6.8 + - - -
230A GLN* 2.5 57.3 + - + +
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Residues in contact with THR 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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222A ARG 3.3 15.0 - - - +
223A LYS* 2.9 18.6 + - + +
225A ALA* 1.3 75.9 - - + +
227A VAL* 1.3 73.1 + - - +
229A ARG* 3.4 30.7 + - - -
230A GLN* 6.1 1.3 - - - +
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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
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201A GLU* 4.6 17.9 - - + +
203A PHE* 4.3 20.0 - - + -
223A LYS* 3.2 15.3 + - + +
224A LYS* 4.2 3.6 - - - +
226A THR* 1.3 86.7 + - - +
228A PHE* 1.3 62.5 + - + +
229A ARG* 3.3 12.3 + - - +
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Residues in contact with PHE 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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224A LYS* 2.7 40.2 + - + +
225A ALA* 3.4 3.1 - - - -
227A VAL* 1.3 74.4 - - + +
229A ARG* 1.3 56.0 + - + +
230A GLN* 2.8 19.0 + - - -
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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