Contacts of the helix formed by residues 211 - 234 (chain A) in PDB entry 1X79
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 ILE 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A SER* 1.3 62.5 + - - +
213A LYS* 3.3 2.8 - - - +
214A ARG* 3.1 59.0 - - - +
215A VAL* 2.7 39.1 + - + +
273A ASN* 5.5 9.0 - - - +
276A ALA* 5.6 0.7 - - + -
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Residues in contact with SER 212 (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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211A ILE* 1.3 81.0 - - - +
213A LYS* 1.3 62.0 + - - +
215A VAL* 3.5 5.8 + - - +
216A ASN* 3.1 37.4 + - - +
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE 4.1 3.2 - - - +
212A SER* 1.3 77.9 - - - +
214A ARG* 1.3 65.8 + - - +
215A VAL 3.1 1.1 - - - -
216A ASN* 4.0 13.1 - - + +
217A ALA* 3.0 25.5 + - - +
266A LEU* 4.5 6.8 - - + +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 3.1 55.9 - - - +
213A LYS* 1.3 78.7 - - - +
215A VAL* 1.3 75.8 + - - +
217A ALA* 3.5 2.6 + - - +
218A ILE* 3.2 37.9 + - + +
266A LEU* 3.9 20.1 - - + +
270A THR* 5.3 2.5 - - - -
276A ALA* 3.5 28.3 - - - +
279A GLU* 3.0 43.5 + - - +
280A ILE* 3.4 27.8 - - + -
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 2.7 27.7 + - + +
212A SER* 3.6 6.7 - - - +
213A LYS 3.1 0.4 - - - -
214A ARG* 1.3 95.8 - - - +
216A ASN* 1.3 63.4 + - - +
218A ILE* 3.1 8.0 + - + +
219A GLU* 2.8 48.9 + - + +
279A GLU* 5.7 1.1 - - - +
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Residues in contact with ASN 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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212A SER* 3.1 27.7 + - - +
213A LYS* 3.3 12.5 + - - +
215A VAL* 1.3 80.0 - - - +
217A ALA* 1.3 63.9 + - - +
219A GLU* 3.9 6.5 - - - +
220A GLU* 2.9 28.0 + - - +
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Residues in contact with ALA 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 LYS 3.0 17.4 + - - +
214A ARG 3.5 0.9 - - - +
216A ASN* 1.3 79.5 - - - +
218A ILE* 1.3 58.2 + - - +
220A GLU* 3.4 3.4 - - - +
221A VAL* 2.9 34.9 + - - +
259A MET* 3.6 10.8 - - + +
262A THR* 4.2 16.6 - - + -
263A LEU* 4.5 3.4 - - + -
266A LEU* 3.5 26.7 - - + -
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Residues in contact with ILE 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 ARG* 3.2 46.8 + - + +
215A VAL* 3.1 7.7 + - - +
217A ALA* 1.3 75.4 - - + +
219A GLU* 1.3 60.1 + - + +
221A VAL* 3.2 7.3 + - - +
222A ASN* 2.8 53.9 + - - +
263A LEU* 5.3 3.4 - - + -
279A GLU* 3.8 32.5 - - + +
280A ILE* 4.2 8.7 - - + +
283A ALA* 4.4 18.2 - - + -
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Residues in contact with GLU 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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215A VAL* 2.8 38.1 + - + +
216A ASN* 3.9 7.0 - - - +
218A ILE* 1.3 75.0 - - + +
220A GLU* 1.3 68.0 + - - +
222A ASN* 3.2 6.6 + - - +
223A ASN* 2.9 46.5 + - - +
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Residues in contact with GLU 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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216A ASN* 2.9 20.0 + - - +
217A ALA* 3.4 5.6 - - - +
219A GLU* 1.3 77.8 - - - +
221A VAL* 1.3 63.1 + - - +
223A ASN* 3.3 6.6 + - - +
224A ASN* 3.1 37.0 + - - +
255A ARG* 4.1 24.0 + - - +
259A MET* 3.7 29.8 - - + +
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Residues in contact with VAL 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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217A ALA 2.9 22.2 + - - +
218A ILE* 3.4 9.4 - - - +
219A GLU 3.2 0.2 - - - -
220A GLU* 1.3 75.5 - - - +
222A ASN* 1.3 72.1 + - - +
224A ASN* 3.0 4.0 + - - -
225A VAL* 2.9 43.9 + - + +
256A CYS* 5.7 2.9 - - - -
259A MET* 3.5 22.9 - - + -
263A LEU* 4.1 20.6 - - + -
283A ALA* 3.9 24.5 - - + +
287A LEU* 4.3 13.5 - - + -
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Residues in contact with ASN 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 ILE* 2.8 43.4 + - - +
219A GLU* 3.9 7.4 + - - +
221A VAL* 1.3 80.2 - - - +
223A ASN* 1.3 63.1 + - - +
224A ASN 3.3 0.3 + - - -
225A VAL* 3.7 4.2 + - - +
226A LYS* 2.8 39.3 + - - +
283A ALA* 4.2 5.1 - - - +
286A ASN* 3.6 24.2 + - - +
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Residues in contact with ASN 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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219A GLU* 2.9 37.9 + - - +
220A GLU* 3.7 7.1 - - - +
222A ASN* 1.3 77.7 - - - +
224A ASN* 1.3 70.1 + - - +
226A LYS* 3.4 18.5 - - - +
227A LEU* 3.5 7.6 + - - +
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Residues in contact with ASN 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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220A GLU* 3.1 28.2 + - - +
221A VAL* 3.0 3.6 + - - +
223A ASN* 1.3 88.2 + - - +
225A VAL* 1.3 66.9 + - - +
226A LYS 3.0 1.3 - - - -
227A LEU* 2.9 10.8 + - - +
228A LEU* 2.8 26.6 + - - +
252A LEU* 4.1 21.5 - - + +
255A ARG* 4.2 16.5 + - - -
256A CYS* 4.2 18.2 - - - -
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Residues in contact with VAL 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 VAL* 2.9 39.7 + - + +
222A ASN* 4.2 5.2 - - - +
224A ASN* 1.3 74.7 - - + +
226A LYS* 1.3 54.4 + - + +
228A LEU* 4.0 2.4 - - - +
229A THR* 2.5 48.9 + - - +
256A CYS* 5.0 3.1 - - - -
286A ASN* 3.4 31.9 - - + +
287A LEU* 4.1 14.1 - - + +
289A GLN* 5.0 5.6 - - - +
290A VAL* 3.5 26.2 - - + -
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Residues in contact with LYS 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 ASN* 2.8 31.8 + - - +
223A ASN* 3.4 12.1 - - - +
225A VAL* 1.3 78.7 - - + +
227A LEU* 1.3 62.4 + - - +
229A THR* 3.4 5.4 + - - -
230A GLU* 3.2 24.5 + - - +
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Residues in contact with LEU 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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223A ASN 3.5 9.1 + - - +
224A ASN* 2.9 17.8 + - - +
226A LYS* 1.3 78.4 - - - +
228A LEU* 1.3 55.1 + - - +
230A GLU* 2.8 36.8 - - - +
231A MET* 3.0 49.8 + - + +
248A LEU* 6.1 2.5 - - + -
252A LEU* 3.3 15.3 - - + -
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Residues in contact with LEU 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 ASN 2.8 16.4 + - - +
225A VAL* 4.0 2.2 - - - +
227A LEU* 1.3 71.5 - - - +
229A THR* 1.3 66.7 + - - +
231A MET* 3.5 4.1 - - + +
232A VAL* 2.9 36.3 + - + +
249A MET* 4.1 22.9 - - + -
252A LEU* 3.3 22.9 - - + -
253A TYR* 3.7 49.8 - - + +
256A CYS* 4.3 17.9 - - + -
290A VAL* 3.5 25.1 - - + +
291A ILE* 5.9 0.2 - - + -
294A TYR* 4.5 1.1 - - + -
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Residues in contact with THR 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 VAL* 2.5 32.9 + - - +
226A LYS* 3.6 6.7 - - - -
228A LEU* 1.3 79.9 - - - +
230A GLU* 1.3 66.1 + - - +
232A VAL* 3.3 4.9 + - - +
233A MET* 3.2 27.5 + - + +
289A GLN* 5.8 1.6 + - - +
290A VAL* 3.6 20.3 - - - +
293A LEU* 4.4 15.4 - - + +
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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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226A LYS* 3.2 14.4 + - - +
227A LEU* 2.8 38.8 - - - +
229A THR* 1.3 77.5 - - - +
231A MET* 1.3 55.0 + - + +
232A VAL 2.6 13.2 + - - -
233A MET* 2.7 20.4 + - - +
234A SER* 2.9 19.7 + - - +
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Residues in contact with MET 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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227A LEU* 3.0 46.3 + - + +
228A LEU* 3.5 8.7 - - - +
230A GLU* 1.3 75.6 - - + +
232A VAL* 1.3 61.7 + - - +
234A SER* 3.8 11.2 - - - +
235A HIS* 3.3 17.2 - - - +
245A SER* 4.2 8.3 - - - +
248A LEU* 3.8 23.1 - - + +
249A MET* 3.4 54.2 - - + +
252A LEU* 4.0 12.3 - - - -
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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
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228A LEU* 2.9 30.7 + - + +
229A THR* 3.5 8.3 - - - +
230A GLU 2.6 5.3 + - - -
231A MET* 1.3 72.5 - - - +
233A MET* 1.3 61.2 + - - +
235A HIS* 2.9 26.7 + - - +
249A MET* 4.1 7.9 - - - -
290A VAL* 4.9 1.8 - - + -
293A LEU* 3.9 23.1 - - + -
294A TYR* 4.2 31.0 - - + -
297A LEU* 4.2 23.4 - - + +
298A VAL* 4.2 15.9 - - + -
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Residues in contact with MET 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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229A THR* 3.3 23.1 - - + +
230A GLU* 2.7 13.1 + - - +
232A VAL* 1.3 67.3 - - - +
234A SER* 1.3 53.7 + - - +
235A HIS 2.4 19.6 + - - -
236A SER* 3.1 19.9 + - - +
293A LEU* 4.2 28.5 - - + -
297A LEU* 4.6 15.0 - - - -
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Residues in contact with SER 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 22.3 + - - +
231A MET* 3.8 7.3 - - - +
233A MET* 1.3 72.0 - - - +
235A HIS* 1.3 59.1 + - - +
236A SER 3.6 4.7 - - - -
245A SER* 5.5 5.9 - - - -
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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