Contacts of the helix formed by residues 218 - 235 (chain A) in PDB entry 2VXO
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.8 33.9 - - + -
215A GLY 4.4 9.0 - - - +
216A THR* 3.0 6.4 + - - +
217A PHE* 1.3 74.6 - - - +
219A VAL* 1.3 65.0 + - - +
220A GLN* 3.7 9.2 + - - +
221A ASN* 3.3 27.1 + - - +
222A ARG* 3.0 30.3 + - - +
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Residues in contact with VAL 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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49A PHE* 6.1 0.2 - - - -
218A THR* 1.3 74.0 - - - +
220A GLN* 1.3 54.2 + - - +
222A ARG* 3.7 13.3 - - - +
223A GLU* 2.7 36.9 + - - +
414A PHE* 4.3 15.6 - - + -
418A GLU* 4.1 36.3 - - + +
421A ILE* 4.0 33.4 - - + -
422A LEU* 4.2 10.3 - - + +
425A GLU* 3.9 12.8 - - - +
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Residues in contact with GLN 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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218A THR* 3.2 9.4 + - - +
219A VAL* 1.3 79.7 - - - +
221A ASN* 1.3 70.6 + - - +
223A GLU* 2.8 30.8 + - - +
224A LEU* 3.2 33.9 + - + +
425A GLU* 3.6 27.6 + - - +
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Residues in contact with ASN 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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216A THR* 2.8 44.1 + - - +
217A PHE* 5.3 0.7 - - - -
218A THR* 3.3 12.6 + - - +
220A GLN* 1.3 80.3 - - - +
222A ARG* 1.3 61.6 + - + +
224A LEU* 3.1 19.4 + - - +
225A GLU* 2.9 27.8 + - - +
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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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46A ARG* 4.2 15.0 - - - +
217A PHE* 3.6 50.7 + - + -
218A THR 3.0 30.1 + - - +
219A VAL* 3.8 11.6 - - - +
221A ASN* 1.3 73.5 - - + +
223A GLU* 1.3 60.7 + - - +
225A GLU* 3.3 8.6 + - - +
226A CYS* 2.8 30.8 + - - +
413A ASP* 2.8 29.5 + - - +
414A PHE* 3.7 23.1 - - + -
415A HIS* 5.1 1.2 - - - -
418A GLU* 2.7 42.6 + - - +
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Residues in contact with GLU 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 VAL 2.7 23.2 + - - +
220A GLN* 2.8 27.7 + - - +
222A ARG* 1.3 74.4 - - - +
224A LEU* 1.3 57.1 + - - +
226A CYS* 3.3 7.9 + - - +
227A ILE* 2.8 47.3 + - + +
255A LEU* 4.1 6.9 - - + +
258A ARG* 4.2 4.5 + - - +
414A PHE* 4.2 5.5 - - - -
422A LEU* 3.5 28.5 - - + -
425A GLU* 4.0 15.0 - - - +
426A LEU* 3.5 26.3 + - - +
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Residues in contact with LEU 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 GLN* 3.2 32.0 + - + +
221A ASN* 3.1 23.1 + - - +
223A GLU* 1.3 75.3 - - - +
225A GLU* 1.3 65.9 + - - +
227A ILE* 3.5 14.4 + - + +
228A ARG* 3.2 21.5 + - - +
258A ARG* 4.0 24.5 - - - +
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Residues in contact with GLU 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 ASN 2.9 15.6 + - - +
222A ARG* 3.7 7.9 - - - +
224A LEU* 1.3 75.0 - - - +
226A CYS* 1.3 64.9 + - - +
228A ARG* 2.8 45.0 + - - +
229A GLU* 2.9 48.8 + - - +
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Residues in contact with CYS 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 2.8 18.4 + - - +
223A GLU* 3.3 9.2 + - - +
225A GLU* 1.3 77.1 - - - +
227A ILE* 1.3 54.7 + - - +
229A GLU* 3.4 14.1 + - - +
230A ILE* 2.9 40.8 + - - +
255A LEU* 3.9 24.0 - - + -
410A PRO* 3.6 25.4 - - - -
414A PHE* 4.1 13.2 - - + -
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Residues in contact with ILE 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 GLU* 2.8 49.3 + - + +
224A LEU* 3.8 12.6 - - + +
225A GLU 3.2 0.2 - - - -
226A CYS* 1.3 75.5 - - - +
228A ARG* 1.3 58.1 + - - +
230A ILE* 3.1 4.7 + - - +
231A LYS* 2.9 39.3 + - - +
255A LEU* 4.0 11.7 - - + -
258A ARG* 3.7 38.1 - - + +
259A ALA* 3.7 39.2 - - + +
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Residues in contact with ARG 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 LEU 3.2 12.2 + - - +
225A GLU* 2.8 44.9 + - - +
227A ILE* 1.3 78.2 - - - +
229A GLU* 1.3 62.7 + - - +
231A LYS* 3.2 11.9 + - + +
232A GLU* 2.9 40.9 + - + +
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Residues in contact with GLU 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 GLU* 2.9 47.9 + - - +
226A CYS* 3.7 13.7 - - - +
228A ARG* 1.3 79.3 - - - +
230A ILE* 1.3 61.5 + - + +
232A GLU* 3.3 7.0 + - - +
233A ARG* 2.9 30.9 + - - +
413A ASP* 5.4 4.0 - - - +
492B GLU* 5.6 6.6 - - - +
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Residues in contact with ILE 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 CYS* 2.9 27.8 + - - +
227A ILE* 3.5 6.5 - - - +
229A GLU* 1.3 73.3 - - + +
231A LYS* 1.3 65.4 + - - +
233A ARG* 3.2 4.7 + - - -
234A VAL* 3.0 31.9 + - + +
255A LEU* 4.1 20.6 - - + -
256A LEU* 4.1 23.3 - - + -
259A ALA* 3.7 23.1 - - + -
260A LEU* 4.1 13.9 - - + -
408A ILE* 5.2 4.5 - - + -
410A PRO* 4.0 28.7 - - + -
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Residues in contact with LYS 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 ILE* 2.9 29.4 + - + +
228A ARG* 3.5 14.1 - - + +
230A ILE* 1.3 71.8 - - - +
232A GLU* 1.3 57.1 + - - +
235A GLY* 3.0 30.2 + - - -
258A ARG* 5.7 3.1 - - - +
259A ALA 3.4 27.8 - - - +
260A LEU* 4.4 9.4 - - + -
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Residues in contact with GLU 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 ARG* 2.9 26.6 + - + +
229A GLU* 3.7 8.7 - - - +
230A ILE 3.2 0.2 - - - -
231A LYS* 1.3 76.4 - - - +
233A ARG* 1.3 63.6 + - - +
235A GLY* 4.4 2.9 + - - -
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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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229A GLU 2.9 16.8 + - - +
230A ILE* 3.2 4.5 + - - +
232A GLU* 1.3 77.5 - - - +
234A VAL* 1.3 65.6 + - + +
363A PHE* 3.6 38.3 - - + -
404A GLU 5.6 1.4 + - - -
405A GLY 3.0 27.1 + - - -
406A LYS* 4.6 9.3 - - - +
408A ILE* 4.3 19.0 - - + +
484B GLN* 4.4 31.8 + - - +
488B ALA* 6.0 1.8 - - - +
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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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230A ILE* 3.0 27.8 + - + +
233A ARG* 1.3 82.7 - - + +
235A GLY* 1.3 61.7 + - - +
236A THR 3.1 4.2 + - - -
237A SER* 3.1 50.9 + - - +
239A VAL* 3.7 27.8 - - + -
260A LEU* 4.2 7.0 - - + -
264A GLN* 3.9 9.6 - - - +
363A PHE* 3.8 14.3 - - + -
408A ILE* 4.2 15.9 - - + -
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Residues in contact with GLY 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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231A LYS 3.0 20.2 + - - +
232A GLU 4.4 2.8 + - - -
233A ARG 3.6 1.0 - - - -
234A VAL* 1.3 75.0 - - - +
236A THR* 1.3 63.0 + - - -
260A LEU* 4.3 5.5 - - - +
264A GLN* 2.8 18.4 + - - +
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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