Contacts of the helix formed by residues 220 - 234 (chain A) in PDB entry 3VPM
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A GLU 4.5 4.0 - - - +
219A ALA* 1.3 77.7 - - - +
221A TYR* 1.3 64.5 + - - +
222A GLY* 3.3 6.8 + - - -
223A GLU* 2.9 40.3 + - - +
224A ARG* 3.0 22.6 + - - -
282A HIS 5.3 7.0 + - - +
284A PRO* 4.8 3.8 - - - +
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Residues in contact with TYR 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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72A LEU* 4.5 8.7 - - + -
73A LEU* 4.1 25.8 - - + +
149A PHE* 3.7 24.2 - + - -
152A GLU* 3.6 24.9 - - + +
153A VAL* 3.7 24.0 - - + +
162A TYR* 2.7 23.0 + - - -
220A THR* 1.3 72.4 - - - +
222A GLY* 1.3 64.1 + - - +
224A ARG* 3.1 16.8 + - - +
225A VAL* 2.9 52.6 + - + +
276A MET* 3.3 21.4 - - + +
280A LEU* 3.9 24.5 - - + -
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR* 3.1 8.2 + - - -
221A TYR* 1.3 79.6 - - - +
223A GLU* 1.3 59.7 + - - +
225A VAL* 3.3 14.9 - - - +
226A VAL* 3.4 15.4 - - - +
277A PHE* 3.5 4.8 - - - -
280A LEU* 3.5 26.3 - - - +
282A HIS 5.4 2.0 - - - -
284A PRO* 4.0 16.4 - - - -
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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
----------------------------------------------------------
213A TRP* 4.5 7.2 - - + -
219A ALA* 3.4 17.4 - - + -
220A THR* 2.9 46.5 + - - +
222A GLY* 1.3 75.8 - - - +
224A ARG* 1.3 60.3 + - - +
226A VAL* 3.1 9.7 + - - +
227A ALA* 2.9 25.1 + - - +
284A PRO* 4.1 21.8 - - + -
288A ARG* 3.2 31.2 + - + +
292A ILE* 4.4 16.8 - - + +
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Residues in contact with ARG 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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144A ASN* 5.1 1.2 + - - +
148A ARG* 3.2 49.8 - - - +
149A PHE* 3.7 27.0 - - + -
152A GLU* 2.6 42.8 + - - -
213A TRP* 3.9 34.0 + - + +
216A ASP 4.4 1.3 - - - -
219A ALA* 3.3 24.0 + - + -
220A THR 3.0 13.9 + - - +
221A TYR* 3.1 25.7 + - - +
223A GLU* 1.3 74.7 - - - +
225A VAL* 1.3 59.6 + - - +
227A ALA* 3.2 8.7 + - + +
228A PHE* 2.9 28.2 + - + -
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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
----------------------------------------------------------
149A PHE* 3.6 18.5 - - + -
162A TYR* 4.0 3.6 - - - +
221A TYR* 2.9 68.0 + - + +
222A GLY* 3.3 18.4 - - - +
224A ARG* 1.3 67.6 - - - +
226A VAL* 1.3 60.5 + - + +
228A PHE 3.9 0.6 - - - +
229A ALA* 2.9 30.7 + - - +
273A ALA* 4.0 20.1 - - + +
276A MET* 4.5 7.4 - - + -
277A PHE* 4.2 17.3 - - + +
280A LEU* 4.7 1.8 - - + -
335A LEU* 6.3 0.4 - - - -
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Residues in contact with VAL 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 GLY 3.4 15.0 - - - +
223A GLU* 3.1 11.9 + - - +
225A VAL* 1.3 77.5 - - - +
227A ALA* 1.3 52.2 + - - +
229A ALA* 3.0 7.6 + - - +
230A ALA* 2.7 33.8 + - - +
277A PHE* 3.6 24.7 - - + -
289A VAL* 4.2 22.0 - - + -
292A ILE* 4.0 18.2 - - + -
293A ILE* 3.9 24.5 - - + +
335A LEU* 4.1 19.1 - - + -
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Residues in contact with ALA 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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209A TRP* 3.4 12.3 - - + -
213A TRP* 3.5 50.5 - - + +
223A GLU 2.9 12.3 + - - +
224A ARG* 3.2 10.1 + - - +
226A VAL* 1.3 76.9 - - - +
228A PHE* 1.3 59.1 + - + +
230A ALA* 3.2 6.5 + - - +
231A VAL* 2.8 28.5 + - - +
292A ILE* 4.4 3.1 - - + +
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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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140A ILE* 4.3 3.1 - - + -
141A VAL* 4.1 25.4 - - + -
144A ASN* 3.3 49.1 - - + +
149A PHE* 4.3 15.0 - + + -
210A ALA* 3.7 26.0 - - + -
213A TRP* 3.9 23.1 - + + -
214A ILE* 3.8 9.6 - - + -
224A ARG* 2.9 21.3 + - + +
225A VAL 4.5 0.7 - - - +
227A ALA* 1.3 78.8 - - + +
229A ALA* 1.3 61.1 + - - +
230A ALA 3.1 0.9 - - - -
231A VAL* 3.5 23.2 - - + +
232A GLU* 2.9 40.2 + - - +
273A ALA* 5.7 0.2 - - - -
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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
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225A VAL 2.9 19.9 + - - +
226A VAL* 3.4 6.7 - - - +
228A PHE* 1.3 75.6 - - - +
230A ALA* 1.3 58.6 + - - +
232A GLU* 5.0 0.7 - - - -
233A GLY* 2.8 28.9 + - - -
270A CYS* 3.5 13.2 - - - +
273A ALA* 3.6 23.5 - - + +
274A CYS* 5.6 0.9 - - - -
331A LEU* 3.9 25.6 - - + +
335A LEU* 5.8 3.8 - - + -
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Residues in contact with ALA 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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209A TRP* 4.1 9.0 - - + -
226A VAL 2.7 12.1 + - - +
227A ALA* 3.3 11.4 - - - +
228A PHE 3.1 0.2 - - - -
229A ALA* 1.3 75.8 - - - +
231A VAL* 1.3 59.5 + - - +
234A ILE* 2.6 34.1 + - + +
235A PHE* 3.1 8.7 + - - -
292A ILE* 5.1 0.7 - - + -
293A ILE* 4.0 15.9 - - + -
296A ALA* 4.0 24.7 - - + -
331A LEU* 4.3 7.1 - - - +
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Residues in contact with VAL 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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137A SER* 5.3 4.7 - - - +
140A ILE* 6.3 0.2 - - + -
141A VAL* 3.9 26.0 - - + -
209A TRP* 4.0 14.8 - - + -
210A ALA* 3.9 28.0 - - + -
227A ALA 2.8 21.2 + - - +
228A PHE* 3.3 22.0 + - + +
230A ALA* 1.3 75.9 - - - +
232A GLU* 1.3 62.3 + - - +
235A PHE* 3.1 40.1 + - + +
236A PHE* 3.5 14.6 + - + -
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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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141A VAL* 3.9 27.2 - - + +
145A LEU* 5.8 0.5 - - - +
165A GLN* 3.0 23.8 + - - -
228A PHE* 2.9 30.0 + - - +
229A ALA* 5.5 0.3 - - - -
231A VAL* 1.3 73.2 - - - +
233A GLY* 1.3 58.8 + - - +
236A PHE* 3.6 24.3 - - + +
240A PHE* 4.5 2.8 - - - -
266A GLU* 2.8 24.4 - - - +
269A HIS* 3.2 14.5 + - - +
270A CYS* 3.7 15.6 - - - -
402A FE 2.0 32.7 - - - -
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Residues in contact with GLY 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 ALA 2.8 18.0 + - - -
232A GLU* 1.3 81.0 - - - +
234A ILE* 1.3 61.7 + - - +
237A SER* 3.3 24.7 + - - -
240A PHE* 6.0 0.2 - - - -
270A CYS* 3.5 13.0 - - - -
327A VAL* 3.4 11.5 - - - +
331A LEU* 5.3 3.1 - - - -
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Residues in contact with ILE 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 ALA* 2.6 20.2 + - + +
233A GLY* 1.3 76.3 - - - +
235A PHE* 1.3 64.9 + - + +
236A PHE 3.1 1.3 - - - -
237A SER* 2.9 20.8 + - - -
293A ILE* 3.8 40.4 - - + +
296A ALA* 3.7 34.1 - - + +
297A VAL* 4.1 1.3 - - + +
300A GLU* 3.3 21.2 - - + -
324A ILE* 4.0 13.2 - - + +
327A VAL* 4.3 13.5 - - + -
328A ALA* 3.9 13.9 - - + +
331A LEU* 4.1 19.1 - - + -
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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