Contacts of the helix formed by residues 221 - 237 (chain B) in PDB entry 2VE7
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 HIS 221 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLU* 3.1 29.4 + - + +
219B ILE* 4.5 0.2 - - - -
220B MET* 1.3 93.4 + - + +
222B ASN* 1.3 59.4 + - - +
223B LYS 3.2 3.1 - - - -
224B LEU* 2.9 30.2 + - + +
225B PHE* 3.1 9.2 + - - +
257B LEU* 3.9 34.0 - - + +
258B PHE* 4.3 17.8 - + - -
138D TYR* 3.4 10.2 + - - +
142D LEU* 4.0 14.2 - - + +
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Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 3.6 6.1 + - - +
213B GLU 2.8 26.1 + - - +
214B GLU* 4.1 1.1 - - - +
215B THR* 3.1 27.9 + - - +
219B ILE* 3.9 10.5 - - + +
220B MET 3.5 0.6 - - - -
221B HIS* 1.3 69.8 - - - +
223B LYS* 1.3 57.5 + - - +
225B PHE* 3.9 14.0 - - - -
226B LEU* 2.8 44.6 + - - +
56D VAL 3.3 22.5 + - - +
57D TYR* 3.5 22.6 + - - +
58D GLY* 3.8 1.4 - - - +
131D ARG* 4.2 0.5 + - - -
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 4.6 3.4 + - - +
213B GLU* 3.6 26.0 + - - +
221B HIS 3.2 0.6 - - - -
222B ASN* 1.3 78.0 - - - +
224B LEU* 1.3 61.8 + - + +
226B LEU* 4.4 7.2 - - - +
227B ASP* 3.5 22.7 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLU* 4.7 0.8 + - - -
221B HIS* 2.9 20.4 + - + +
223B LYS* 1.3 81.4 - - + +
225B PHE* 1.3 58.8 + - - +
227B ASP* 3.5 4.4 + - + +
228B TYR* 3.1 25.7 + - + +
250B LEU* 4.0 19.1 - - + -
253B LYS* 3.5 46.4 - - + +
254B LEU* 4.0 23.8 - - + -
257B LEU* 4.7 10.1 - - + -
138D TYR* 3.9 14.6 - - - +
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ILE* 3.3 45.5 - - + -
221B HIS 3.1 7.4 + - - +
222B ASN* 3.7 15.9 - - - +
224B LEU* 1.3 75.3 - - - +
226B LEU* 1.3 57.3 + - + +
228B TYR* 3.1 5.4 + + - +
229B THR* 2.6 61.4 + - - -
131D ARG* 3.5 42.2 - - + -
134D CYS* 3.6 11.2 - - + -
135D ARG* 3.5 26.9 - - + -
138D TYR* 3.5 33.3 - + + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 2.8 36.3 + - - +
223B LYS* 4.4 5.6 - - - +
225B PHE* 1.3 75.5 - - + +
227B ASP* 1.3 57.8 + - - +
229B THR* 4.3 5.8 - - - -
230B ILE* 2.8 55.1 + - + +
56D VAL* 3.7 34.8 - - + +
57D TYR* 3.5 35.7 - - + -
98D ILE* 5.5 1.6 - - + -
127D PHE* 4.8 8.7 - - + -
131D ARG* 5.8 2.2 - - - +
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Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LYS* 3.5 20.6 + - - +
224B LEU* 3.7 6.8 - - - +
225B PHE 3.2 0.6 - - - -
226B LEU* 1.3 77.1 - - - +
228B TYR* 1.3 65.1 + - - +
230B ILE* 4.0 5.9 - - - +
231B LYS* 3.1 59.0 + - - +
249B GLU* 4.5 0.2 - - - +
253B LYS* 2.9 29.2 + - - +
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.1 12.6 + - + +
225B PHE* 3.3 23.1 - + - +
227B ASP* 1.3 81.0 + - - +
229B THR* 1.3 60.3 + - - +
231B LYS* 3.2 8.5 + - - +
232B CYS* 2.9 46.6 + - - -
246B MET* 3.8 25.8 - - + -
247B ASN* 2.7 28.4 + - - -
250B LEU* 3.9 32.3 - - + -
134D CYS* 3.9 22.2 - - + -
137D THR* 3.1 9.4 - - + +
138D TYR* 4.3 7.6 - + + -
2198D IPH 2.6 29.1 + - - -
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B PHE* 2.6 54.4 + - - -
226B LEU* 3.9 8.3 - - + -
228B TYR* 1.3 73.0 - - - +
230B ILE* 1.3 66.5 + - - +
232B CYS* 3.4 3.7 + - - +
233B TYR* 2.9 21.3 + - - +
127D PHE* 4.0 19.3 - - + -
130D PHE* 4.0 2.9 - - + -
131D ARG* 3.4 34.5 - - + -
134D CYS* 3.9 13.1 - - - +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 2.8 42.5 + - + +
227B ASP* 4.0 5.2 - - - +
229B THR* 1.3 71.6 - - - +
231B LYS* 1.3 67.5 + - + +
233B TYR* 2.9 17.8 + - + +
234B GLU* 3.1 31.4 + - + +
57D TYR* 6.1 1.1 - - + -
98D ILE* 3.7 45.3 - - + -
127D PHE* 5.2 3.4 - - + -
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 3.1 50.4 + - - +
228B TYR* 3.5 5.8 - - - +
230B ILE* 1.3 78.8 - - + +
232B CYS* 1.3 60.8 - - - +
234B GLU* 3.3 11.4 + - + +
235B SER* 3.3 21.0 + - - -
246B MET* 4.1 22.1 - - + +
249B GLU* 2.9 41.0 + - - +
253B LYS* 4.0 1.4 - - - +
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Residues in contact with CYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 2.9 52.3 + - - -
229B THR 3.6 7.6 - - - +
231B LYS* 1.3 75.7 - - - +
233B TYR* 1.3 58.4 + - - +
235B SER* 3.3 1.4 + - - -
236B PHE* 2.8 30.0 + - - +
243B PHE* 3.4 25.1 - - + -
246B MET* 3.7 16.6 - - - +
130D PHE* 3.7 15.3 - - + -
134D CYS* 4.1 4.5 - - - -
2198D IPH 3.9 9.9 - - - +
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B THR 2.9 12.7 + - - +
230B ILE* 2.9 13.6 + - + +
232B CYS* 1.3 76.6 - - - +
234B GLU* 1.3 53.8 + - + +
236B PHE* 3.2 20.9 + + - +
237B MET* 2.7 51.0 + - - +
98D ILE* 3.5 28.0 - - + -
99D CYS* 4.7 1.1 + - - -
100D ARG* 4.2 22.1 - - + +
123D GLY 4.8 0.9 + - - -
126D ASN* 3.8 12.9 - - - +
127D PHE* 3.7 41.2 + + + +
130D PHE* 3.2 43.5 - + + -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE* 3.1 31.6 + - + +
231B LYS* 3.3 9.6 + - + +
233B TYR* 1.3 74.3 - - + +
235B SER* 1.3 61.9 + - - +
237B MET* 3.3 4.0 + - - +
238B SER* 2.8 28.2 + - - -
100D ARG* 2.7 35.6 + - - +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LYS 3.3 9.1 + - - -
232B CYS 3.5 8.3 - - - -
233B TYR 3.2 0.4 - - - -
234B GLU* 1.3 76.1 - - - +
236B PHE* 1.3 58.2 + - - +
238B SER* 2.8 26.8 + - - -
240B ALA* 3.1 33.9 + - - +
243B PHE* 4.4 3.8 - - - -
246B MET* 3.1 32.3 - - - +
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B CYS 2.8 21.4 + - - +
233B TYR* 3.4 29.2 - + - +
235B SER* 1.3 72.0 - - - +
237B MET* 1.3 70.4 + - - +
239B GLY* 2.9 22.0 + - - -
240B ALA 3.9 15.9 + - - -
243B PHE* 4.0 12.9 - + + -
130D PHE* 3.5 29.4 - + + -
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Residues in contact with MET 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B TYR* 2.7 34.8 + - + +
234B GLU 3.6 6.1 - - - +
235B SER 3.2 0.4 - - - -
236B PHE* 1.3 90.6 - - - +
238B SER* 1.3 58.4 + - - +
239B GLY 3.4 0.7 - - - -
100D ARG* 3.5 59.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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