Contacts of the helix formed by residues 231 - 243 (chain B) in PDB entry 1VLP
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 ALA 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B TYR* 3.4 27.8 - - + -
19B MSE 3.1 25.3 - - + +
229B THR 3.6 1.0 + - - -
230B VAL* 1.3 79.0 - - - +
232B HIS* 1.3 67.5 + - + +
233B GLU* 3.1 6.3 - - + +
234B TRP* 3.1 19.9 + - - +
235B VAL* 4.2 1.4 + - - +
269B LEU* 3.6 7.2 - - - +
294B ARG* 4.4 5.8 - - - +
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Residues in contact with HIS 232 (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 ALA* 1.3 74.8 - - + +
233B GLU* 1.3 61.4 + - - +
234B TRP 3.0 0.7 + - - -
235B VAL* 3.2 6.3 + - - +
236B MSE 3.0 31.5 + - - +
269B LEU* 3.4 18.1 - - + +
271B ASP* 3.0 37.1 + - - -
272B THR* 2.8 24.3 + - - +
294B ARG* 5.5 1.6 - - - -
296B ASP* 3.1 25.7 + - - -
390B LYS* 3.4 40.1 - - + +
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Residues in contact with GLU 233 (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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15B TYR* 3.9 6.8 - - - -
16B LYS* 2.7 28.9 + - - -
19B MSE 3.3 20.6 - - + -
34B TYR* 2.6 36.5 + - - -
125B TRP* 3.5 15.2 + - + -
129B ILE* 3.0 14.0 - - + +
132B GLU* 3.4 8.5 - - - +
231B ALA* 4.2 2.6 - - + +
232B HIS* 1.3 78.6 - - - +
234B TRP* 1.3 55.2 + - - +
236B MSE 4.1 11.6 - - - -
237B GLY 2.9 23.2 + - - -
380B LEU* 3.9 19.6 - - + +
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Residues in contact with TRP 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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19B MSE 3.7 17.9 - - - -
22B ALA* 3.6 41.7 - - + -
23B VAL* 3.9 12.6 - - + -
26B ASN* 3.9 4.7 - - - -
27B PHE* 3.5 28.3 - + - -
125B TRP* 4.1 8.6 - + - -
230B VAL* 3.5 24.7 - - + -
231B ALA 3.1 13.6 + - - +
232B HIS 3.0 0.2 + - - -
233B GLU* 1.3 82.4 - - - +
235B VAL* 1.3 58.9 + - + +
237B GLY* 3.7 0.5 - - - -
238B VAL* 3.0 36.5 + - + +
252B ALA* 3.0 37.9 + - + +
255B CYS* 3.5 24.5 - - + -
256B TRP* 3.8 17.9 - + + -
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Residues in contact with VAL 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 ALA 4.2 1.1 + - - +
232B HIS* 3.2 5.2 + - - +
234B TRP* 1.3 77.6 - - + +
236B MSE 1.3 62.6 + - - +
238B VAL* 4.2 1.3 - - + -
239B ALA* 2.9 29.1 + - - +
248B ALA* 3.7 13.0 - - + +
249B ASN* 3.7 20.0 - - - +
252B ALA* 3.7 28.5 - - + -
269B LEU 5.7 1.8 - - - +
272B THR* 3.3 40.6 - - + +
273B PHE* 3.8 15.3 - - + -
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Residues in contact with MSE 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 HIS* 3.0 37.7 + - - +
233B GLU* 3.9 9.9 - - - +
235B VAL* 1.3 76.8 - - - +
237B GLY* 1.3 56.7 + - - +
239B ALA* 3.4 2.1 + - - +
240B SER* 3.0 32.7 + - - -
245B TYR* 5.0 0.5 + - - -
272B THR* 3.6 14.1 - - + -
273B PHE* 4.1 8.0 - - - -
380B LEU* 3.8 34.1 - - + +
388B ALA* 3.9 5.8 - - + +
389B ILE* 3.3 43.7 + - - +
390B LYS* 4.2 10.5 - - - +
399B MSE 4.4 15.0 - - - +
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Residues in contact with GLY 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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125B TRP* 3.8 17.3 - - - -
233B GLU 2.9 19.3 + - - -
234B TRP 3.7 0.4 - - - -
236B MSE 1.3 74.1 - - - +
238B VAL* 1.3 64.0 + - - +
240B SER* 3.2 1.9 + - - -
241B ILE* 3.1 31.2 + - - +
380B LEU* 4.0 1.9 - - - +
383B VAL* 4.2 17.7 - - - +
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Residues in contact with VAL 238 (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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27B PHE* 3.8 29.8 - - + -
125B TRP* 4.5 1.0 - - + -
234B TRP* 3.0 37.4 + - + +
235B VAL* 3.8 7.2 - - - +
237B GLY* 1.3 74.6 - - - +
239B ALA* 1.3 63.9 + - - +
241B ILE* 3.8 17.1 + - - +
242B SER* 4.4 2.8 + - - -
244B ASP* 5.1 2.1 + - - +
248B ALA* 4.0 16.4 - - - +
251B ASN* 4.0 29.8 - - + +
252B ALA* 4.0 8.5 - - + +
255B CYS* 5.2 2.7 - - - -
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Residues in contact with ALA 239 (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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235B VAL 2.9 18.9 + - - +
236B MSE 3.7 1.8 - - - +
238B VAL* 1.3 77.1 - - - +
240B SER* 1.3 59.2 + - - +
242B SER 3.7 0.2 + - - -
243B GLU* 2.9 30.9 + - - -
244B ASP 3.4 8.0 + - - -
245B TYR* 3.5 35.0 - - + -
248B ALA* 3.6 16.8 - - + -
273B PHE* 3.6 10.1 - - + -
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Residues in contact with SER 240 (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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236B MSE 3.0 17.8 + - - -
237B GLY 3.2 0.8 + - - -
239B ALA* 1.3 74.4 - - - +
241B ILE* 1.3 55.2 + - - +
242B SER 3.4 0.3 + - - -
243B GLU* 3.7 5.7 + - - +
245B TYR* 3.4 10.0 + - - -
383B VAL* 3.7 27.1 - - - +
386B ASN* 2.7 37.2 + - - +
387B HIS 3.0 25.8 + - - -
388B ALA* 3.3 11.3 - - - -
389B ILE 4.6 0.2 + - - -
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PRO* 5.8 4.3 - - - +
27B PHE* 3.6 43.7 - - + -
30B VAL* 3.7 19.5 - - + -
125B TRP* 4.7 1.8 - - + -
237B GLY 3.1 21.0 + - - +
238B VAL* 4.1 7.0 - - - +
239B ALA 3.4 0.6 - - - -
240B SER* 1.3 78.1 - - - +
242B SER* 1.3 63.4 + - - +
383B VAL* 3.8 18.8 - - + +
384B ASN* 4.1 18.9 + - - +
386B ASN* 3.3 12.0 + - - +
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Residues in contact with SER 242 (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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238B VAL 4.4 3.6 + - - -
239B ALA 3.7 2.0 + - - -
241B ILE* 1.3 82.2 - - - +
243B GLU* 1.3 74.5 + - - +
244B ASP* 3.0 14.3 + - - +
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Residues in contact with GLU 243 (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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113A THR* 4.8 4.7 + - - +
114A HIS* 5.0 1.2 + - - -
239B ALA 2.9 12.9 + - - -
240B SER* 3.7 2.5 + - - +
241B ILE 3.6 0.4 - - - -
242B SER* 1.3 80.3 - - - +
244B ASP* 1.3 59.1 + - - +
245B TYR* 3.2 25.3 + - + -
386B ASN* 3.1 42.9 - - - +
387B HIS 4.9 2.4 + - - +
404B THR* 4.8 3.3 + - - +
407B ARG* 2.8 45.6 + - - +
411B GLU* 4.3 3.6 - - - +
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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