Contacts of the helix formed by residues 231 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.5 37.7 - - + -
19A MSE 4.5 8.1 - - + +
229A THR 3.7 0.6 + - - -
230A VAL* 1.3 79.5 - - - +
232A HIS* 1.3 67.4 + - - +
233A GLU* 3.1 16.7 + - + +
234A TRP* 3.2 16.5 + - - +
235A VAL* 4.3 1.4 + - - +
269A LEU* 3.5 7.9 - - - +
294A ARG* 4.4 5.2 - - - +
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Residues in contact with HIS 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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231A ALA* 1.3 73.4 - - - +
233A GLU* 1.3 62.1 + - - +
234A TRP 3.1 1.4 + - - -
235A VAL* 3.3 6.9 + - - +
236A MSE 3.1 38.3 + - - +
269A LEU* 3.3 18.7 - - + +
271A ASP* 3.0 37.4 + - - -
272A THR* 2.9 27.1 + - + +
294A ARG* 5.0 3.6 - - - -
296A ASP* 2.7 27.4 + - - -
390A LYS* 3.7 30.7 + - + +
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Residues in contact with GLU 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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15A TYR* 4.4 3.8 - - - -
16A LYS* 2.6 35.4 + - - -
19A MSE 3.4 24.7 - - + +
34A TYR* 2.3 40.1 + - - -
125A TRP* 3.5 16.3 + - + -
129A ILE* 3.6 2.1 - - - +
132A GLU* 4.0 4.7 - - - +
231A ALA* 3.1 9.2 - - + +
232A HIS* 1.3 78.8 - - - +
234A TRP* 1.3 56.1 + - - +
236A MSE 3.8 11.6 - - - +
237A GLY* 2.8 25.3 + - - -
380A LEU* 3.9 17.8 - - + +
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Residues in contact with TRP 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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19A MSE 3.4 31.2 - - + -
22A ALA* 3.7 40.6 - - + -
23A VAL* 4.0 9.2 - - + -
26A ASN* 4.0 4.7 - - - -
27A PHE* 3.6 29.8 - + - -
125A TRP* 4.1 7.3 - + - -
230A VAL* 3.6 22.0 - - + -
231A ALA 3.2 10.8 + - - +
232A HIS 3.1 0.6 + - - -
233A GLU* 1.3 81.4 - - - +
235A VAL* 1.3 64.8 + - + +
237A GLY* 3.8 0.5 - - - -
238A VAL* 3.0 30.2 + - + +
252A ALA* 3.1 36.0 + - + +
255A CYS* 3.6 25.6 - - + -
256A TRP* 3.8 18.4 - + + +
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Residues in contact with VAL 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 ALA 4.3 1.4 + - - +
232A HIS* 3.3 4.0 + - - +
234A TRP* 1.3 79.6 - - + +
236A MSE 1.3 59.6 + - - +
238A VAL* 4.3 1.1 - - + -
239A ALA* 2.9 28.2 + - - +
248A ALA* 3.4 40.8 - - + +
249A ASN* 3.8 18.2 - - - +
252A ALA* 3.8 15.5 - - + -
269A LEU 5.6 1.6 - - - +
272A THR* 3.4 39.0 - - + +
273A PHE* 3.9 8.3 - - + -
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Residues in contact with MSE 236 (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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232A HIS* 3.1 38.4 + - - +
233A GLU* 3.8 9.0 - - - +
235A VAL* 1.3 76.2 - - - +
237A GLY* 1.3 56.6 + - - +
239A ALA* 3.4 1.7 + - - +
240A SER* 3.0 33.2 + - - -
245A TYR* 5.2 0.3 + - - -
272A THR* 3.6 13.0 - - + -
273A PHE* 4.2 8.3 - - - -
380A LEU* 3.7 35.4 - - + +
388A ALA* 3.9 7.4 - - + +
389A ILE* 3.4 42.8 - - - +
390A LYS* 4.3 10.1 - - - +
399A MSE 4.5 14.8 - - - +
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Residues in contact with GLY 237 (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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125A TRP* 3.7 15.9 - - - -
233A GLU 2.8 21.3 + - - -
236A MSE 1.3 70.3 - - - +
238A VAL* 1.3 64.1 + - - +
240A SER* 3.2 1.6 + - - -
241A ILE* 3.0 34.0 + - - +
380A LEU* 4.0 2.1 - - - +
383A VAL* 4.1 18.4 - - - -
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Residues in contact with VAL 238 (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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27A PHE* 4.0 27.4 - - + -
125A TRP* 4.5 1.0 - - + -
234A TRP* 3.0 38.7 + - + +
235A VAL* 3.8 7.0 - - - +
237A GLY* 1.3 74.8 - - - +
239A ALA* 1.3 61.7 + - - +
241A ILE* 3.7 18.1 + - - +
242A SER* 4.4 4.9 + - - -
244A ASP* 5.1 1.7 + - - +
248A ALA* 4.0 9.2 - - - +
251A ASN* 3.9 29.8 - - + +
252A ALA* 4.0 14.8 - - + +
255A CYS* 5.4 1.8 - - - -
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Residues in contact with ALA 239 (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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235A VAL 2.9 18.3 + - - +
236A MSE 3.8 2.9 - - - +
238A VAL* 1.3 76.3 - - - +
240A SER* 1.3 51.2 + - - +
241A ILE 3.4 0.2 + - - -
243A GLU* 2.6 38.9 + - - -
244A ASP 3.4 6.9 + - - -
245A TYR* 3.5 37.5 - - + -
248A ALA* 3.6 20.4 - - + +
273A PHE* 3.8 3.6 - - + -
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Residues in contact with SER 240 (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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236A MSE 3.0 17.9 + - - -
237A GLY 3.2 0.4 + - - -
239A ALA* 1.3 74.6 - - - +
241A ILE* 1.3 57.9 + - - +
242A SER 3.2 0.2 - - - -
243A GLU* 3.8 6.5 + - - +
245A TYR* 3.5 9.1 + - - -
383A VAL* 3.6 26.4 - - - +
386A ASN* 2.7 37.9 + - - +
387A HIS 3.1 24.0 + - - -
388A ALA* 3.4 10.6 - - - -
389A ILE 4.7 0.2 + - - -
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Residues in contact with ILE 241 (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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27A PHE* 3.6 46.0 - - + -
30A VAL* 3.9 17.9 - - + -
125A TRP* 4.6 2.0 - - + -
237A GLY 3.0 25.6 + - - +
238A VAL* 4.0 8.7 - - - +
239A ALA 3.3 0.6 - - - -
240A SER* 1.3 79.5 - - - +
242A SER* 1.3 65.1 + - - +
383A VAL* 3.8 18.4 - - + -
384A ASN* 4.2 19.9 + - - +
386A ASN* 3.4 10.0 + - - -
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Residues in contact with SER 242 (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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238A VAL 4.4 4.0 + - - -
239A ALA 3.6 1.6 + - - -
241A ILE* 1.3 82.5 - - - +
243A GLU* 1.3 73.4 + - - +
244A ASP* 3.2 14.5 + - - +
386A ASN* 4.8 1.6 - - - +
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Residues in contact with GLU 243 (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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239A ALA 2.6 20.5 + - - +
240A SER* 4.0 14.1 - - - +
242A SER* 1.3 76.2 - - - +
244A ASP* 1.3 57.1 + - - +
245A TYR* 3.2 26.2 + - + +
386A ASN* 4.0 27.5 - - + +
387A HIS* 4.6 10.4 + - - +
404A THR* 4.8 6.6 + - - +
407A ARG* 3.4 26.9 + - - +
411A GLU* 4.5 6.2 - - - +
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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