Contacts of the helix formed by residues 247 - 261 (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 HIS 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASP* 2.9 34.2 + - - +
246A LEU* 1.3 104.2 - - + +
248A ALA* 1.3 58.4 + - - +
249A ASN 3.4 2.7 - - - -
250A LYS* 3.5 10.9 + - + +
251A ASN* 2.9 46.1 + - - +
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Residues in contact with ALA 248 (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* 3.4 12.1 - - + +
238A VAL* 4.0 4.0 - - - +
239A ALA* 3.6 28.9 - - + +
244A ASP 3.4 18.7 + - - +
245A TYR* 3.2 12.0 + - - +
247A HIS* 1.3 76.0 - - - +
249A ASN* 1.3 61.5 + - - +
251A ASN* 3.8 5.6 - - - +
252A ALA* 2.8 33.8 + - - +
273A PHE* 4.1 4.9 - - + -
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Residues in contact with ASN 249 (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* 3.8 22.8 - - - +
245A TYR 4.7 1.4 + - - -
246A LEU 5.4 0.4 + - - -
247A HIS 3.4 0.6 - - - -
248A ALA* 1.3 77.3 - - - +
250A LYS* 1.3 63.9 + - - +
252A ALA* 3.7 2.5 - - - +
253A MSE 3.0 29.8 + - - +
269A LEU 4.8 3.6 - - - +
270A THR 5.1 1.6 + - - +
272A THR* 5.3 2.3 - - - -
273A PHE* 4.4 17.6 - - - +
274A GLY 4.9 1.2 + - - -
277A ASP* 2.9 30.5 + - - +
278A PHE* 3.5 44.0 - - + +
281A SER* 4.4 9.0 - - - +
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Residues in contact with LYS 250 (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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247A HIS* 3.5 12.6 + - + +
248A ALA 3.3 0.4 - - - -
249A ASN* 1.3 77.4 - - - +
251A ASN* 1.3 66.7 + - - +
253A MSE 3.2 13.0 + - - +
254A ASP* 2.9 35.8 + - - +
281A SER* 4.1 23.8 + - - +
286A TYR* 3.0 35.9 + - + +
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Residues in contact with ASN 251 (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* 3.9 16.0 - - + +
244A ASP* 4.6 10.1 + - - +
247A HIS* 2.9 38.8 + - - +
248A ALA* 3.8 4.1 - - - +
250A LYS* 1.3 79.4 - - - +
252A ALA* 1.3 57.4 + - - +
254A ASP* 3.4 11.1 + - - +
255A CYS* 3.0 35.4 + - - +
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Residues in contact with ALA 252 (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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234A TRP* 3.1 34.0 + - + +
235A VAL* 3.8 23.1 - - + -
238A VAL* 4.0 11.6 - - + +
248A ALA 2.8 17.9 + - - +
249A ASN 3.7 4.0 - - - +
251A ASN* 1.3 74.7 - - - +
253A MSE 1.3 65.1 + - + +
255A CYS* 3.4 1.2 + - - +
256A TRP* 3.0 19.8 + - - +
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Residues in contact with MSE 253 (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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249A ASN 3.0 12.3 + - - +
250A LYS* 3.2 15.9 + - - +
252A ALA* 1.3 72.2 - - + +
254A ASP* 1.3 68.1 + - - +
256A TRP* 3.1 1.3 + - - +
257A ILE* 2.8 29.7 + - - +
278A PHE* 3.9 31.0 - - + -
281A SER* 3.6 33.7 - - - +
282A PHE* 4.3 3.4 - - - +
286A TYR* 3.6 46.9 - - + -
290A TYR* 3.6 30.7 - - + +
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Residues in contact with ASP 254 (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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250A LYS* 2.9 41.0 + - - +
251A ASN* 3.6 11.0 - - - +
253A MSE 1.3 77.4 - - - +
255A CYS* 1.3 60.0 + - - +
257A ILE* 3.3 3.0 + - - -
258A ASN* 2.8 47.2 + - - +
286A TYR* 2.6 29.5 + - - -
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Residues in contact with CYS 255 (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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26A ASN* 4.1 16.1 + - - +
27A PHE* 4.3 22.2 - - - -
234A TRP* 3.6 21.1 - - + -
238A VAL* 5.4 2.5 - - - -
251A ASN* 3.0 22.1 + - - +
252A ALA* 3.8 1.8 - - - +
254A ASP* 1.3 79.2 - - - +
256A TRP* 1.3 58.8 + - - +
258A ASN* 3.9 5.6 - - - +
259A THR* 2.7 33.2 + - - -
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Residues in contact with TRP 256 (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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18A THR* 3.9 26.0 - - + -
19A MSE 4.2 14.4 - - + -
22A ALA* 3.7 21.8 - - + -
229A THR 4.7 1.1 - - - -
230A VAL* 3.7 44.2 - - + +
234A TRP* 3.8 23.1 - + + +
252A ALA 3.0 18.1 + - - +
253A MSE 3.1 4.7 + - - +
255A CYS* 1.3 77.2 - - - +
257A ILE* 1.3 62.3 + - - +
259A THR* 3.2 6.4 + - - -
260A PHE* 3.1 53.5 + + - +
264A ASN 4.5 1.6 + - - -
265A ALA* 3.1 37.4 + - + +
290A TYR* 3.9 17.7 - + - +
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Residues in contact with ILE 257 (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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253A MSE 2.8 19.0 + - - +
254A ASP* 3.9 3.6 - - - +
256A TRP* 1.3 76.7 - - - +
258A ASN* 1.3 64.3 + - - +
261A GLY* 2.8 33.7 + - - +
262A ALA* 3.7 25.4 - - + +
265A ALA* 4.2 20.0 - - + +
285A PRO* 5.9 1.3 - - + -
286A TYR* 3.7 32.3 - - + -
289A ALA* 4.4 13.5 - - + -
290A TYR* 4.1 15.5 - - + +
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Residues in contact with ASN 258 (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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26A ASN* 6.0 1.3 - - - +
254A ASP* 2.8 35.2 + - - +
255A CYS* 4.0 5.5 - - - +
257A ILE* 1.3 82.4 - - - +
259A THR* 1.3 60.3 + - - +
261A GLY 4.7 0.9 + - - -
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Residues in contact with THR 259 (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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22A ALA* 4.2 7.8 - - - +
25A THR* 4.0 30.8 - - + +
26A ASN* 2.8 22.3 + - - -
79A TYR 4.4 2.1 - - - +
81A PRO* 4.0 15.0 - - + +
255A CYS 2.7 22.5 + - - -
256A TRP* 3.5 5.2 - - - -
257A ILE 3.1 0.4 - - - -
258A ASN* 1.3 79.8 - - - +
260A PHE* 1.3 89.6 + - + +
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Residues in contact with PHE 260 (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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18A THR* 3.3 29.8 - - + -
21A ALA* 4.0 7.2 - - + -
22A ALA* 4.0 7.2 - - + -
79A TYR* 3.6 46.6 - + + +
80A LEU* 4.2 8.1 - - + -
81A PRO* 3.9 14.6 - - + -
256A TRP* 3.1 63.7 + + + +
259A THR* 1.3 96.0 - - + +
261A GLY* 1.3 61.4 + - - +
264A ASN* 2.8 35.5 + - + +
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Residues in contact with GLY 261 (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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257A ILE* 2.8 19.2 + - - +
258A ASN 4.6 0.8 + - - -
259A THR 3.7 1.4 - - - -
260A PHE* 1.3 81.4 - - - +
262A ALA* 1.3 66.7 + - - +
263A LYS* 3.2 3.6 - - - -
264A ASN* 2.9 15.3 + - - -
265A ALA* 3.4 8.5 + - - +
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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