Contacts of the helix formed by residues 274 - 280 (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 GLY 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ASN* 4.9 0.5 + - - -
270A THR 3.3 9.1 - - - +
271A ASP 2.9 11.1 + - - -
273A PHE* 1.3 83.1 + - - +
275A THR* 1.3 66.4 + - - -
276A ASP 3.3 3.1 - - - -
277A ASP 3.3 5.4 + - - -
278A PHE* 3.5 5.9 + - - +
391A ILE* 4.8 1.1 - - - -
392A SER 3.9 10.3 + - - -
393A ASP* 3.5 10.5 - - - -
414A TYR* 3.3 13.7 + - - -
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Residues in contact with THR 275 (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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270A THR* 2.8 40.2 + - - +
271A ASP* 3.6 0.5 - - - +
274A GLY* 1.3 71.4 - - - -
276A ASP* 1.3 58.6 + - - +
278A PHE* 3.2 2.6 + - - +
279A LEU* 2.9 48.5 + - + +
303A TYR* 3.5 11.9 - - + -
306A LYS* 4.1 17.5 - - + -
307A ILE* 4.3 4.9 - - + -
393A ASP* 2.6 37.3 + - - -
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Residues in contact with ASP 276 (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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274A GLY 3.3 1.0 - - - -
275A THR* 1.3 75.3 - - - +
277A ASP* 1.3 61.4 + - - +
279A LEU* 3.4 10.6 + - - +
280A LYS* 3.4 24.7 + - - +
306A LYS* 3.1 36.7 + - - +
414A TYR* 4.0 22.5 - - + -
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Residues in contact with ASP 277 (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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245A TYR 4.6 5.9 - - - +
246A LEU* 4.8 8.6 - - - +
249A ASN* 2.9 28.4 + - - +
273A PHE* 3.7 10.8 - - - +
274A GLY 3.3 1.3 + - - +
276A ASP* 1.3 75.9 - - - +
278A PHE* 1.3 63.2 + - - +
280A LYS* 3.3 36.2 + - - +
281A SER* 4.2 3.5 + - - -
412A LEU* 3.6 40.1 - - + +
414A TYR* 3.1 24.0 + - + +
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Residues in contact with PHE 278 (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* 3.5 34.2 - - + +
253A MSE 3.9 26.7 - - + -
268A ALA* 3.6 24.0 - - + -
269A LEU 4.2 9.6 - - - -
270A THR* 3.3 52.0 - - + +
274A GLY 3.5 2.2 + - - -
275A THR 3.2 4.7 + - - +
277A ASP* 1.3 79.7 - - - +
279A LEU* 1.3 69.6 + - + +
281A SER* 3.2 19.8 + - - -
282A PHE* 3.4 43.4 + + + +
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Residues in contact with LEU 279 (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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270A THR* 5.4 0.4 - - + -
275A THR* 2.9 34.9 + - + +
276A ASP* 3.8 9.4 - - - +
277A ASP 3.3 0.6 - - - -
278A PHE* 1.3 83.2 - - + +
280A LYS* 1.3 64.2 + - - +
281A SER 3.1 1.0 + - - -
282A PHE* 3.1 26.0 + - + +
306A LYS* 4.3 21.1 - - + -
307A ILE* 4.2 17.3 - - + -
310A HIS* 3.7 58.6 - - + +
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Residues in contact with LYS 280 (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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246A LEU* 5.6 7.7 - - - +
276A ASP 3.4 16.3 + - - +
277A ASP* 3.3 26.6 + - - +
278A PHE 3.2 1.4 + - - -
279A LEU* 1.3 75.8 - - - +
281A SER* 1.3 57.9 + - - +
283A ARG* 3.6 24.6 + - - -
412A LEU* 4.3 17.7 + - - +
413A GLY* 5.8 0.6 - - - -
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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