Contacts of the helix formed by residues 267 - 272 (chain B) in PDB entry 3VI4
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 ASP 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TYR* 3.5 17.2 - - - +
254A LYS* 3.3 20.5 + - - +
284A TYR* 2.7 36.2 + - - -
175B TYR* 2.5 21.7 + - - +
263B HIS* 3.0 43.6 - - + -
264B PHE* 3.2 17.0 + - - +
266B GLY* 1.3 75.5 - - - +
268B GLY* 1.3 56.8 + - - +
269B LYS 3.1 2.5 - - - -
270B LEU* 3.0 17.5 + - - +
296B TYR* 3.8 5.6 - - + -
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Residues in contact with GLY 268 (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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175B TYR* 3.1 8.5 + - - -
266B GLY 3.3 0.2 - - - -
267B ASP* 1.3 79.1 - - - +
269B LYS* 1.3 51.0 + - - +
271B GLY* 2.7 25.3 + - - -
273B ILE* 2.7 33.3 + - - +
295B ASP* 3.0 24.9 + - - -
296B TYR* 3.9 7.0 - - - -
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Residues in contact with LYS 269 (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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21A PHE* 4.7 22.2 - - + -
118A LEU* 5.1 1.0 - - - +
168A PHE* 3.7 28.4 - - + -
233A TYR* 3.4 33.1 + - - +
287A TYR* 3.6 34.3 + - - +
266B GLY* 3.6 5.4 + - - +
268B GLY* 1.3 75.1 - - - +
270B LEU* 1.3 64.1 + - - +
272B GLY* 2.8 14.9 + - - +
273B ILE 2.8 13.8 + - - +
274B VAL* 4.7 16.8 - - + -
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Residues in contact with LEU 270 (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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118A LEU* 3.6 14.6 - - - +
165A GLN* 2.9 44.3 - - - +
168A PHE* 4.0 14.0 - - + -
183A PRO* 4.3 14.8 - - + -
188A TRP* 3.8 25.8 - - + +
230A TYR* 3.7 34.3 - - + +
233A TYR* 3.7 25.1 - - + -
174B PRO* 3.9 11.8 - - + +
175B TYR* 3.8 5.2 - - + +
267B ASP 3.0 14.6 + - - +
269B LYS* 1.3 78.0 - - - +
271B GLY* 1.3 55.7 + - - +
272B GLY 3.7 0.3 + - - -
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Residues in contact with GLY 271 (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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100A TRP* 5.3 0.7 + - - -
118A LEU* 4.0 11.2 - - - +
172B VAL* 5.2 4.0 - - - +
173B MET 3.4 24.6 - - - +
175B TYR* 3.2 11.2 + - - -
268B GLY 2.7 13.1 + - - -
270B LEU* 1.3 71.6 - - - +
272B GLY* 1.3 57.4 + - - -
273B ILE* 3.1 15.6 + - - +
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Residues in contact with GLY 272 (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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18A PHE* 5.1 1.6 - - - -
41A LYS* 5.0 2.1 + - - -
100A TRP* 3.6 45.7 - - - -
118A LEU* 3.9 4.4 - - - +
269B LYS* 2.8 14.8 + - - -
270B LEU 3.4 1.0 + - - -
271B GLY* 1.3 75.5 - - - +
273B ILE* 1.3 61.0 + - - +
274B VAL* 3.5 9.6 + - - +
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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