Contacts of the helix formed by residues 271 - 277 (chain D) in PDB entry 1VI9
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 271 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D GLU 4.1 2.9 - - - +
254D ILE* 3.8 33.4 - - + +
257D THR* 3.9 14.1 - - - +
267D GLN 3.2 16.4 + - - +
268D VAL 3.8 2.2 - - - +
269D VAL 3.1 1.0 - - - -
270D ALA* 1.3 74.8 - - - +
272D GLN* 1.3 65.2 + - - +
273D ASP 3.3 2.5 - - - -
274D ARG* 2.9 28.0 + - + +
275D ILE* 3.1 11.3 + - + +
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Residues in contact with GLN 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ARG 3.1 22.6 + - - -
28C ARG* 3.2 32.6 + - - +
30C GLY* 3.9 7.7 - - - +
24D PHE* 3.5 23.0 - - + -
28D ARG* 3.0 32.6 + - - +
268D VAL 3.3 6.4 + - - +
269D VAL* 3.1 24.2 + - - +
270D ALA 3.3 1.9 - - - +
271D ALA* 1.3 77.8 - - - +
273D ASP* 1.3 77.1 + - - +
275D ILE* 3.2 18.3 + - - +
276D ALA 3.4 8.7 + - - -
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Residues in contact with ASP 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 4.4 4.2 + - - -
28D ARG* 2.8 20.6 + - - +
270D ALA 5.2 0.8 + - - -
271D ALA 3.1 1.2 + - - -
272D GLN* 1.3 88.5 - - - +
274D ARG* 1.3 67.8 + - + +
275D ILE 3.2 0.4 - - - -
276D ALA 3.6 0.3 + - - -
277D LYS* 2.9 52.4 + - - +
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D ALA* 4.1 0.3 - - - -
253D GLU* 3.5 41.7 + - + +
256D VAL* 5.7 1.2 - - - +
257D THR* 2.9 31.1 + - - +
270D ALA 3.7 21.0 + - - -
271D ALA* 2.9 15.1 + - - +
273D ASP* 1.3 85.2 - - + +
275D ILE* 1.3 60.6 + - - +
277D LYS 3.6 11.2 - - - +
278D PRO* 3.1 29.2 - - - +
279D GLU* 3.7 30.5 - - + +
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Residues in contact with ILE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 5.4 0.9 - - + -
25D PRO* 4.1 31.4 - - + +
28D ARG* 4.8 5.2 - - + -
29D LEU* 3.6 14.4 - - + +
229D LEU* 4.3 11.2 - - + -
246D HIS* 2.8 27.9 + - - -
250D ALA* 3.7 18.7 - - + +
254D ILE* 3.6 35.0 - - + -
268D VAL 3.4 25.6 - - - +
271D ALA* 3.1 7.8 + - + +
272D GLN* 3.2 14.6 + - + +
274D ARG* 1.3 79.2 - - - +
276D ALA* 1.3 60.8 + - - +
278D PRO* 3.8 0.3 - - - +
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.6 35.2 - - + +
29D LEU* 3.7 12.8 - - + -
246D HIS* 3.5 16.1 + - - -
272D GLN 3.4 2.2 + - - -
273D ASP 3.7 0.9 - - - +
275D ILE* 1.3 84.2 - - - +
277D LYS* 1.3 82.1 + - + +
278D PRO* 3.7 1.3 - - - +
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.5 24.5 - - - +
273D ASP* 2.9 49.2 + - - +
274D ARG* 3.6 10.5 - - - +
276D ALA* 1.3 88.4 - - + +
278D PRO* 1.3 72.4 - - - +
279D GLU* 3.6 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