Contacts of the helix formed by residues 272 - 282 (chain B) in PDB entry 6V9A
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 THR 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 3.7 37.7 - - + +
26B LEU* 3.4 12.9 - - - +
270B VAL 3.8 0.2 - - - +
271B GLY* 1.3 79.4 - - - +
273B ILE* 1.3 59.9 + - - +
274B ASP* 3.5 9.2 + - - +
275B ALA* 3.0 23.8 + - + +
276B TYR 2.8 24.9 + - - -
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Residues in contact with ILE 273 (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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25B ARG 3.9 4.6 + - - +
26B LEU* 3.5 39.5 - - + +
27B LYS* 3.9 8.1 - - + -
29B LEU* 5.6 3.6 - - + -
272B THR* 1.3 73.7 - - - +
274B ASP* 1.3 57.4 + - - +
276B TYR* 3.8 3.9 - - + +
277B TRP* 3.0 28.9 + - - +
376B VAL* 4.7 8.7 - - + +
401B ARG* 3.8 29.2 - - + +
403B THR* 4.0 20.0 - - + -
407B ILE* 4.5 13.5 - - + +
409B LEU* 3.8 28.0 - - + +
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Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 3.1 8.8 + - - +
273B ILE* 1.3 78.6 - - - +
275B ALA* 1.3 57.6 + - - +
277B TRP* 3.9 5.6 - - - +
278B GLN* 2.9 31.2 + - - +
403B THR* 3.1 25.7 + - + +
404B GLU* 5.1 0.5 + - - +
405B SER* 2.6 33.6 + - - -
407B ILE* 3.5 12.5 - - - +
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Residues in contact with ALA 275 (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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269B ASP* 6.3 0.2 - - + -
270B VAL* 3.9 19.8 - - - +
271B GLY 4.1 1.6 - - - +
272B THR* 3.0 24.5 + - + +
274B ASP* 1.3 73.4 - - - +
276B TYR* 1.3 60.7 + - - +
278B GLN* 3.6 5.8 - - - +
279B ALA* 2.9 32.2 + - - +
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Residues in contact with TYR 276 (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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26B LEU* 4.2 11.0 - - + -
29B LEU* 3.9 23.6 - - + -
38B VAL* 3.5 20.8 - - + +
39B TYR* 2.8 32.3 + - - +
40B PHE* 5.0 2.0 - + - -
46B ILE* 4.9 3.6 - - + -
270B VAL* 4.0 28.0 - - + +
272B THR 2.8 17.0 + - - +
273B ILE* 3.8 5.2 - - - +
275B ALA* 1.3 74.5 - - - +
277B TRP* 1.3 67.7 + - - +
279B ALA* 3.2 1.4 + - - +
280B ASN* 3.1 48.4 + - - -
344B PHE* 4.6 1.9 - - - -
359B VAL* 4.3 7.2 - - + -
361B LEU* 3.7 19.9 - - + +
376B VAL* 4.0 26.2 - - + -
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Residues in contact with TRP 277 (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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273B ILE 3.0 15.4 + - - +
274B ASP* 3.9 4.5 - - - +
276B TYR* 1.3 80.5 - - - +
278B GLN* 1.3 105.7 + - + +
280B ASN* 3.8 0.5 - - - +
281B ILE* 2.9 39.7 + - + +
340B ARG* 4.4 13.2 - - - -
357B ASN* 2.9 42.1 + - + -
359B VAL* 4.0 12.8 - - + -
374B ASN* 3.5 23.6 - - - -
375B VAL 3.6 18.4 + - - +
376B VAL* 3.7 20.0 - - + -
407B ILE* 3.3 33.1 - - + +
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Residues in contact with GLN 278 (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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274B ASP 2.9 20.8 + - - +
275B ALA* 3.6 7.2 - - - +
277B TRP* 1.3 102.6 - - - +
279B ALA* 1.3 57.4 + - - +
281B ILE* 4.0 1.0 - - - +
282B ASP* 2.9 68.3 + - - +
340B ARG* 5.0 7.9 - - - +
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Residues in contact with ALA 279 (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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40B PHE* 4.0 15.1 - - + -
266B TYR* 4.0 17.2 + - - +
268B ARG* 4.5 14.4 - - - +
270B VAL* 3.9 20.0 - - + -
275B ALA 2.9 21.1 + - - +
276B TYR 3.8 2.7 - - - +
278B GLN* 1.3 73.8 - - - +
280B ASN* 1.3 61.9 + - - +
282B ASP* 3.8 15.9 - - - +
283B LEU* 3.9 11.6 - - - +
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Residues in contact with ASN 280 (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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40B PHE* 3.6 11.5 - - - -
41B GLY* 2.8 34.5 + - - +
276B TYR* 3.1 58.7 + - - +
279B ALA* 1.3 74.6 - - - +
281B ILE* 1.3 65.8 + - - +
283B LEU* 3.0 25.7 + - - +
284B THR 4.2 0.3 + - - -
342B LEU* 3.9 17.0 - - + +
344B PHE* 4.3 1.2 - - - -
359B VAL* 3.7 27.6 - - + -
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Residues in contact with ILE 281 (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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277B TRP* 2.9 50.9 + - + +
278B GLN* 4.1 2.5 - - - +
280B ASN* 1.3 72.5 - - - +
282B ASP* 1.3 58.8 + - - +
284B THR* 2.8 36.5 + - + -
285B ASP* 4.3 0.7 - - - +
340B ARG* 3.4 65.1 - - + +
341B SER* 4.3 3.8 - - - -
342B LEU 4.3 3.8 - - - +
357B ASN 3.9 7.4 - - - -
358B ALA 3.7 12.8 - - - +
359B VAL* 3.6 17.5 - - + -
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Residues in contact with ASP 282 (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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268B ARG* 5.6 3.8 + - - -
278B GLN* 2.9 56.1 + - - +
279B ALA* 3.8 10.8 - - - +
280B ASN 3.2 0.2 - - - -
281B ILE* 1.3 76.9 - - - +
283B LEU* 1.3 61.0 + - + +
285B ASP* 3.0 41.6 + - - +
288B PRO* 3.6 7.1 - - - +
289B ASP* 5.2 12.6 - - + +
340B ARG* 5.3 2.3 + - - -
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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