Contacts of the helix formed by residues 272 - 282 (chain A) in PDB entry 6V99
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.7 43.7 - - - +
26A LEU* 3.8 6.0 - - - +
270A VAL 4.1 0.2 - - - +
271A GLY* 1.3 81.2 - - - +
273A ILE* 1.3 59.6 + - - +
274A ASP* 3.5 9.2 + - - +
275A ALA* 3.1 22.5 + - + +
276A TYR* 2.9 29.1 + - - +
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Residues in contact with ILE 273 (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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25A ARG 4.2 7.6 + - - +
26A LEU* 3.9 27.3 - - + +
27A LYS* 4.2 8.7 - - + -
29A LEU* 5.4 6.3 - - + -
272A THR* 1.3 73.8 - - - +
274A ASP* 1.3 57.9 + - - +
276A TYR* 3.3 7.6 + - + +
277A TRP* 2.8 28.9 + - - +
376A VAL* 4.9 7.6 - - + -
401A ARG* 3.6 35.9 - - + -
403A THR* 5.2 9.6 - - - -
407A ILE* 4.3 26.2 - - + +
409A LEU* 4.3 20.6 - - + -
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Residues in contact with ASP 274 (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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272A THR* 3.3 7.9 + - - +
273A ILE* 1.3 79.2 - - - +
275A ALA* 1.3 52.0 + - - +
277A TRP* 3.3 7.7 + - + +
278A GLN* 2.7 36.8 + - - +
403A THR* 2.9 40.6 + - - +
404A GLU* 5.5 0.5 - - - +
405A SER* 2.9 25.9 + - - -
407A ILE* 3.2 15.8 - - - +
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Residues in contact with ALA 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 VAL* 3.8 20.5 - - + +
271A GLY 4.3 1.6 - - - +
272A THR* 3.1 22.7 + - + +
274A ASP* 1.3 78.1 - - - +
276A TYR* 1.3 58.2 + - - +
278A GLN* 3.3 6.0 + - - +
279A ALA* 2.8 32.7 + - - +
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Residues in contact with TYR 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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26A LEU* 4.3 11.2 - - + -
29A LEU* 3.8 24.0 - - + -
38A VAL* 3.3 22.7 - - + +
39A TYR 2.7 30.2 + - - -
40A PHE* 4.8 4.5 - + - -
46A ILE* 5.0 1.6 - - + -
270A VAL* 3.7 30.4 - - + +
272A THR 2.9 16.5 + - - +
273A ILE* 3.6 5.6 - - + +
275A ALA* 1.3 77.5 - - - +
277A TRP* 1.3 64.6 + - - +
279A ALA* 3.9 1.4 - - - +
280A ASN* 2.9 47.7 + - - +
344A PHE* 4.4 1.6 - - - -
359A VAL* 4.3 6.5 - - + -
361A LEU* 3.6 23.6 - - + +
376A VAL* 3.8 25.1 - - + -
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Residues in contact with TRP 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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273A ILE 2.8 17.0 + - - +
274A ASP* 3.7 6.7 - - + +
276A TYR* 1.3 78.3 - - - +
278A GLN* 1.3 105.9 + - + +
280A ASN* 3.3 2.9 + - - +
281A ILE* 2.9 50.7 + - + +
357A ASN* 2.9 37.8 + - + -
359A VAL* 3.8 12.3 - - + +
374A ASN* 3.6 24.2 - - - -
375A VAL 3.6 17.5 + - - -
376A VAL* 3.6 22.4 - - + -
407A ILE* 3.4 34.9 - - + +
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Residues in contact with GLN 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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274A ASP 2.7 22.1 + - - +
275A ALA* 3.7 6.3 - - - +
277A TRP* 1.3 96.7 - - - +
279A ALA* 1.3 63.0 + - - +
281A ILE* 3.7 10.5 - - - +
282A ASP* 2.8 62.6 + - - +
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Residues in contact with ALA 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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40A PHE* 3.6 19.1 - - + -
266A TYR* 4.2 12.3 + - - +
268A ARG* 4.9 13.5 - - + +
270A VAL* 3.6 22.7 - - + -
275A ALA 2.8 21.0 + - - +
276A TYR 3.9 0.9 - - - +
278A GLN* 1.3 74.4 - - - +
280A ASN* 1.3 63.3 + - - +
282A ASP* 3.8 10.9 + - - +
283A LEU* 3.7 16.1 + - - +
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Residues in contact with ASN 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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40A PHE* 3.5 18.8 - - - +
41A GLY* 2.9 36.0 - - - +
276A TYR* 2.9 37.6 + - - +
279A ALA* 1.3 75.8 - - - +
281A ILE* 1.3 65.8 + - - +
283A LEU* 3.1 23.5 + - - +
284A THR 4.3 0.5 + - - -
342A LEU* 3.5 15.5 - - + +
344A PHE* 3.8 12.7 - - - -
359A VAL* 3.6 30.5 - - + -
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Residues in contact with ILE 281 (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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277A TRP* 2.9 38.9 + - + +
278A GLN* 3.5 21.1 - - - +
280A ASN* 1.3 76.9 - - - +
282A ASP* 1.3 68.4 + - - +
284A THR* 2.8 35.9 + - + +
285A ASP 4.3 0.3 + - - -
340A ARG* 3.2 33.6 + - + +
341A SER* 4.3 2.0 - - - -
342A LEU* 4.6 2.9 - - - +
357A ASN* 3.6 26.2 - - - +
358A ALA 3.7 7.0 - - - +
359A VAL* 3.8 17.3 - - + -
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Residues in contact with ASP 282 (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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268A ARG* 5.5 4.2 + - - -
278A GLN* 2.8 58.2 + - - +
279A ALA* 4.0 8.1 - - - +
280A ASN 3.2 0.4 - - - -
281A ILE* 1.3 77.1 - - - +
283A LEU* 1.3 62.3 + - + +
284A THR 3.1 0.2 - - - -
285A ASP* 3.1 38.6 + - - +
288A PRO* 3.7 8.0 - - - +
289A ASP* 4.3 18.5 - - + +
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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