Contacts of the helix formed by residues 269 - 281 (chain A) in PDB entry 6O0Z
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLU* 5.6 1.1 - - - -
268A LYS* 1.3 77.7 - - - +
270A THR* 1.3 61.6 + - - +
271A TYR 3.2 3.1 + - - -
272A ASP* 3.9 11.6 + - - +
273A ASP* 4.6 2.4 + - - +
627A GLU 6.1 0.7 - - - +
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Residues in contact with THR 270 (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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265A GLN* 6.2 1.3 - - - -
268A LYS* 4.5 3.1 - - - +
269A ASP* 1.3 77.7 - - - +
271A TYR* 1.3 57.1 + - - +
272A ASP 3.4 0.9 - - - -
273A ASP* 3.5 9.4 + - - +
274A ASP* 2.9 41.0 + - - +
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Residues in contact with TYR 271 (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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243A ALA 5.4 4.8 + - - -
264A LEU* 3.7 21.1 - - + -
265A GLN* 3.2 37.6 - - + +
266A LEU 3.3 22.4 - - - +
267A SER* 5.2 4.0 - - - -
268A LYS* 3.9 13.2 + - + +
269A ASP 3.2 1.8 - - - -
270A THR* 1.3 76.5 - - - +
272A ASP* 1.3 62.9 + - + +
274A ASP* 3.7 3.3 - - + -
275A LEU* 2.9 42.0 + - + +
290A PHE* 4.7 18.4 + - - +
293A ALA* 5.8 3.3 - - - +
294A LYS* 6.3 3.1 - - + -
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Residues in contact with ASP 272 (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 LYS 4.8 1.0 + - - -
269A ASP 3.9 9.0 + - - +
270A THR 3.4 0.4 - - - -
271A TYR* 1.3 81.8 - - + +
273A ASP* 1.3 58.3 + - - +
275A LEU* 3.4 6.9 + - - +
276A ASP* 2.9 28.5 + - - +
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Residues in contact with ASP 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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269A ASP 4.6 2.5 + - - +
270A THR* 3.5 13.5 + - - +
272A ASP* 1.3 78.5 - - - +
274A ASP* 1.3 60.2 + - - +
276A ASP* 3.4 7.2 + - - +
277A ASN* 2.9 28.2 + - - +
653A ARG* 4.3 19.5 + - + -
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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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262A ALA* 5.1 6.6 - - - +
263A LYS 3.5 30.3 + - - +
264A LEU* 4.5 13.2 - - + +
265A GLN* 5.9 1.7 - - - +
270A THR* 2.9 33.0 + - - +
271A TYR* 3.8 6.5 - - - +
273A ASP* 1.3 76.4 - - - +
275A LEU* 1.3 58.0 + - - +
277A ASN* 3.4 8.4 + - - +
278A LEU* 2.9 29.1 + - - +
653A ARG* 5.2 5.5 - - - -
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Residues in contact with LEU 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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264A LEU* 6.2 0.9 - - - -
271A TYR* 2.9 36.6 + - + +
272A ASP* 3.8 6.5 - - - +
273A ASP 3.3 0.2 - - - -
274A ASP* 1.3 74.9 - - - +
276A ASP* 1.3 58.9 + - - +
278A LEU* 3.3 6.1 + - - +
279A LEU* 2.9 31.5 + - - +
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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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272A ASP 2.9 17.6 + - - +
273A ASP* 3.7 7.6 - - - +
275A LEU* 1.3 76.1 - - - +
277A ASN* 1.3 57.8 + - - +
279A LEU* 3.8 4.7 - - - +
280A ALA* 2.9 32.9 + - - +
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Residues in contact with ASN 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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262A ALA* 5.7 7.0 - - + -
273A ASP 2.9 17.4 + - - +
274A ASP* 3.7 9.4 - - - +
276A ASP* 1.3 77.5 - - - +
278A LEU* 1.3 60.1 + - - +
280A ALA* 3.9 3.8 - - - +
281A GLN* 3.2 29.5 + - - +
653A ARG* 3.8 38.1 - - - +
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Residues in contact with LEU 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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262A ALA* 5.0 17.2 - - + +
264A LEU* 6.4 1.6 - - + -
274A ASP 2.9 18.3 + - - +
275A LEU* 3.3 7.2 + - - +
277A ASN* 1.3 76.5 - - - +
279A LEU* 1.3 58.1 + - - +
281A GLN* 4.2 2.0 - - - -
282A ILE* 3.4 26.9 + - - +
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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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275A LEU 2.9 18.0 + - - +
276A ASP* 4.2 4.3 - - - +
278A LEU* 1.3 79.2 - - - +
280A ALA* 1.3 57.3 + - - +
281A GLN 3.3 1.1 - - - -
282A ILE 3.3 18.1 - - - +
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Residues in contact with ALA 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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276A ASP 2.9 20.7 + - - +
277A ASN* 3.5 3.3 + - - +
279A LEU* 1.3 75.3 - - - +
281A GLN* 1.3 57.5 + - - +
282A ILE 3.8 0.4 - - - -
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Residues in contact with GLN 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 ASN 3.2 17.6 + - - +
278A LEU* 5.1 1.3 - - - +
280A ALA* 1.3 79.6 - - - +
282A ILE* 1.3 58.0 + - - +
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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