Contacts of the helix formed by residues 269 - 280 (chain A) in PDB entry 1A9Z
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 VAL 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.9 30.1 - - + -
215A LEU* 4.4 4.3 - - + -
217A ILE* 3.9 31.0 - - + -
218A PHE 6.1 0.4 - - - +
228A THR* 3.2 12.2 + - - +
229A GLY 3.0 26.3 + - - +
268A SER* 1.3 75.0 - - - +
270A LEU* 1.3 61.8 + - - +
272A VAL* 3.1 4.9 + - - +
273A VAL* 3.0 22.4 + - + +
341A UPG 3.8 34.1 - - - +
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Residues in contact with LEU 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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217A ILE* 3.8 23.6 - - + -
226A ASP* 3.2 36.1 - - + +
228A THR* 3.6 15.9 + - + -
268A SER* 3.2 1.2 + - - -
269A VAL* 1.3 73.2 - - - +
271A ASP* 1.3 67.1 + - - +
273A VAL* 3.2 6.0 + - + +
274A ASN* 2.9 38.5 + - - +
286A TYR* 3.9 28.5 - - + +
288A PHE* 4.5 9.2 - - + -
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 4.4 3.5 - - - +
266A GLY 5.0 0.2 - - - +
267A ASN* 3.7 26.4 + - + +
268A SER* 3.0 38.7 + - - +
270A LEU* 1.3 78.2 - - - +
272A VAL* 1.3 62.8 + - - +
274A ASN* 3.5 7.5 + - - +
275A ALA* 3.0 23.0 + - - +
318A LEU* 4.1 5.8 - - + +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 4.1 14.1 - - + -
201A MET* 3.9 34.1 - - + -
204A ILE* 3.9 14.4 - - + -
233A TYR* 3.6 36.1 - - + -
267A ASN* 4.5 3.6 - - + -
268A SER 3.4 13.7 - - - +
269A VAL 3.1 7.4 + - - +
271A ASP* 1.3 72.1 - - - +
273A VAL* 1.3 65.0 + - - +
275A ALA* 3.1 8.0 + - + +
276A PHE* 2.9 21.8 + - - +
318A LEU* 4.4 12.3 - - + -
322A ALA* 5.1 1.3 - - + +
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Residues in contact with VAL 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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204A ILE* 4.1 14.6 - - + -
215A LEU* 3.6 31.0 - - + -
217A ILE* 5.0 2.5 - - + -
269A VAL* 3.0 17.3 + - + +
270A LEU* 3.4 11.4 - - + +
272A VAL* 1.3 72.8 - - - +
274A ASN* 1.3 64.7 + - - +
276A PHE* 2.9 6.7 + - - +
277A SER* 2.8 38.4 + - - +
284A VAL* 4.2 17.3 - - + +
286A TYR* 3.8 29.6 - - + -
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Residues in contact with ASN 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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270A LEU* 2.9 29.6 + - - +
271A ASP* 3.7 8.0 - - - +
273A VAL* 1.3 89.0 - - - +
275A ALA* 1.3 61.7 + - - +
277A SER* 3.3 10.0 + - - -
278A LYS* 3.1 24.6 + - - +
286A TYR* 5.2 6.9 + - - -
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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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271A ASP 3.0 14.4 + - - +
272A VAL* 3.1 8.9 + - + +
274A ASN* 1.3 76.3 - - - +
276A PHE* 1.3 58.5 + - - +
278A LYS* 3.5 6.4 - - - +
279A ALA* 3.0 25.8 + - - +
318A LEU* 3.9 24.2 - - + +
319A ASP* 3.6 24.0 - - - +
322A ALA* 3.7 14.1 - - + +
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Residues in contact with PHE 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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201A MET* 3.9 19.1 - - - -
204A ILE* 3.3 31.4 - - + -
205A ALA* 3.6 23.3 - - + -
208A ALA* 3.6 23.1 - - + -
272A VAL 2.9 12.7 + - - +
273A VAL 2.9 7.4 + - - +
275A ALA* 1.3 76.1 - - - +
277A SER* 1.3 56.9 + - - +
279A ALA* 3.0 1.5 + - - -
280A CYS* 2.8 42.4 + - + -
284A VAL* 4.1 4.7 - - + -
322A ALA* 3.9 18.8 - - + +
325A THR* 3.8 22.9 - - + -
326A TRP* 3.9 30.5 - + + -
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Residues in contact with SER 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 VAL* 2.8 21.9 + - - +
274A ASN* 3.4 16.0 + - - -
276A PHE* 1.3 71.0 - - - +
278A LYS* 1.3 56.4 + - - +
281A GLY* 3.0 26.7 + - - -
282A LYS 3.2 24.8 + - - +
283A PRO* 3.8 6.5 - - - +
284A VAL* 3.0 27.8 + - - +
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Residues in contact with LYS 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 ASN 3.1 14.0 + - - +
275A ALA* 3.5 7.2 - - - +
277A SER* 1.3 81.9 - - - +
279A ALA* 1.3 63.2 + - - +
280A CYS 3.4 0.2 + - - -
281A GLY* 3.5 8.7 + - - -
319A ASP* 3.2 37.5 + - - +
323A GLN* 5.4 4.5 - - - +
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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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275A ALA 3.0 17.9 + - - +
276A PHE* 3.0 6.1 + - - +
278A LYS* 1.3 79.4 - - - +
280A CYS* 1.3 58.0 + - - +
281A GLY 3.6 0.3 + - - -
322A ALA* 4.0 7.9 - - + +
323A GLN* 3.8 44.7 - - + +
326A TRP* 3.5 17.8 - - + -
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Residues in contact with CYS 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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208A ALA* 4.1 8.3 - - - -
276A PHE* 2.8 40.2 + - + +
277A SER* 4.1 1.3 - - - -
279A ALA* 1.3 73.1 - - - +
281A GLY* 1.3 54.6 + - - +
282A LYS* 3.2 56.7 + - - -
284A VAL* 4.2 2.7 - - - -
326A TRP* 3.6 42.3 + - + +
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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