Contacts of the helix formed by residues 268 - 276 (chain A) in PDB entry 5UAK
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 ASN 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A GLU* 3.4 13.9 + - - +
265A MET 3.3 7.0 + - - +
267A GLU* 1.3 87.9 - - - +
269A ILE* 1.3 60.6 + - - +
270A GLN* 3.4 2.9 - - - +
271A SER* 2.7 31.0 + - - +
272A VAL* 3.5 13.5 - - - +
1292A LYS* 4.2 24.7 - - - +
1293A VAL 5.0 3.8 + - - -
1294A PHE* 3.5 30.8 - - + +
1295A ILE 5.3 0.8 - - - +
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Residues in contact with ILE 269 (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 MET* 3.4 23.6 - - - +
266A ILE* 3.2 35.0 - - + +
267A GLU 3.6 2.8 + - - -
268A ASN* 1.3 73.7 - - - +
270A GLN* 1.3 56.1 + - - +
272A VAL* 3.1 9.0 + - + +
273A LYS* 2.8 64.0 + - + +
956A VAL* 5.8 3.8 - - + +
957A LEU* 5.6 10.8 - - + -
961A MET* 4.8 9.9 - - + -
964A LEU* 3.7 31.4 - - + -
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 3.4 1.3 - - - +
269A ILE* 1.3 76.5 - - - +
271A SER* 1.3 56.9 + - - +
273A LYS* 3.7 8.7 - - - +
274A ALA* 2.8 29.2 + - - +
961A MET* 3.4 35.8 - - + +
965A ASN* 5.8 0.9 + - - -
1255A SER* 4.5 9.7 + - - -
1260A LEU* 3.7 35.7 - - + +
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 2.7 36.7 + - - +
270A GLN* 1.3 76.4 - - - +
272A VAL* 1.3 55.0 + - - +
274A ALA* 3.5 6.5 - - - +
275A TYR* 2.8 53.0 + - - -
277A TRP* 5.0 0.4 - - - -
1290A PRO* 6.1 4.5 - - - -
1294A PHE* 3.6 25.8 - - - -
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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
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265A MET* 4.1 15.5 - - + -
268A ASN 3.5 13.5 - - - +
269A ILE* 3.1 11.1 + - + +
271A SER* 1.3 83.8 + - - +
273A LYS* 1.3 54.8 + - + +
276A CYS* 2.8 27.0 + - - -
277A TRP* 3.0 51.9 + - + +
278A GLU* 4.3 3.3 - - - +
281A MET* 3.9 20.9 - - - -
957A LEU* 4.1 20.0 - - + -
1294A PHE* 4.3 11.9 - - + -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 2.8 37.9 + - + +
270A GLN 3.7 4.5 - - - +
272A VAL* 1.3 75.3 - - + +
274A ALA* 1.3 63.1 + - - +
276A CYS* 3.2 12.9 + - - +
278A GLU* 4.7 10.3 - - - +
957A LEU* 6.1 3.6 - - + +
958A GLN 5.6 4.3 - - - +
959A ALA* 3.7 26.5 + - - +
960A PRO 4.6 0.4 - - - -
961A MET* 3.1 38.8 - - - +
964A LEU* 4.9 5.7 - - - +
1260A LEU* 3.8 25.8 - - + -
1283A ARG* 3.2 30.1 + - - +
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Residues in contact with ALA 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 GLN 2.8 22.1 + - - +
271A SER* 3.1 8.7 + - - +
273A LYS* 1.3 74.3 - - - +
275A TYR* 1.3 67.3 + - + +
1258A LEU* 3.5 29.7 - - + +
1260A LEU* 5.3 0.4 - - - +
1283A ARG* 3.6 32.7 - - - +
1288A VAL* 5.2 7.9 - - + -
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Residues in contact with TYR 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 SER* 2.8 39.6 + - - +
274A ALA* 1.3 77.7 - - + +
276A CYS* 1.3 71.7 + - - +
277A TRP* 3.3 48.4 + + + +
1284A LYS* 4.8 7.6 + - - +
1287A GLY* 6.1 1.3 - - - -
1288A VAL* 3.6 15.4 + - + -
1290A PRO* 4.9 4.7 - - + +
1293A VAL* 5.8 0.5 - - - +
1294A PHE* 5.1 3.6 - - + -
1307A TYR* 5.6 0.5 - - - -
1355A CYS* 2.9 33.8 - - - +
1358A ARG* 3.8 35.6 + - + -
1359A SER* 4.8 8.7 - - - -
1362A SER* 6.1 1.1 - - - -
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Residues in contact with CYS 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 VAL 2.8 13.1 + - - -
273A LYS 3.2 12.0 + - - +
274A ALA 4.6 2.0 - - - +
275A TYR* 1.3 82.3 - - - +
277A TRP* 1.3 61.4 + - - +
278A GLU* 3.7 11.2 - - - -
1280A GLN* 3.8 50.5 - - - +
1283A ARG* 5.3 2.5 - - + -
1284A LYS* 3.9 23.6 + - + +
1307A TYR* 3.0 24.3 + - - -
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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