Contacts of the helix formed by residues 265 - 272 (chain B) in PDB entry 2CKE
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 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B GLU* 6.3 3.1 - - + -
200B MET* 4.2 4.7 - - - -
261B ARG 6.1 0.4 - - - +
263B ARG 4.6 4.3 - - - +
264B LEU* 1.3 75.6 - - - +
266B ILE* 1.3 68.3 + - - +
267B GLN* 3.8 7.6 + - - +
268B GLU* 2.8 48.7 + - - +
269B ALA* 2.9 10.0 + - - +
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Residues in contact with ILE 266 (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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124B LEU* 3.3 46.9 - - + +
127B VAL* 4.0 10.1 - - + -
128B ASN* 3.5 46.2 - - + +
131B HIS* 4.0 26.0 + - + +
200B MET* 3.6 28.7 - - + +
203B ILE* 4.4 0.4 - - + -
265B THR* 1.3 73.6 - - - +
267B GLN* 1.3 62.7 + - + +
269B ALA* 3.2 3.6 + - - +
270B LEU* 2.9 28.8 + - + +
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Residues in contact with GLN 267 (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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128B ASN* 3.0 34.4 + - - +
265B THR* 3.1 8.3 + - - +
266B ILE* 1.3 83.6 - - + +
268B GLU* 1.3 63.2 + - + +
270B LEU* 3.4 14.1 + - - +
271B ARG* 3.1 54.4 + - - +
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Residues in contact with GLU 268 (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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263B ARG 3.9 3.8 - - - +
264B LEU* 3.5 31.3 - - + +
265B THR* 2.8 45.7 + - - +
267B GLN* 1.3 76.9 - - + +
269B ALA* 1.3 57.6 + - - +
271B ARG* 3.4 25.1 + - - +
272B HIS* 3.0 27.5 + - - +
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Residues in contact with ALA 269 (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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124B LEU* 4.0 17.0 - - + -
200B MET* 3.8 22.0 - - + -
251B PHE* 3.9 13.1 - - + -
255B LEU* 4.8 0.7 - - + -
264B LEU* 4.2 15.8 - - + +
265B THR 2.9 10.2 + - - +
266B ILE 3.3 8.7 - - - +
268B GLU* 1.3 74.0 - - - +
270B LEU* 1.3 66.0 + - - +
271B ARG 3.2 0.9 + - - -
272B HIS* 3.2 11.8 + - - +
275B ILE* 3.4 17.7 - - - +
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Residues in contact with LEU 270 (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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121B LYS* 4.3 18.6 - - + +
124B LEU* 3.8 27.8 - - + +
125B ASP* 3.6 24.5 - - - +
128B ASN* 4.1 34.8 - - + +
266B ILE* 2.9 15.1 + - + +
267B GLN* 3.4 20.6 + - - +
269B ALA* 1.3 76.8 - - - +
271B ARG* 1.3 58.5 + - + +
275B ILE* 3.7 7.5 - - + +
276B THR* 2.7 28.6 + - - -
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Residues in contact with ARG 271 (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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267B GLN* 3.1 49.3 + - - +
268B GLU* 3.7 22.7 - - - +
269B ALA 3.1 0.8 - - - -
270B LEU* 1.3 78.7 - - + +
272B HIS* 1.3 68.0 + - - +
273B PRO* 3.5 3.6 - - - +
276B THR* 4.0 13.0 - - - +
278B VAL* 5.8 2.3 - - - +
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Residues in contact with HIS 272 (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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247B LEU* 3.4 27.1 - - + -
250B ASP* 2.8 29.0 + - + -
251B PHE* 3.6 29.9 + + + +
254B LYS* 4.2 18.6 - - + -
264B LEU* 4.7 7.6 - - + -
268B GLU 3.0 12.2 + - - +
269B ALA* 3.2 16.0 + - - +
271B ARG* 1.3 76.7 - - - +
273B PRO* 1.3 88.8 - - + +
274B TRP* 3.1 25.3 + - + +
275B ILE* 2.9 7.0 + - + -
276B THR 2.9 18.9 + - - -
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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