Contacts of the helix formed by residues 252 - 262 (chain B) in PDB entry 1CKJ
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 GLU 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B PRO* 2.7 24.4 + - - +
251B SER* 1.3 82.8 + - - +
253B PHE* 1.3 56.6 + - + +
255B THR* 3.2 9.9 + - - -
256B TYR* 2.8 30.2 + - - +
277B LEU* 3.8 42.6 - - + +
278B PHE* 4.2 14.8 - - + -
280B ASN* 5.3 1.7 - - - +
281B LEU* 3.9 24.0 + - + +
284B ARG* 3.2 28.7 + - - -
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Residues in contact with PHE 253 (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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105B LEU* 4.2 17.7 - - + -
108B VAL* 4.6 8.1 - - + -
109B LEU* 4.2 8.1 - - + -
112B ALA* 5.9 0.4 - - + -
208B LEU* 4.3 21.3 - - + -
209B MET* 3.7 26.0 - - + -
212B ASN* 3.5 28.3 - - - -
246B CYS* 4.3 7.2 - - + -
249B TYR* 4.4 4.3 - - + -
250B PRO* 3.0 47.5 + - + +
252B GLU* 1.3 74.6 - - - +
254B ALA* 1.3 62.9 + - - +
256B TYR* 3.1 8.3 + - + +
257B LEU* 3.0 26.9 + - - +
278B PHE* 3.5 28.0 - + - -
281B LEU* 4.2 7.9 - - + -
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Residues in contact with ALA 254 (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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242B ILE* 4.0 9.8 - - + +
243B GLU* 4.3 19.7 - - - +
246B CYS* 3.7 29.3 - - + +
251B SER* 2.7 19.3 + - - +
253B PHE* 1.3 74.8 - - - +
255B THR* 1.3 62.4 + - - +
257B LEU* 3.5 1.2 + - - +
258B ASN* 3.0 31.9 + - - +
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Residues in contact with THR 255 (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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251B SER* 2.8 23.2 + - - -
252B GLU* 3.3 13.1 + - - -
254B ALA* 1.3 78.2 - - - +
256B TYR* 1.3 56.4 + - - +
258B ASN* 3.6 6.4 - - - +
259B PHE* 3.0 31.5 + - + +
273B TYR* 4.2 15.0 - - + +
277B LEU* 4.0 23.6 - - + +
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Residues in contact with TYR 256 (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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116B ILE* 3.8 21.9 - - + +
201B LEU* 2.8 44.6 + - + +
202B GLU* 4.8 0.7 - - - -
204B LEU* 3.7 17.5 - - + +
205B GLY* 3.7 21.8 - - - -
208B LEU* 5.0 4.5 - - + -
252B GLU 2.8 13.8 + - - +
253B PHE* 3.3 12.3 - - - +
255B THR* 1.3 73.6 - - - +
257B LEU* 1.3 73.1 + - + +
259B PHE* 3.1 4.2 + - - +
260B CYS* 3.0 38.4 + - - -
274B LEU* 3.8 29.2 - - + -
277B LEU* 4.4 7.4 - - + -
278B PHE* 3.6 24.9 - + + -
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Residues in contact with LEU 257 (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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202B GLU* 3.6 35.2 - - + +
205B GLY* 3.8 15.5 - - - +
206B TYR* 3.7 24.5 - - + +
209B MET* 4.5 11.7 - - + -
242B ILE* 3.9 25.1 - - + -
245B LEU* 3.9 27.6 - - + -
246B CYS* 4.4 5.8 - - - -
253B PHE 3.0 13.7 + - - +
256B TYR* 1.3 80.7 - - + +
258B ASN* 1.3 56.6 + - - +
260B CYS* 3.2 3.3 + - - +
261B ARG* 2.8 38.8 + - - +
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Residues in contact with ASN 258 (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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242B ILE* 4.0 22.2 - - - +
243B GLU* 4.2 22.5 + - - +
254B ALA 3.0 28.2 + - - +
255B THR* 3.6 7.0 - - - +
257B LEU* 1.3 75.7 - - - +
259B PHE* 1.3 64.3 + - - +
261B ARG* 3.2 13.1 + - - +
262B SER* 3.0 16.6 + - - -
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Residues in contact with PHE 259 (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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255B THR* 3.0 20.3 + - + +
256B TYR 3.1 4.2 + - - +
258B ASN* 1.3 75.1 - - - +
260B CYS* 1.3 62.7 + - - +
262B SER* 2.6 22.5 + - - -
263B LEU* 3.4 45.6 + - + +
270B ASP* 4.3 22.7 - - + -
273B TYR* 3.7 34.5 - + + -
274B LEU* 3.7 37.0 - - + -
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Residues in contact with CYS 260 (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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188B ASN* 5.8 0.7 + - - -
198B ARG* 4.2 14.2 - - - +
201B LEU* 4.0 15.5 - - - -
202B GLU* 4.1 25.1 - - + +
256B TYR* 3.0 51.6 + - - -
257B LEU* 3.5 6.7 - - - +
259B PHE* 1.3 78.9 - - - +
261B ARG* 1.3 58.1 + - - +
262B SER 3.0 5.1 + - - -
263B LEU* 3.5 25.3 + - + +
274B LEU* 4.4 11.4 - - - -
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Residues in contact with ARG 261 (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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187B ILE* 3.6 28.6 - - - +
188B ASN* 5.9 3.1 - - - +
202B GLU* 3.5 25.3 + - + +
206B TYR* 2.7 40.9 + - - -
218B TRP* 5.6 1.2 - - - -
237B LYS* 5.0 6.3 + - - +
240B THR 4.9 9.3 + - - -
242B ILE* 3.3 37.9 - - + +
245B LEU* 4.8 6.9 - - - +
257B LEU* 2.8 26.0 + - - +
258B ASN* 3.2 6.7 + - - +
260B CYS* 1.3 70.4 - - - +
262B SER* 1.3 58.0 + - - +
263B LEU 5.1 1.1 - - - -
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Residues in contact with SER 262 (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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258B ASN 3.0 11.1 + - - -
259B PHE* 2.6 26.3 + - - -
261B ARG* 1.3 79.6 - - - +
263B LEU* 1.3 68.5 + - - +
264B ARG* 3.4 7.4 + - - +
267B ASP* 4.8 0.3 - - - +
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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