Contacts of the helix formed by residues 265 - 276 (chain B) in PDB entry 1CK4
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 ARG 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ALA* 3.8 10.1 + - + -
228B LEU* 3.7 41.6 - - - +
231B ASP* 3.8 21.6 + - - -
262B ASP* 2.9 25.6 + - - +
263B ASN 2.8 2.8 + - - -
264B TYR* 1.3 106.1 + - + +
266B LEU* 1.3 65.4 + - - +
267B LYS 3.5 1.8 - - - -
268B GLN* 3.2 12.1 + - + +
269B VAL* 2.9 35.8 + - + +
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Residues in contact with LEU 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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226B THR* 5.2 2.0 - - + -
227B ALA* 3.9 26.0 - - + +
230B ILE* 5.1 3.4 - - + -
260B SER* 4.2 6.5 - - - +
263B ASN* 2.8 21.0 + - - +
264B TYR 3.5 0.2 - - - -
265B ARG* 1.3 74.6 - - - +
267B LYS* 1.3 60.5 + - + +
269B VAL* 3.2 2.6 + - + -
270B ILE* 2.7 49.7 + - + +
302B GLU* 3.4 40.8 - - + +
305B SER* 4.6 9.0 - - - +
306B ILE* 4.1 26.9 - - + -
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN 5.3 5.2 - - - -
264B TYR* 4.8 19.3 + - - +
265B ARG 3.4 1.0 + - - -
266B LEU* 1.3 75.7 - - + +
268B GLN* 1.3 58.8 + - - +
270B ILE* 3.7 5.0 - - - +
271B GLN* 2.8 32.7 + - - +
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Residues in contact with GLN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR 5.6 0.4 + - - +
265B ARG* 3.2 12.2 + - + +
266B LEU 3.2 0.4 - - - -
267B LYS* 1.3 79.3 - - - +
269B VAL* 1.3 66.0 + - + +
271B GLN* 3.0 12.1 + - - +
272B ASP* 3.0 45.7 + - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ALA* 3.7 29.8 - - + +
230B ILE* 3.3 32.3 - - + -
231B ASP* 3.8 26.2 - - + +
234B ARG* 4.1 2.9 + - - +
265B ARG* 2.9 34.9 + - - +
266B LEU* 3.8 4.3 - - - +
268B GLN* 1.3 78.2 - - + +
270B ILE* 1.3 68.3 + - + +
272B ASP* 3.3 9.4 + - - +
273B CYS* 3.1 21.8 + - - -
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 4.5 9.6 - - + -
266B LEU* 2.7 34.9 + - + +
267B LYS* 3.8 4.9 - - - +
269B VAL* 1.3 86.2 - - + +
271B GLN* 1.3 60.4 + - - +
273B CYS* 3.2 6.6 + - - +
274B GLU* 2.9 26.4 + - + +
280B ARG* 3.9 28.6 + - - +
305B SER* 4.2 16.4 - - - +
306B ILE* 3.9 39.9 - - + -
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Residues in contact with GLN 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 LYS 2.8 19.9 + - - +
268B GLN* 3.0 13.4 + - - +
270B ILE* 1.3 75.6 - - - +
272B ASP* 1.3 66.4 + - - +
274B GLU* 3.3 14.9 + - - +
275B ASP* 3.1 50.7 + - - +
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Residues in contact with ASP 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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231B ASP* 4.7 0.3 - - - +
234B ARG* 3.1 42.4 + - - +
268B GLN* 3.0 39.4 + - - +
269B VAL* 3.6 3.8 - - - +
271B GLN* 1.3 76.6 - - - +
273B CYS* 1.3 64.1 + - - +
275B ASP* 3.4 12.1 + - - +
276B GLU* 3.2 26.4 + - - +
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Residues in contact with CYS 273 (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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230B ILE* 3.7 27.6 - - - -
234B ARG* 4.1 17.9 - - - +
252B MET* 4.1 16.8 - - - -
269B VAL* 3.1 18.1 + - - -
270B ILE* 3.4 9.4 - - - +
272B ASP* 1.3 78.2 - - - +
274B GLU* 1.3 61.8 + - - +
276B GLU* 3.1 3.6 + - - +
277B ASN 3.0 17.2 + - - -
278B ILE* 3.1 19.6 + - + +
280B ARG* 3.7 25.4 - - - +
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Residues in contact with GLU 274 (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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270B ILE* 2.9 13.5 + - + +
271B GLN* 3.4 26.7 - - - +
273B CYS* 1.3 77.1 - - - +
275B ASP* 1.3 59.0 + - - +
277B ASN* 2.9 31.3 + - - +
278B ILE 4.7 1.1 - - - +
280B ARG* 2.6 43.0 + - - +
308B SER* 4.6 2.9 + - - -
309B GLU* 5.9 2.6 + - - -
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Residues in contact with ASP 275 (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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263A ASN* 4.0 8.7 - - - +
264A TYR* 3.4 48.0 + - + +
271B GLN* 3.1 38.2 + - - +
272B ASP* 3.8 11.0 - - - +
274B GLU* 1.3 76.2 - - - +
276B GLU* 1.3 58.1 + - + +
277B ASN* 3.1 12.1 + - - +
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Residues in contact with GLU 276 (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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261A HIS 5.1 5.2 - - - +
263A ASN* 5.8 0.9 - - - -
264A TYR* 4.6 19.4 + - + -
234B ARG* 3.1 48.3 + - - +
238B PHE* 5.9 0.3 - - - +
250B LYS* 4.1 24.8 + - - +
272B ASP* 3.2 12.5 + - - +
273B CYS 3.1 6.0 + - - +
275B ASP* 1.3 77.0 - - + +
277B ASN* 1.3 71.8 + - - +
278B ILE* 3.4 15.7 + - + +
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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