Contacts of the helix formed by residues 252 - 263 (chain B) in PDB entry 1ZKK
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 ILE 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B GLU* 1.3 74.3 - - + +
253B THR* 1.3 67.4 + - - +
255B ALA* 3.3 6.5 + - - +
256B LYS* 2.9 58.5 + - + +
274B TYR* 4.5 9.2 - - + -
281B THR* 3.2 52.5 + - + +
282B TYR* 4.3 2.0 - - - +
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Residues in contact with THR 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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251B GLU* 3.3 3.6 - - - +
252B ILE* 1.3 84.8 - - - +
254B ASP* 1.3 62.1 + - - +
256B LYS* 3.4 6.4 + - - +
257B LYS* 3.1 36.6 + - + +
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Residues in contact with ASP 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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250B ILE* 3.5 22.8 - - - +
251B GLU* 3.2 17.5 + - + +
253B THR* 1.3 77.0 - - - +
255B ALA* 1.3 59.4 + - - +
257B LYS* 3.3 10.8 + - - +
258B ARG* 2.9 48.5 + - - +
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Residues in contact with ALA 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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250B ILE* 3.6 14.1 - - + +
251B GLU 2.8 20.5 + - - +
252B ILE* 3.3 3.6 + - - +
254B ASP* 1.3 73.6 - - - +
256B LYS* 1.3 56.4 + - - +
258B ARG* 3.2 1.3 + - - -
259B GLU* 2.8 30.8 + - - +
272B MET* 3.5 7.0 - - + +
274B TYR* 3.5 31.8 + - + +
283B CYS* 3.6 19.1 - - + -
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Residues in contact with LYS 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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252B ILE* 2.9 45.9 + - + +
253B THR* 3.9 6.5 - - - +
255B ALA* 1.3 75.5 - - - +
257B LYS* 1.3 58.0 + - + +
259B GLU* 3.5 4.3 + - - +
260B ALA* 3.1 28.2 + - - +
274B TYR* 4.0 13.6 - - - +
19F ARG* 3.2 36.7 - - - +
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Residues in contact with LYS 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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253B THR* 3.1 27.9 + - + +
254B ASP* 3.6 11.7 - - - +
255B ALA 3.2 0.2 - - - -
256B LYS* 1.3 75.0 - - + +
258B ARG* 1.3 65.2 + - + +
260B ALA* 3.4 7.5 + - - +
261B LEU* 3.3 29.3 + - + +
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Residues in contact with ARG 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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248B ASP* 3.4 28.3 + - - +
250B ILE* 3.6 30.4 - - - +
254B ASP* 2.9 33.3 + - - +
255B ALA 3.5 7.6 - - - +
257B LYS* 1.3 75.3 - - - +
259B GLU* 1.3 59.1 + - - +
261B LEU* 3.2 13.4 + - + +
262B TYR* 2.9 49.7 + - + -
272B MET* 4.3 1.3 - - + -
285B ASP* 3.0 33.4 + - - +
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Residues in contact with GLU 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 ALA 2.8 15.9 + - - +
256B LYS* 3.9 5.6 - - - +
257B LYS 3.2 0.4 - - - -
258B ARG* 1.3 77.6 - - - +
260B ALA* 1.3 55.0 + - - +
262B TYR* 3.2 9.3 + - - +
263B ALA* 2.8 30.1 + - + +
272B MET* 3.8 14.1 - - - +
274B TYR* 2.7 27.3 + - - +
17F ARG* 3.0 39.0 + - - +
18F HIS 4.2 0.3 - - - +
19F ARG* 3.0 41.6 + - - +
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Residues in contact with ALA 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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256B LYS 3.1 17.6 + - - +
257B LYS* 3.8 7.4 - - - +
258B ARG 3.3 0.2 - - - -
259B GLU* 1.3 76.2 - - - +
261B LEU* 1.3 60.3 + - + +
263B ALA* 3.7 12.2 + - - +
264B GLN* 3.4 22.3 + - - +
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Residues in contact with LEU 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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257B LYS* 3.3 18.8 + - + +
258B ARG* 3.2 10.7 + - - +
259B GLU 3.2 0.6 - - - -
260B ALA* 1.3 74.4 - - + +
262B TYR* 1.3 66.9 + - + +
263B ALA 3.1 1.3 - - - -
264B GLN* 3.1 41.7 + - - +
265B ASP* 4.0 3.6 + - - +
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Residues in contact with TYR 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 ARG* 2.9 35.4 + - + -
259B GLU* 3.2 6.5 + - - +
261B LEU* 1.3 78.5 - - + +
263B ALA* 1.3 56.8 + - - +
264B GLN 3.1 0.2 - - - -
265B ASP* 2.9 32.7 + - - +
268B THR* 3.2 22.7 + - + -
272B MET* 3.7 25.6 - - - -
285B ASP* 2.6 28.7 + - - -
287B THR* 3.4 33.3 + - + -
17F ARG* 3.6 23.7 + - - +
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Residues in contact with ALA 263 (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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259B GLU* 2.8 16.8 + - + +
260B ALA* 3.8 11.7 - - - +
261B LEU 3.1 0.4 - - - -
262B TYR* 1.3 75.9 - - - +
264B GLN* 1.3 61.1 + - + +
265B ASP 3.2 3.9 + - - -
266B PRO* 4.7 5.0 - - - +
17F ARG* 3.9 21.3 - - + +
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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