Contacts of the helix formed by residues 252 - 263 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLU* 1.3 78.4 - - - +
253A THR* 1.3 70.6 + - - +
255A ALA* 3.7 6.9 - - + +
256A LYS* 2.9 59.6 + - + +
274A TYR* 5.7 0.2 - - + -
280A LYS* 5.2 2.0 - - - +
281A THR* 3.5 23.8 + - + +
222B LEU* 3.8 15.7 - - + +
223B ILE 3.8 2.9 - - - -
224B ASP* 3.5 58.3 - - + +
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Residues in contact with THR 253 (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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251A GLU* 3.0 18.7 + - - -
252A ILE* 1.3 83.7 - - - +
254A ASP* 1.3 58.2 + - - +
256A LYS* 3.8 5.8 - - - +
257A LYS* 3.0 30.1 + - + +
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Residues in contact with ASP 254 (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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250A ILE* 3.6 16.4 - - + +
251A GLU* 2.9 21.2 + - - +
253A THR* 1.3 73.8 - - - +
255A ALA* 1.3 61.9 + - - +
257A LYS* 3.3 18.4 + - - +
258A ARG* 2.9 66.5 + - - +
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Residues in contact with ALA 255 (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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250A ILE* 3.6 19.4 - - + +
251A GLU 3.0 18.9 + - - +
252A ILE* 3.2 8.3 + - + +
254A ASP* 1.3 76.4 - - - +
256A LYS* 1.3 56.7 + - - +
258A ARG 3.4 0.2 + - - -
259A GLU* 2.9 32.9 + - - +
272A MET* 3.6 4.9 - - + +
274A TYR* 3.8 31.6 - - + +
283A CYS* 4.0 8.7 - - + -
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Residues in contact with LYS 256 (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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252A ILE* 2.9 38.5 + - + +
253A THR* 3.8 6.1 - - - +
255A ALA* 1.3 72.8 - - - +
257A LYS* 1.3 65.9 + - - +
259A GLU* 3.6 9.5 - - - +
260A ALA* 3.1 24.4 + - - +
221B ASP* 3.0 30.4 + - - +
222B LEU* 2.7 45.6 + - + -
223B ILE* 5.4 0.6 - - - +
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Residues in contact with LYS 257 (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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253A THR* 3.0 20.2 + - + +
254A ASP* 3.5 17.5 + - - +
256A LYS* 1.3 78.2 - - - +
258A ARG* 1.3 62.0 + - + +
260A ALA* 3.3 6.4 + - - +
261A LEU* 3.2 38.9 + - + +
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Residues in contact with ARG 258 (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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248A ASP* 3.1 34.2 + - - +
250A ILE* 3.8 22.3 - - - +
254A ASP* 2.9 47.0 + - - +
255A ALA 3.8 3.4 - - - +
257A LYS* 1.3 75.5 - - + +
259A GLU* 1.3 60.1 + - - +
261A LEU* 3.1 12.6 + - + +
262A TYR* 2.8 56.6 + - + +
272A MET* 4.2 3.1 - - + -
285A ASP* 2.9 27.4 + - - +
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Residues in contact with GLU 259 (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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255A ALA 2.9 15.3 + - - +
256A LYS* 3.4 9.3 + - - +
258A ARG* 1.3 75.1 - - - +
260A ALA* 1.3 58.1 + - - +
262A TYR* 3.2 9.3 + - - +
263A ALA* 2.9 32.3 + - - +
272A MET* 3.6 14.0 - - - +
274A TYR* 2.7 34.1 + - - +
222B LEU* 4.4 3.5 - - - +
17E ARG* 4.5 11.4 + - - +
19E ARG* 2.9 44.5 + - - +
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Residues in contact with ALA 260 (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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256A LYS 3.1 13.8 + - - +
257A LYS* 3.6 7.2 - - - +
258A ARG 3.3 0.2 - - - -
259A GLU* 1.3 79.7 - - - +
261A LEU* 1.3 61.4 + - + +
263A ALA* 3.8 10.4 + - - +
264A GLN* 3.2 25.8 + - - +
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Residues in contact with LEU 261 (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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257A LYS* 3.2 36.9 + - + +
258A ARG* 3.1 12.9 + - + +
260A ALA* 1.3 77.8 - - + +
262A TYR* 1.3 70.4 + - + +
264A GLN* 3.2 34.8 + - - +
265A ASP* 3.8 6.1 + - - +
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Residues in contact with TYR 262 (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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258A ARG* 2.8 40.3 + - + +
259A GLU 3.7 2.2 - - - +
261A LEU* 1.3 76.8 - - + +
263A ALA* 1.3 58.1 + - - +
265A ASP* 2.9 32.9 + - - +
268A THR* 3.8 20.1 - - + -
272A MET* 3.7 25.6 - - - -
285A ASP* 2.7 26.5 + - - -
287A THR* 3.3 36.8 - - + +
17E ARG* 3.5 29.8 + - - +
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Residues in contact with ALA 263 (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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259A GLU 2.9 16.9 + - - +
260A ALA* 3.8 9.2 - - - +
261A LEU 3.2 0.2 - - - -
262A TYR* 1.3 75.5 - - - +
264A GLN* 1.3 60.3 + - + +
265A ASP 3.6 2.7 + - - -
266A PRO* 5.0 1.4 - - - +
17E ARG* 3.7 19.6 - - - +
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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