Contacts of the helix formed by residues 293 - 297 (chain C) 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 LEU 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C GLU* 2.8 34.2 + - + +
218C MET* 3.7 45.3 - - + +
219C LYS* 4.7 2.0 - - - +
220C ILE* 3.5 36.8 - - + -
230C VAL* 3.6 21.1 - - + +
243C VAL* 4.8 0.4 - - + -
291C ASN 4.1 10.1 - - - +
292C ARG* 1.3 77.0 - - - +
294C GLY* 1.3 66.7 + - - +
295C ARG 3.2 2.5 - - - -
296C LEU* 2.9 23.9 + - + +
297C ILE* 3.6 2.6 + - - +
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Residues in contact with GLY 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C VAL* 3.9 18.6 - - - +
244C GLU 3.7 23.1 + - - -
245C TYR* 3.6 21.1 - - - -
246C HIS 5.1 0.8 - - - +
292C ARG* 3.7 2.4 - - - +
293C LEU* 1.3 76.9 - - - +
295C ARG* 1.3 60.6 + - - +
296C LEU 3.1 1.4 + - - -
297C ILE* 3.1 22.6 + - - +
320C LEU* 5.3 1.7 - - - +
334C TYR* 4.6 1.9 + - - -
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C TYR* 3.6 16.1 - - + +
246C HIS 4.7 8.1 + - - +
271C TYR* 3.5 25.7 - - + -
286C ALA* 2.8 42.9 + - + -
287C THR 3.1 23.8 + - - -
288C ARG 3.4 10.1 + - - -
289C GLU* 3.0 45.8 + - - +
290C THR* 3.6 22.7 + - - +
292C ARG* 3.4 25.2 + - + +
294C GLY* 1.3 74.7 - - - +
296C LEU* 1.3 73.4 + - + +
297C ILE 3.4 0.2 - - - -
2802C SAH 3.5 9.5 - - - +
20G LYS* 3.3 17.8 + - - -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ILE* 3.7 41.3 - - + -
228C ARG* 3.6 43.7 - - + +
229C GLY* 3.4 22.7 - - - -
230C VAL* 3.7 10.1 - - + -
271C TYR* 4.5 1.3 - - + -
290C THR 6.1 0.7 - - - +
292C ARG 4.4 3.8 - - - +
293C LEU* 2.9 17.9 + - + +
295C ARG* 1.3 101.6 - - + +
297C ILE* 1.3 63.4 + - - +
298C ASN 3.5 0.5 + - - -
2802C SAH 3.4 24.0 - - + +
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Residues in contact with ILE 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C VAL* 3.7 21.1 - - + +
242C VAL* 5.2 0.4 - - + -
243C VAL* 3.8 20.4 - - + -
293C LEU 3.7 9.9 - - - +
294C GLY* 3.1 14.1 + - - +
295C ARG 3.4 0.2 - - - -
296C LEU* 1.3 78.8 - - - +
298C ASN* 1.3 58.8 + - - +
305C CYS* 5.5 0.4 - - - -
320C LEU* 3.7 23.1 - - + -
332C LEU* 3.3 46.0 - - + +
333C LEU 3.9 0.9 - - - +
334C TYR* 3.5 28.1 + - + -
336C TYR* 2.7 28.6 + - - -
2802C SAH 3.8 1.4 - - - +
20G LYS* 4.6 1.6 + - - -
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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