Contacts of the helix formed by residues 293 - 297 (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 LEU 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLU* 2.9 25.4 + - + +
218B MET* 3.6 46.4 - - + +
219B LYS* 5.2 0.9 - - - -
220B ILE* 3.4 39.0 - - + -
230B VAL* 3.6 21.6 - - + +
243B VAL* 4.6 6.3 - - + -
291B ASN 4.1 11.4 - - - +
292B ARG* 1.3 72.7 - - - +
294B GLY* 1.3 67.7 + - - +
295B ARG 3.2 3.4 - - - -
296B LEU* 2.9 25.7 + - + +
297B ILE* 3.7 3.0 + - + +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL* 3.8 22.2 - - - +
244B GLU 3.6 20.8 + - - -
245B TYR* 3.7 20.4 - - - -
246B HIS 5.2 0.6 - - - +
292B ARG* 3.6 2.4 - - - +
293B LEU* 1.3 77.2 - - - +
295B ARG* 1.3 62.7 + - - +
296B LEU 3.1 1.8 + - - -
297B ILE* 3.2 21.3 + - - +
320B LEU* 5.2 1.5 - - - +
334B TYR* 4.7 1.9 + - - -
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Residues in contact with ARG 295 (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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245B TYR* 3.6 16.8 - - + +
246B HIS 4.8 8.5 + - - +
271B TYR* 3.6 22.6 - - + -
286B ALA* 2.7 42.3 + - + +
287B THR 3.1 24.4 + - - -
288B ARG 3.4 9.5 + - - -
289B GLU* 3.0 45.0 + - - +
290B THR* 3.7 22.6 + - - +
292B ARG* 3.3 24.2 - - + +
294B GLY* 1.3 74.9 - - - +
296B LEU* 1.3 74.4 + - + +
297B ILE 3.4 0.4 - - - -
2801B SAH 3.5 12.6 - - - +
20F LYS* 3.5 17.2 + - - -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 3.7 41.7 - - + -
228B ARG* 3.6 44.0 - - + +
229B GLY* 3.5 19.4 - - - -
230B VAL* 3.8 9.2 - - + -
271B TYR* 4.8 0.7 - - + -
290B THR 5.9 2.5 - - - +
292B ARG 4.5 4.0 - - - +
293B LEU* 2.9 17.9 + - + +
295B ARG* 1.3 103.1 - - + +
297B ILE* 1.3 63.8 + - - +
298B ASN 3.5 2.1 + - - -
2801B SAH 3.4 23.8 - - + +
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Residues in contact with ILE 297 (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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218B MET* 5.1 0.7 - - - -
230B VAL* 3.7 26.5 - - + +
242B VAL* 5.2 0.2 - - + -
243B VAL* 3.7 20.4 - - + -
293B LEU 3.7 4.5 - - - +
294B GLY* 3.2 13.5 + - - +
296B LEU* 1.3 77.8 - - - +
298B ASN* 1.3 58.6 + - - +
305B CYS* 5.7 0.2 - - - -
320B LEU* 3.7 22.0 - - + -
332B LEU* 3.3 45.5 - - + +
333B LEU 4.0 0.7 - - - +
334B TYR* 3.5 30.2 + - + -
336B TYR* 2.7 27.9 + - - -
2801B SAH 3.8 1.4 - - - +
20F LYS* 4.6 1.4 + - - -
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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