Contacts of the helix formed by residues 293 - 297 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D GLU* 2.9 35.3 + - + +
218D MET* 3.7 38.6 - - + +
219D LYS* 4.7 1.6 - - - +
220D ILE* 3.5 37.0 - - + +
230D VAL* 3.5 22.6 - - + +
243D VAL* 4.6 5.6 - - + -
291D ASN 4.1 9.9 - - - +
292D ARG* 1.3 76.2 - - - +
294D GLY* 1.3 68.5 + - - +
295D ARG 3.2 2.7 - - - -
296D LEU* 2.9 23.5 + - + +
297D ILE* 3.5 3.4 + - - +
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Residues in contact with GLY 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D GLU* 4.8 0.6 + - - -
243D VAL* 3.9 19.0 - - - +
244D GLU 3.6 24.5 + - - -
245D TYR* 3.6 21.1 - - - -
246D HIS 5.1 0.6 - - - +
292D ARG* 3.7 2.0 - - - +
293D LEU* 1.3 78.4 - - - +
295D ARG* 1.3 60.7 + - - +
296D LEU 3.2 1.2 + - - -
297D ILE* 3.2 20.4 + - - +
320D LEU* 5.3 1.3 - - - +
334D TYR* 4.6 2.6 + - - -
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Residues in contact with ARG 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ARG* 4.5 0.6 - - - +
245D TYR* 3.6 16.7 - - - +
246D HIS 4.7 6.4 + - - +
271D TYR* 3.6 22.0 - - + -
286D ALA* 2.8 50.8 + - + -
287D THR 3.1 16.2 + - - -
288D ARG 3.4 13.1 + - - -
289D GLU* 3.0 40.4 + - - +
290D THR* 3.6 28.5 + - - +
292D ARG* 3.3 22.4 + - + +
294D GLY* 1.3 75.1 - - - +
296D LEU* 1.3 74.6 + - + +
297D ILE 3.4 0.2 - - - -
2803D SAH 3.4 21.8 - - - +
20H LYS* 3.5 9.6 + - - -
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ILE* 3.6 37.0 - - + -
228D ARG* 3.5 51.4 - - + +
229D GLY* 3.5 17.8 - - - -
230D VAL* 3.8 10.1 - - + -
271D TYR* 4.8 0.2 - - + -
290D THR 5.9 2.0 - - - +
291D ASN 6.2 0.4 - - - -
292D ARG 4.0 13.5 - - - +
293D LEU* 2.9 18.7 + - + +
295D ARG* 1.3 94.7 - - - +
297D ILE* 1.3 63.6 + - - +
298D ASN 3.5 1.7 + - - -
2803D SAH 3.4 23.1 - - + +
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Residues in contact with ILE 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D MET* 5.2 0.4 - - - -
230D VAL* 3.7 20.2 - - + +
243D VAL* 3.6 31.2 - - + -
293D LEU 3.7 12.3 - - - +
294D GLY* 3.2 10.7 + - - +
295D ARG 3.4 0.2 - - - -
296D LEU* 1.3 79.1 - - - +
298D ASN* 1.3 59.3 - - - +
320D LEU* 3.6 13.5 - - + -
332D LEU* 3.2 44.4 - - + +
333D LEU 3.9 0.7 - - - +
334D TYR* 3.5 28.8 + - + -
336D TYR* 2.7 29.2 + - - -
2803D SAH 3.8 1.4 - - - +
20H 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