Contacts of the strand formed by residues 241 - 245 (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 PHE 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D ARG* 6.2 0.9 - - + -
206D ILE* 3.9 32.4 - - + +
209D LEU* 3.6 48.3 - - + +
210D ILE* 3.7 24.2 - - + -
215D GLU* 6.5 0.9 - - + -
236D PHE* 3.8 15.2 - - - -
239D GLY 3.6 2.6 + - - -
240D ASP* 1.3 74.2 - - - +
242D VAL* 1.3 66.5 + - - +
243D VAL* 3.6 16.4 - - + -
244D GLU* 3.4 21.3 - - + -
319D ILE* 3.6 38.4 - - + -
320D LEU 4.5 0.4 - - - -
321D ILE* 3.8 9.1 - - + +
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Residues in contact with VAL 242 (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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215D GLU* 5.4 0.9 - - - -
216D GLU 5.3 0.2 - - - +
218D MET* 3.3 23.8 - - - +
236D PHE* 4.0 28.2 - - + -
240D ASP 3.8 1.3 - - - +
241D PHE* 1.3 84.3 - - - +
243D VAL* 1.3 66.4 + - + +
297D ILE* 5.2 0.2 - - + -
305D CYS* 4.0 18.2 - - - -
320D LEU* 2.8 17.6 + - + +
322D ALA* 3.6 30.1 - - + +
326D ILE* 4.4 2.7 - - + -
332D LEU* 3.6 35.2 - - + -
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Residues in contact with VAL 243 (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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215D GLU* 3.4 38.8 - - + +
218D MET* 3.9 16.2 - - + -
241D PHE* 3.5 14.2 - - - -
242D VAL* 1.3 85.5 - - + +
244D GLU* 1.3 68.7 + - - +
293D LEU* 4.6 0.7 - - + -
294D GLY* 3.9 17.3 - - - +
297D ILE* 3.6 30.7 - - + -
319D ILE 3.8 0.2 - - - -
320D LEU* 2.8 35.1 + - + +
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Residues in contact with GLU 244 (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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210D ILE* 3.4 27.8 - - + +
215D GLU* 4.4 1.7 + - - +
241D PHE* 3.4 16.1 - - + -
243D VAL* 1.3 84.5 - - - +
245D TYR* 1.3 71.8 + - - +
246D HIS* 3.2 40.9 + - + +
292D ARG* 4.7 5.9 + - - +
294D GLY* 3.6 16.1 + - - -
317D HIS* 2.7 36.0 + - - +
318D LEU 3.2 14.8 + - - +
319D ILE* 4.3 5.6 - - + +
320D LEU* 4.8 0.2 - - - -
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Residues in contact with TYR 245 (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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243D VAL 3.9 1.8 + - - -
244D GLU* 1.3 78.8 - - - +
246D HIS* 1.3 56.3 + - - +
271D TYR* 2.7 32.8 + - - +
273D TYR* 3.6 28.5 - + + -
284D VAL* 3.4 34.8 - - + +
286D ALA* 3.7 15.1 - - + +
294D GLY* 3.6 19.5 - - - -
295D ARG* 3.6 21.7 - - - -
318D LEU* 2.8 28.5 + - + +
320D LEU* 4.2 13.7 - - + +
334D TYR* 3.7 13.0 - + - -
20H LYS* 3.0 31.8 + - + +
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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