Contacts of the strand formed by residues 272 - 277 (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 MET 272 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D ILE* 4.3 1.6 - - + -
255D ALA* 3.6 23.6 - - - +
258D ARG* 4.2 7.6 - - + -
259D GLU* 3.6 22.2 - - - +
262D TYR* 3.7 19.3 - - - -
270D CYS* 3.7 1.6 - - - +
271D TYR* 1.3 77.1 - - - +
273D TYR* 1.3 60.1 + - - +
274D TYR* 3.5 27.5 - - + +
283D CYS* 3.7 18.8 - - - -
284D VAL 3.7 4.5 - - - -
285D ASP* 3.6 27.6 - - - +
287D THR* 4.1 4.9 - - - +
17H ARG* 3.9 14.6 - - - +
18H HIS 6.2 0.2 - - - +
19H ARG* 4.0 4.0 - - + +
20H LYS* 3.0 26.8 + - - +
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Residues in contact with TYR 273 (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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245D TYR* 3.6 44.6 - + + -
272D MET* 1.3 72.7 - - - +
274D TYR* 1.3 67.7 + - - +
275D PHE* 3.8 5.7 - - - -
283D CYS* 3.3 3.0 - - - -
284D VAL 2.8 36.3 + - - +
307D THR* 2.8 39.3 + - + -
318D LEU* 3.6 19.0 - - + +
320D LEU* 5.2 0.4 - - + -
334D TYR* 3.3 33.5 - + - -
335D ASP 4.2 5.7 + - - -
336D TYR 5.0 0.4 - - - -
20H LYS* 3.2 21.1 - - + -
21H VAL 3.6 9.8 + - - -
22H LEU* 3.5 27.6 - - + +
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Residues in contact with TYR 274 (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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222C LEU* 3.6 24.1 - - + +
252D ILE* 5.7 1.1 - - + -
255D ALA* 3.8 22.5 - - + +
259D GLU* 2.5 44.3 + - - +
272D MET* 3.5 24.9 - - + +
273D TYR* 1.3 75.1 - - - +
275D PHE* 1.3 62.9 + - - +
276D GLN* 5.1 3.4 - - - +
281D THR* 4.1 17.5 - - + -
282D TYR 3.3 14.6 - - - -
283D CYS* 3.9 9.9 - - + -
19H ARG* 3.5 25.1 - - + -
20H LYS 2.9 15.5 + - - +
21H VAL* 3.5 12.3 - - + +
22H LEU* 3.0 26.5 + - - +
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Residues in contact with PHE 275 (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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249D LEU* 3.8 21.1 - - + -
273D TYR 3.8 3.4 - - - -
274D TYR* 1.3 75.1 - - - +
276D GLN* 1.3 81.9 + - - +
277D TYR* 3.8 11.0 - - + -
281D THR* 3.5 3.5 - - - -
282D TYR* 2.9 63.3 + - + +
283D CYS 4.0 0.4 - - - -
284D VAL* 4.0 16.2 - - + -
309D LEU* 3.7 28.0 - - + -
316D PRO* 3.7 19.1 - - + -
317D HIS* 5.8 0.2 - - - -
318D LEU* 3.7 23.3 - - + -
21H VAL* 5.9 0.2 - - - -
22H LEU* 3.7 29.6 - - + +
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Residues in contact with GLN 276 (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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225C GLY* 3.3 25.9 - - - +
226C LYS 3.7 0.6 + - - -
227C GLY* 4.0 20.9 - - - +
274D TYR* 5.1 3.2 - - - +
275D PHE* 1.3 95.7 + - - +
277D TYR* 1.3 61.5 - - - +
279D SER* 5.4 2.9 - - - +
280D LYS 3.3 6.3 - - - +
281D THR* 2.5 37.9 + - - +
309D LEU* 3.5 18.5 - - - +
21H VAL* 6.0 3.6 - - - +
22H LEU* 5.4 3.2 + - - +
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Residues in contact with TYR 277 (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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275D PHE* 3.8 10.9 + - + -
276D GLN* 1.3 76.8 - - - +
278D LEU* 1.3 105.7 + - + +
279D SER 3.2 0.6 - - - +
280D LYS* 2.9 18.9 + - - +
282D TYR* 3.5 37.5 + + + -
309D LEU* 3.9 19.7 - - + -
311D ASP* 2.6 38.7 + - + -
314D GLY* 3.4 19.6 + - - -
316D PRO* 3.8 36.3 - - + -
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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