Contacts of the strand formed by residues 272 - 276 (chain D) in PDB entry 2UZ1
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 272 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D LEU* 4.1 26.0 - - + +
201D LEU* 3.8 29.6 - - + -
204D ALA* 3.6 19.3 - - + -
206D ARG 3.9 1.2 - - - +
207D PRO* 3.4 4.3 - - + +
208D VAL* 2.9 27.4 + - - +
270D PRO* 3.4 0.8 - - - +
271D ASP* 1.3 82.8 + - - +
273D VAL* 1.3 74.5 + - - +
274D LEU* 4.2 4.0 - - + +
296D ALA* 4.1 0.2 - - - +
297D GLN* 3.2 31.9 - - + +
299D ILE* 3.9 29.8 - - + -
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Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 3.4 16.6 - - + -
210D VAL* 3.8 28.3 - - + -
260D LEU* 5.9 0.7 - - + -
270D PRO* 4.1 3.4 - - + -
272D LEU* 1.3 82.1 - - - +
274D LEU* 1.3 61.4 + - - +
275D MET* 3.7 17.8 + - + -
291D LEU 5.5 0.2 - - - +
292D ILE* 4.0 30.5 - - + -
293D PRO* 4.0 18.8 - - + -
296D ALA* 4.1 7.9 - - + -
297D GLN 3.0 6.7 + - - -
298D VAL* 3.4 7.7 - - + +
299D ILE 2.9 28.6 + - - +
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Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ALA* 5.2 4.7 - - + -
201D LEU* 4.9 9.6 - - + -
208D VAL 2.9 13.5 + - - +
209D ILE* 3.3 24.1 - - + +
210D VAL 2.8 26.1 + - - +
227D PHE* 4.3 20.4 - - + -
272D LEU* 4.2 10.7 - - + +
273D VAL* 1.3 70.3 - - - +
275D MET* 1.3 60.2 + - - +
276D LEU* 3.9 24.5 - - + -
299D ILE* 3.4 37.5 - - + +
301D VAL* 4.3 5.4 - - + -
329D LEU* 4.3 18.6 - - + -
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Residues in contact with MET 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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210D VAL* 3.5 10.3 - - + +
273D VAL* 3.8 19.1 - - + -
274D LEU* 1.3 70.5 - - - +
276D LEU* 1.3 64.2 + - - +
277D GLY 3.8 1.1 - - - -
278D ALA* 3.3 37.7 - - + +
279D ARG 4.2 6.1 - - - +
280D PHE* 3.5 34.1 - - + -
284D THR* 4.7 0.2 - - + -
292D ILE* 3.3 30.1 - - + -
298D VAL* 3.5 26.5 - - + -
299D ILE 2.8 12.1 + - - +
300D GLN* 3.6 9.6 - - + -
301D VAL* 2.9 29.7 + - - +
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Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ILE* 3.8 22.2 - - + -
210D VAL 2.8 13.3 + - - +
211D LEU* 3.7 15.3 - - + -
212D GLY* 3.0 23.0 + - - +
215D ALA* 4.3 0.3 - - - +
224D LEU* 5.3 3.4 - - + -
227D PHE* 5.3 2.5 - - + -
274D LEU* 3.9 27.1 - - + +
275D MET* 1.3 71.9 - - - +
277D GLY* 1.3 57.5 + - - +
278D ALA 3.1 2.2 - - - +
301D VAL* 3.8 31.9 - - + -
322D VAL* 3.8 24.9 - - + +
325D THR* 4.3 14.6 - - + -
326D ILE* 4.1 19.1 - - + -
329D LEU* 4.6 5.8 - - + -
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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