Contacts of the helix formed by residues 277 - 282 (chain A) in PDB entry 4ZTZ
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 HIS 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A VAL* 3.5 30.5 - - + +
201A VAL* 4.0 13.8 - - + +
207A THR* 4.4 9.9 + - - -
209A PRO* 3.5 31.6 - - + -
241A PRO* 3.5 9.4 - - - +
242A ALA* 2.9 28.8 + - - +
273A PHE* 3.5 39.2 + + - -
274A ASP 3.0 14.4 + - - +
276A ALA* 1.3 84.5 + - + +
278A ILE* 1.3 57.7 + - - +
812A MET* 3.6 24.9 - - + +
843A GLN* 5.9 0.2 - - - -
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.6 33.2 - - + -
241A PRO* 4.0 2.0 - - - -
242A ALA* 3.3 6.7 - - + +
244A LEU* 3.7 28.7 - - + -
245A ILE* 5.3 0.9 - - + +
274A ASP 3.4 9.4 - - - +
275A ARG* 3.0 24.7 + - - +
276A ALA 3.3 0.2 - - - -
277A HIS* 1.3 82.5 - - - +
279A ARG* 1.3 66.1 + - - +
280A GLU* 3.5 17.1 + - + +
281A GLN* 3.6 26.1 + - + +
282A TYR* 3.3 23.2 - - - -
289A MET* 4.8 5.8 - - + -
291A PHE* 4.5 7.2 - - + -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 5.3 4.2 - - - +
239A LEU* 2.4 75.5 + - + +
240A SER* 4.4 5.7 + - - +
241A PRO* 3.4 23.8 + - - +
242A ALA* 2.5 18.3 + - - +
243A ASP* 3.3 29.2 + - - +
278A ILE* 1.3 74.0 - - - +
280A GLU* 1.3 79.2 + - + +
281A GLN 3.5 0.7 + - - -
282A TYR* 4.1 7.0 + - - +
283A LEU* 4.1 4.9 - - - +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ILE* 4.9 2.4 - - - +
243A ASP* 3.4 23.2 - - - +
244A LEU 3.2 20.6 + - - -
245A ILE* 3.3 50.6 + - + +
278A ILE* 3.4 6.6 - - + +
279A ARG* 1.3 88.7 - - + +
281A GLN* 1.3 64.0 + - - +
282A TYR 3.3 3.4 + - - -
283A LEU* 3.6 31.1 + - + +
285A GLN 5.5 0.7 - - - +
287A SER* 5.2 7.3 + - - -
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 4.8 4.0 - - - +
275A ARG* 2.6 43.0 + - - +
278A ILE* 3.6 32.3 + - + +
279A ARG 3.3 1.6 - - - -
280A GLU* 1.3 77.8 - - - +
282A TYR* 1.3 61.5 + - - +
283A LEU 3.3 4.4 + - - +
287A SER* 3.9 19.3 + - - -
289A MET* 3.7 40.9 + - - +
291A PHE* 3.7 10.7 - - + -
432A VAL* 4.9 0.9 - - - +
434A TYR* 4.0 6.6 - - - -
841A LEU* 4.0 21.1 - - + +
1129A PHE* 4.3 10.1 - - - -
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Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 5.2 3.1 - - + -
241A PRO* 4.8 3.4 - - + -
276A ALA* 2.3 37.1 + - - +
278A ILE 3.3 25.6 - - - -
279A ARG* 4.1 9.6 + - - +
280A GLU 3.3 0.6 - - - -
281A GLN* 1.3 76.4 - - - +
283A LEU* 1.3 62.5 + - + +
434A TYR* 2.9 26.7 + - - -
812A MET* 3.2 19.1 - - - +
814A VAL* 3.5 43.2 - - + +
816A LEU* 3.2 17.2 - - + +
839A ALA* 3.3 34.0 - - + +
840A ILE* 4.0 10.8 - - + +
841A LEU* 3.4 24.7 - - + +
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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