Contacts of the helix formed by residues 271 - 276 (chain A) in PDB entry 1Z3Z
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 SER 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A THR* 4.0 0.9 - - - -
111A GLY* 3.2 34.8 - - - -
114A SER* 4.5 0.2 + - - -
244A GLU 4.7 0.4 + - - -
245A ALA* 2.9 27.6 - - - +
270A LEU* 1.3 79.7 - - - +
272A LYS* 1.3 63.5 + - - +
273A THR* 3.4 2.0 + - - -
274A LEU* 2.6 28.6 + - - +
275A GLY* 3.0 10.9 + - - -
278A LEU 6.1 0.2 - - - -
280A LEU 3.5 14.2 - - - +
281A ALA* 3.7 6.3 - - - +
434A PLP 5.1 1.3 - - - -
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 2.9 31.4 - - - +
53A MET* 3.5 11.2 - - + +
54A SER* 3.5 25.0 - - - +
245A ALA* 2.9 16.1 + - + +
246A GLN* 2.9 19.2 - - + +
271A SER* 1.3 82.6 + - - +
273A THR* 1.3 61.2 + - - +
275A GLY* 3.4 2.4 + - - -
276A ALA 3.3 14.0 + - - -
277A GLY 4.1 0.5 + - - -
278A LEU 5.2 1.2 - - - +
434A PLP 1.3 91.0 + - + +
435A MES 3.8 9.9 - - - -
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET 3.9 5.6 - - - +
54A SER 3.7 7.6 - - - -
56A VAL* 3.6 29.1 - - + +
244A GLU 4.3 2.1 + - - -
245A ALA 3.2 15.1 + - - +
246A GLN 3.7 13.9 - - - +
248A GLY* 2.8 30.8 + - - +
249A VAL* 3.6 11.6 - - - +
251A ARG* 3.4 30.5 - - + +
270A LEU* 5.4 0.5 - - - +
271A SER 3.1 0.9 + - - -
272A LYS* 1.3 76.4 - - - +
274A LEU* 1.3 63.9 + - - +
275A GLY 3.4 0.2 - - - -
276A ALA* 3.5 6.6 + - - -
317A VAL* 4.1 2.1 - - - +
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Residues in contact with LEU 274 (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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90A LEU* 5.1 3.1 - - + -
94A LEU* 4.6 16.4 - - + -
249A VAL* 4.0 9.4 - - + -
270A LEU* 4.1 18.8 - - + -
271A SER* 2.6 24.2 + - - +
273A THR* 1.3 76.0 + - - +
275A GLY* 1.3 59.5 + - - +
276A ALA 3.6 0.2 + - - -
280A LEU* 3.9 22.0 - - + +
281A ALA* 4.2 8.1 - - - -
282A ALA* 4.1 26.7 - - + -
314A GLY* 4.0 10.3 - - - +
317A VAL* 3.9 16.1 - - + +
318A LEU* 4.2 32.5 - - + -
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Residues in contact with GLY 275 (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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271A SER 3.0 10.8 + - - -
272A LYS 3.4 1.8 + - - -
274A LEU* 1.3 76.0 - - - +
276A ALA* 1.3 57.1 + - - +
277A GLY 2.8 16.5 + - - -
278A LEU* 2.9 44.2 + - - +
280A LEU* 3.9 17.4 + - - -
313A VAL* 4.3 3.6 - - - +
317A VAL* 4.5 1.3 - - - -
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Residues in contact with ALA 276 (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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54A SER 3.6 15.0 - - - -
55A ALA* 3.3 23.2 - - - +
56A VAL* 4.2 9.9 - - + +
57A LEU* 4.5 3.1 + - + +
58A GLY 4.7 4.0 - - - +
64A ILE* 4.2 16.7 - - + +
272A LYS 3.3 5.5 + - - -
273A THR 3.5 3.5 + - - -
274A LEU 3.2 2.8 - - - -
275A GLY* 1.3 78.2 - - - +
277A GLY* 1.3 53.8 + - - +
278A LEU* 4.6 3.1 - - - +
317A VAL* 3.5 33.2 - - + -
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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