Contacts of the helix formed by residues 334 - 340 (chain H) in PDB entry 2POZ
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 TYR 334 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129H ASN* 2.9 51.8 + - + -
130H GLY 3.9 1.6 - - - -
132H TYR* 4.5 5.4 - - - -
157H LYS* 5.2 0.2 + - - -
307H HIS* 4.5 5.2 + - - -
308H VAL* 3.2 26.9 - - + -
309H CYS* 3.5 28.1 - - + +
315H GLU* 5.3 1.2 + - - -
332H GLU* 3.1 14.3 + - + -
333H HIS* 1.3 81.1 + - - +
335H PRO* 1.3 66.8 - - - +
336H ALA 3.4 2.9 + - - -
337H PHE* 3.3 55.3 + + + +
338H LYS* 4.0 9.9 - - - -
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Residues in contact with PRO 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H ALA* 4.5 6.3 - - + -
129H ASN 3.6 12.3 - - - +
131H TRP* 5.7 4.7 - - + +
147H ARG* 4.4 25.0 + - - +
148H PRO* 6.1 0.4 - - + -
151H GLU* 4.8 2.9 - - - +
153H TYR* 3.6 30.3 - - + +
333H HIS* 3.1 32.3 - - + +
334H TYR* 1.3 85.1 - - - +
336H ALA* 1.3 61.3 + - + +
337H PHE 3.3 1.0 + - - -
338H LYS* 3.7 17.1 + - + +
339H ALA* 4.9 0.9 + - - +
353H ILE* 5.4 2.7 - - + -
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Residues in contact with ALA 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ARG* 4.4 9.8 + - - +
129H ASN 5.1 0.4 + - - -
130H GLY 4.2 22.4 - - - +
131H TRP* 5.4 2.0 - - - -
147H ARG* 4.5 16.4 - - - +
334H TYR 3.4 1.6 - - - -
335H PRO* 1.3 78.6 - - + +
337H PHE* 1.3 67.6 + - + +
338H LYS 3.2 2.9 - - - -
339H ALA* 3.0 23.5 + - + +
340H ASP* 3.5 8.4 - - - +
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Residues in contact with PHE 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H SER 5.7 0.2 - - - +
17H ARG* 3.1 45.5 - - + -
18H LEU* 3.5 44.9 - - + -
130H GLY* 4.9 3.1 - - - -
309H CYS* 3.7 13.9 - - - -
310H GLY 5.0 4.7 - - - -
334H TYR* 3.3 57.7 - + + +
335H PRO 3.3 1.2 - - - -
336H ALA* 1.3 79.2 - - + +
338H LYS* 1.3 69.4 + - - +
340H ASP* 3.2 26.8 + - - +
343H TYR* 3.5 14.9 - - + -
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Residues in contact with LYS 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311H SER 6.5 0.2 - - - -
312H SER* 4.2 12.3 + - - +
315H GLU* 4.7 8.2 + - - -
333H HIS* 4.6 15.7 - - + +
334H TYR 4.0 14.4 - - - +
335H PRO* 3.7 18.4 - - + +
336H ALA 3.2 0.8 + - - -
337H PHE* 1.3 83.4 - - - +
339H ALA* 1.3 59.6 + - - +
340H ASP 3.3 0.4 - - - +
343H TYR* 3.7 54.2 + - + +
345H GLU* 5.0 2.5 + - - +
350H PRO* 5.6 2.8 - - - +
351H PRO* 5.2 8.9 + - - +
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Residues in contact with ALA 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335H PRO 4.9 0.6 + - - +
336H ALA* 3.0 16.3 + - + +
338H LYS* 1.3 77.0 - - - +
340H ASP* 1.3 67.7 + - - +
341H ASP* 3.4 6.2 + - - +
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Residues in contact with ASP 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H SER 4.9 0.4 - - - +
16H GLY* 3.6 17.0 - - - -
17H ARG* 2.9 65.5 + - - +
336H ALA 3.5 6.8 - - - +
337H PHE* 3.2 17.3 + - - +
338H LYS 4.4 0.3 - - - +
339H ALA* 1.3 79.8 - - - +
341H ASP* 1.3 64.9 + - - +
342H GLY 3.0 0.7 + - - -
343H TYR* 3.0 19.7 + - + +
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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