Contacts of the helix formed by residues 364 - 369 (chain B) in PDB entry 5H9U
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 364 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 3.2 12.0 - - - +
29B LEU* 3.7 23.6 - - + -
30B ASP* 3.1 18.8 + - - +
33B ILE* 3.8 13.0 - - + -
278B LYS 5.6 0.2 - - - -
280B PRO* 3.3 10.3 - - + +
285B ARG* 3.6 32.8 - - - +
289B TYR* 4.0 22.9 - + - -
359B LEU* 2.4 45.6 + - + +
361B ARG 3.2 21.5 - - - -
363B ILE* 1.3 91.8 - - + +
365B THR* 1.3 65.7 + - - +
366B PRO 3.3 2.5 - - - -
367B THR* 2.4 29.5 + - - -
380B TRP* 4.5 5.6 - + - -
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 3.4 47.2 + - + +
26B ASP* 3.8 7.1 + - - +
27B ALA* 3.7 19.3 - - + +
30B ASP* 2.8 26.3 + - - +
76B GLU* 4.6 3.6 - - - +
364B TYR* 1.3 75.7 - - - +
366B PRO* 1.3 68.8 - - + +
368B SER* 2.2 33.8 + - - +
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 4.6 9.2 - - - +
30B ASP* 4.7 1.1 - - - +
362B PRO 5.7 0.2 - - - +
363B ILE* 3.5 16.8 - - - +
364B TYR 3.5 3.8 - - - -
365B THR* 1.3 94.8 - - + +
367B THR* 1.3 57.0 + - - +
368B SER 3.5 0.2 + - - -
369B ALA 3.4 5.4 + - - +
370B TYR* 5.5 0.3 - - - -
375B ARG* 3.0 32.7 + - - +
378B PHE* 4.2 16.8 - - + -
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 3.5 0.3 + - - -
262B ASP* 4.6 0.5 - - - +
285B ARG* 3.0 18.2 + - - -
289B TYR* 4.1 1.6 - - - +
363B ILE 4.4 4.3 - - - +
364B TYR* 2.4 28.4 + - + +
366B PRO* 1.3 72.3 - - - +
368B SER* 1.3 62.0 + - - +
369B ALA* 3.0 12.0 + - - +
371B GLY 4.3 2.8 - - - -
372B HIS* 3.2 39.9 + - + +
375B ARG* 4.0 6.7 - - - +
378B PHE* 3.7 28.3 - - + -
380B TRP* 3.9 24.7 - - + -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS* 3.2 30.4 + - - +
22B ASP* 3.8 11.1 - - - +
23B ARG* 3.4 48.2 + - - +
26B ASP* 4.1 12.3 - - - -
276B SER* 4.3 5.8 - - - -
365B THR* 2.2 28.9 + - - -
367B THR* 1.3 77.4 + - - +
369B ALA* 1.3 57.9 + - - +
372B HIS* 4.8 1.3 - - - -
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL 5.3 0.2 - - - +
13B THR 4.9 0.2 - - - -
14B GLU* 4.0 18.2 - - + +
19B LYS* 3.9 20.6 - - + +
23B ARG* 5.9 3.6 - - + +
366B PRO 3.4 4.5 + - - +
367B THR 3.0 1.0 + - - +
368B SER* 1.3 82.9 + - - +
370B TYR* 1.3 92.5 + - + +
371B GLY 3.2 2.9 - - - -
375B ARG* 3.0 20.8 + - - -
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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