Contacts of the helix formed by residues 378 - 382 (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 PHE 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ILE* 4.1 16.6 - - + -
366B PRO* 4.2 19.5 - - + -
367B THR* 3.7 25.8 - - + -
372B HIS 4.3 12.6 - - - -
375B ARG* 3.4 56.7 + - + -
376B PRO 3.3 5.5 - - - -
377B GLY* 1.3 85.8 + - - +
379B PRO* 1.3 73.2 - - + +
380B TRP* 3.7 30.5 - + + -
381B GLU* 2.9 27.0 + - + +
382B GLU* 3.6 8.6 + - - +
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Residues in contact with PRO 379 (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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293B TYR* 3.9 2.8 - - - -
357B LEU* 3.2 42.4 - - + +
359B LEU* 4.6 0.9 - - + -
361B ARG* 3.4 27.6 - - - +
363B ILE* 4.1 12.8 - - + -
377B GLY 4.0 4.9 - - - +
378B PHE* 1.3 87.4 - - + +
380B TRP* 1.3 75.7 + - + +
381B GLU 3.3 3.1 + - - -
382B GLU* 3.3 25.5 + - + +
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Residues in contact with TRP 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B TYR* 3.4 71.3 - + + +
292B ARG* 4.0 7.5 - - + +
293B TYR* 3.5 34.2 + - + -
296B LYS* 4.7 2.6 - - - +
357B LEU* 4.1 6.7 - - + -
359B LEU* 3.9 17.0 - - + -
363B ILE* 4.3 7.9 - - + -
364B TYR* 4.5 7.0 - + - -
367B THR* 3.9 15.7 - - + -
372B HIS 2.8 22.0 + - - -
373B PHE* 3.6 25.4 - + - -
378B PHE* 3.7 33.1 - + + +
379B PRO* 1.3 97.3 - - + +
381B GLU* 1.3 67.4 + - + +
382B GLU 3.4 0.9 - - - -
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Residues in contact with GLU 381 (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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292B ARG* 3.0 33.9 + - - +
296B LYS* 2.7 54.8 + - - +
373B PHE* 3.2 9.1 - - - +
374B GLY* 2.8 29.6 + - - -
375B ARG 3.1 26.7 + - - +
376B PRO* 5.2 2.7 - - + -
377B GLY 5.3 0.4 - - - +
378B PHE* 2.9 23.6 + - + +
380B TRP* 1.3 86.1 - - + +
382B GLU* 1.3 61.2 + - - +
383B THR* 3.6 2.6 + - - +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 3.0 27.8 - - + -
296B LYS* 5.6 0.3 - - - +
297B ASN* 3.3 4.0 + - - -
377B GLY* 5.9 3.5 + - - -
378B PHE 4.2 8.5 - - - +
379B PRO* 3.3 19.2 + - + +
380B TRP 4.8 0.2 - - - +
381B GLU* 1.3 79.0 - - - +
383B THR* 1.3 63.3 + - - +
384B ASP* 3.4 19.5 + - - +
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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