Contacts of the helix formed by residues 372 - 379 (chain B) in PDB entry 4U7C
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 THR 372 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B LYS 3.8 0.3 + - - -
348B ASP* 4.1 29.1 + - + +
349B LEU 3.4 13.5 - - - +
350B PRO* 4.5 3.4 - - + -
351B ILE* 3.7 6.9 - - - +
370B ILE* 3.9 1.0 - - - +
371B ILE* 1.3 94.6 - - + +
373B CYS* 1.3 61.0 + - - +
374B THR* 2.9 27.5 - - - +
375B GLU* 3.3 15.7 + - - +
376B LEU* 3.0 22.7 + - - +
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Residues in contact with CYS 373 (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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346B ILE* 3.6 29.0 + - + +
349B LEU* 3.2 37.1 + - - -
351B ILE* 4.3 11.7 - - - -
354B VAL* 5.7 1.1 - - - -
372B THR* 1.3 73.9 - - - +
374B THR* 1.3 61.1 + - - +
376B LEU* 3.5 9.2 - - + +
377B TYR* 2.9 24.1 + - - +
398B ILE* 3.9 28.9 - - - -
399B SER* 3.6 17.0 - - - +
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Residues in contact with THR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 4.8 1.9 - - - +
347B LYS* 3.3 27.6 + - - +
348B ASP* 4.8 3.4 - - - +
372B THR* 2.9 25.1 - - - +
373B CYS* 1.3 78.6 - - - +
375B GLU* 1.3 70.8 + - + +
377B TYR* 3.0 10.1 + - - +
378B GLN* 2.9 44.9 + - - +
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Residues in contact with GLU 375 (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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369B GLY 2.7 21.5 - - - +
370B ILE* 4.0 12.4 - - + +
371B ILE* 2.7 37.6 + - - +
372B THR* 3.3 24.7 + - - +
374B THR* 1.3 79.5 - - + +
376B LEU* 1.3 64.9 + - - +
378B GLN* 3.7 19.3 - - - +
379B GLN* 3.2 31.7 + - + +
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Residues in contact with LEU 376 (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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351B ILE* 4.4 11.4 - - + -
357B ILE* 6.4 1.6 - - + -
365B LEU* 3.9 27.8 - - + -
370B ILE* 3.7 14.5 - - + +
372B THR 3.0 14.4 + - - +
373B CYS* 3.5 10.8 - - - +
374B THR 3.2 0.2 - - - -
375B GLU* 1.3 78.6 - - - +
377B TYR* 1.3 60.4 + - - +
380B ARG* 3.9 6.1 + - - +
383B LEU* 3.6 34.6 - - + +
395B PHE* 3.3 43.8 - - + +
396B LEU* 5.8 0.2 - - - +
398B ILE* 4.0 22.9 - - + -
399B SER* 4.0 7.2 + - - -
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Residues in contact with TYR 377 (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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87B ASP* 4.3 4.0 + - - -
90B ALA* 5.0 7.8 - - + +
373B CYS 2.9 13.3 + - - +
374B THR* 3.0 10.0 + - - +
376B LEU* 1.3 75.8 - - - +
378B GLN* 1.3 68.9 + - + +
380B ARG* 2.9 75.3 + - - +
396B LEU* 4.2 6.7 - - + -
399B SER* 3.6 25.3 - - - +
400B LEU* 3.9 26.7 - - + -
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Residues in contact with GLN 378 (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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83B GLN* 4.6 6.8 + - - +
374B THR* 2.9 34.2 + - - +
375B GLU* 3.4 22.2 + - - +
377B TYR* 1.3 82.7 - - + +
379B GLN* 1.3 63.0 + - + +
380B ARG* 3.2 19.9 + - - +
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Residues in contact with GLN 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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368B LEU 3.2 25.7 + - - -
369B GLY 5.0 2.8 + - - -
370B ILE* 3.9 22.9 - - + +
375B GLU* 3.2 21.5 + - + +
377B TYR 3.3 0.2 - - - -
378B GLN* 1.3 80.0 - - + +
380B ARG* 1.3 63.6 + - - +
381B ALA 3.2 3.4 + - - -
382B LEU* 3.3 33.5 + - + +
383B LEU* 3.0 25.5 + - + +
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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