Contacts of the helix formed by residues 372 - 379 (chain B) in PDB entry 4R7P
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 VAL 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 5.2 7.6 - - + -
223B HIS* 3.8 32.0 - - + +
226B ILE* 3.9 11.9 - - + -
227B TYR* 3.2 42.9 + - + +
249B VAL* 5.2 8.7 - - + -
278B PHE* 4.1 2.3 - - - -
330B ASN* 4.0 17.9 - - - +
332B LEU* 3.7 24.7 - - + -
334B ILE* 4.4 5.8 - - + -
350B MET* 3.6 10.3 - - - +
371B ALA* 1.3 72.0 - - + +
373B GLY* 1.3 66.9 + - - +
375B ALA* 3.3 10.0 + - - +
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.1 1.3 - - - -
280B MET* 4.1 9.3 - - - +
304B LEU* 3.6 17.9 - - - -
328B ASN* 4.8 0.2 - - - -
330B ASN* 4.6 6.1 + - - -
332B LEU* 4.2 12.3 - - - -
371B ALA* 3.2 3.0 - - - +
372B VAL* 1.3 86.5 - - - +
374B ALA* 1.3 63.6 + - - +
375B ALA 2.8 2.1 + - - -
376B ILE* 2.9 25.5 + - - +
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Residues in contact with ALA 374 (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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303B ARG* 5.4 0.5 - - - +
304B LEU* 3.6 28.9 + - + +
349B ASP 3.8 2.7 - - - +
350B MET* 4.1 9.2 - - + -
351B GLU* 3.9 25.1 - - + +
371B ALA* 3.2 20.5 + - + +
373B GLY* 1.3 73.9 - - - +
375B ALA* 1.3 57.7 + - - +
376B ILE* 3.0 8.2 + - - +
377B LYS* 3.4 22.5 + - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TYR* 3.6 14.1 - - - +
348B ILE* 3.6 24.0 - - + -
349B ASP 3.4 13.9 + - - +
350B MET* 3.6 14.1 - - + +
371B ALA 3.9 1.8 + - - -
372B VAL 3.3 15.7 + - - +
373B GLY 2.8 0.8 + - - -
374B ALA* 1.3 73.8 - - - +
376B ILE* 1.3 64.2 + - - +
377B LYS 3.0 4.0 - - - -
378B SER* 2.8 17.6 + - - -
379B PHE* 3.2 12.8 - - + -
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Residues in contact with ILE 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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278B PHE* 3.4 40.9 - - + +
280B MET* 4.1 26.0 - - + +
295B LEU* 4.4 4.9 - - + -
302B LEU* 4.0 18.4 - - + +
303B ARG* 4.0 6.3 - - - -
304B LEU* 3.7 29.8 - - + +
373B GLY 2.9 19.0 + - - +
374B ALA 3.8 2.7 - - - +
375B ALA* 1.3 77.3 - - - +
377B LYS* 1.3 63.4 + - - +
378B SER 3.2 1.0 + - - -
379B PHE* 3.4 10.3 + - - +
382B SER* 3.5 32.5 + - - +
383B LEU 4.8 1.8 - - - +
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Residues in contact with LYS 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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301B LYS* 3.1 28.4 + - + +
302B LEU 3.3 17.9 - - - +
303B ARG* 3.6 41.0 - - + +
349B ASP* 2.2 48.9 + - - +
351B GLU* 3.4 34.0 + - - -
374B ALA 3.4 12.1 - - - +
375B ALA 2.9 0.4 + - - -
376B ILE* 1.3 81.0 - - - +
378B SER* 1.3 64.4 + - - +
379B PHE 3.3 1.1 - - - -
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Residues in contact with SER 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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301B LYS* 5.1 2.9 - - - +
341B ARG* 4.8 1.4 + - - -
342B LEU* 3.2 23.7 - - - +
347B ALA 3.3 17.0 + - - -
348B ILE* 4.0 6.5 - - - -
349B ASP* 3.1 38.6 + - - +
375B ALA 2.8 11.3 + - - -
377B LYS* 1.3 81.0 - - - +
379B PHE* 1.3 62.3 + - - +
380B GLU* 5.0 3.3 - - - +
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Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TYR* 4.1 13.9 - + - -
277B GLU* 3.8 15.0 - - + +
278B PHE* 3.7 37.5 - + + -
301B LYS* 3.5 23.7 + - - +
334B ILE* 4.0 14.6 - - + -
338B ALA* 3.7 26.9 - - + -
339B VAL* 4.0 9.2 - - + -
341B ARG* 5.1 0.2 - - - +
342B LEU* 3.4 23.1 - - + -
348B ILE* 3.6 26.5 - - + -
375B ALA* 3.2 24.2 - - + -
376B ILE 3.4 7.5 + - - +
377B LYS 3.3 0.8 - - - -
378B SER* 1.3 81.5 - - - +
380B GLU* 1.3 66.3 + - - +
381B ASN 4.0 0.2 + - - -
382B SER* 4.1 4.3 + - - -
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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
------------------------------------------------------------
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