Contacts of the helix formed by residues 430 - 438 (chain F) in PDB entry 4R8A
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 ARG 430 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401F ALA 3.2 26.4 + - - +
402F ILE 4.1 3.8 + - - -
404F ALA* 4.4 3.8 + - + +
406F ILE* 3.8 23.7 - - + +
409F ALA* 3.6 12.3 - - - +
418F PRO* 3.4 16.8 - - - +
420F ASP* 2.8 42.2 + - - -
426F PHE* 3.1 41.8 + - - +
427F ARG 3.1 5.4 + - - +
428F GLN 3.0 0.4 - - - -
429F ARG* 1.3 88.5 - - - +
431F ALA* 1.3 58.9 + - - +
432F ALA 3.2 3.1 - - - -
433F LEU* 2.9 33.8 + - + -
434F PHE* 2.9 34.6 + - + -
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Residues in contact with ALA 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427F ARG* 2.8 16.4 + - + +
428F GLN* 3.0 25.1 + - + +
429F ARG 3.6 0.4 - - - -
430F ARG* 1.3 77.6 - - - +
432F ALA* 1.3 61.5 + - - +
434F PHE* 3.7 4.4 + - - +
435F GLU* 3.1 33.3 + - + +
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Residues in contact with ALA 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430F ARG 3.2 0.6 - - - -
431F ALA* 1.3 78.7 - - - +
433F LEU* 1.3 70.7 + - + +
435F GLU* 3.6 4.7 + - - +
436F ALA* 3.3 22.7 + - - +
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Residues in contact with LEU 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F GLU* 3.6 27.8 - - + +
401F ALA* 4.0 12.1 - - + +
404F ALA* 3.7 19.5 - - + -
406F ILE* 5.4 4.5 - - + -
429F ARG 4.9 2.9 - - - +
430F ARG* 2.9 24.2 + - + +
432F ALA* 1.3 87.4 - - + +
434F PHE* 1.3 58.8 + - - +
436F ALA* 3.3 7.0 + - - +
437F CYS* 3.1 34.7 + - - -
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Residues in contact with PHE 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F PHE* 3.9 11.7 - + - -
398F CYS* 3.8 31.2 - - + -
401F ALA* 3.7 16.6 - - + -
402F ILE* 4.6 8.3 - - + -
426F PHE* 3.9 25.8 - + - -
427F ARG* 4.2 14.6 - - + +
430F ARG* 2.9 53.6 + - + +
431F ALA* 4.2 5.8 - - - +
432F ALA 3.3 0.2 - - - -
433F LEU* 1.3 73.4 - - - +
435F GLU* 1.3 68.4 + - - +
436F ALA 3.1 2.0 - - - -
437F CYS* 3.1 3.2 + - - +
438F LEU* 2.8 36.6 + - + +
495F LEU* 3.6 32.1 - - + -
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Residues in contact with GLU 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427F ARG* 3.1 31.0 + - - -
431F ALA* 3.1 21.6 + - + +
432F ALA* 4.1 4.7 - - - +
434F PHE* 1.3 81.2 - - - +
436F ALA* 1.3 56.5 + - - +
438F LEU* 4.6 5.3 - - - +
439F GLY* 3.0 25.2 + - - +
488F ARG* 4.0 16.9 + - - +
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Residues in contact with ALA 436 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432F ALA 3.3 17.3 + - - +
433F LEU* 3.5 8.7 - - - +
434F PHE 3.1 0.6 - - - -
435F GLU* 1.3 78.9 - - - +
437F CYS* 1.3 59.6 + - - +
439F GLY* 3.8 2.2 - - - -
440F ARG* 3.3 23.6 + - - +
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Residues in contact with CYS 437 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397F LEU* 3.3 41.2 - - - +
398F CYS* 4.1 19.3 - - - -
400F GLU* 3.6 33.9 - - - -
401F ALA* 4.4 4.5 - - - -
433F LEU 3.1 24.4 + - - +
434F PHE* 3.1 4.5 + - - +
436F ALA* 1.3 77.8 - - - +
438F LEU* 1.3 61.7 + - - +
439F GLY 3.0 4.3 - - - -
440F ARG* 3.2 25.2 + - - +
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Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F PHE* 5.7 0.2 - - + -
397F LEU* 4.2 5.8 - - + -
398F CYS* 3.8 21.5 - - - -
427F ARG* 4.6 9.6 - - - +
434F PHE* 2.8 22.8 + - + +
435F GLU* 4.7 0.9 - - - +
437F CYS* 1.3 73.7 - - - +
439F GLY* 1.3 59.9 + - - +
440F ARG 3.2 0.9 - - - -
441F LEU* 3.2 24.1 + - + +
442F GLU* 3.5 1.0 - - - +
488F ARG* 2.8 44.7 + - + +
491F PHE* 3.7 39.7 - - + -
492F GLU* 4.0 24.7 - - + +
495F LEU* 4.8 12.1 - - + -
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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