Contacts of the helix formed by residues 421 - 432 (chain N) in PDB entry 5A31
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 CYS 421 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400N TYR* 3.4 42.2 - - + +
403N ALA* 4.9 7.2 - - - -
404N ILE* 4.9 0.4 - - - -
407N LEU* 4.8 9.6 - - - -
417N LEU* 2.9 35.6 + - + +
418N GLU* 4.6 1.6 - - - +
420N ALA* 1.3 76.5 - - - +
422N GLU* 1.3 64.7 + - - +
423N PRO 3.3 1.1 - - - -
424N ILE* 3.1 16.3 + - + -
425N ARG* 3.0 32.0 + - - +
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Residues in contact with GLU 422 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379N LYS* 5.7 3.1 + - - -
418N GLU 3.8 12.2 + - - +
419N VAL* 3.3 24.9 + - - +
420N ALA 3.3 0.2 - - - -
421N CYS* 1.3 76.9 - - - +
423N PRO* 1.4 70.2 - - + +
425N ARG* 3.5 8.0 - - - +
426N ARG* 3.4 24.9 + - + +
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Residues in contact with PRO 423 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379N LYS* 4.1 36.1 - - + +
382N LEU* 5.2 2.9 - - + -
383N GLU* 4.8 5.2 - - - +
387N LEU* 3.8 20.3 - - + +
419N VAL 3.7 4.5 - - - +
420N ALA 3.1 23.8 - - - +
422N GLU* 1.4 90.5 - - + +
424N ILE* 1.3 64.2 + - - +
426N ARG* 3.4 9.1 + - + +
427N TYR* 2.9 25.8 + - - +
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Residues in contact with ILE 424 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382N LEU* 3.4 26.0 - - + -
386N LEU* 5.0 1.6 - - + -
387N LEU* 3.5 24.7 - - + -
396N ILE* 4.5 6.1 - - + -
399N LEU* 4.5 11.4 - - + -
400N TYR* 3.6 62.4 - - + +
403N ALA* 5.2 2.2 - - + -
421N CYS* 3.1 19.5 + - - +
423N PRO* 1.3 80.7 - - - +
425N ARG* 1.3 65.3 + - - +
427N TYR* 3.2 2.8 + - - +
428N LEU* 2.9 31.8 + - + +
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Residues in contact with ARG 425 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400N TYR* 2.9 30.7 + - - -
417N LEU* 5.6 4.4 - - - +
418N GLU* 4.8 19.4 + - - +
421N CYS* 3.0 19.3 + - - +
422N GLU* 3.5 13.0 - - - +
424N ILE* 1.3 78.5 - - - +
426N ARG* 1.3 64.8 + - + +
428N LEU* 3.2 6.8 + - - +
429N ARG* 3.0 48.2 + - - +
503N SER* 4.8 7.7 + - - -
507N SER* 3.0 45.4 + - - +
508N ILE* 5.5 3.4 - - - +
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Residues in contact with ARG 426 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422N GLU* 3.4 15.2 + - + +
423N PRO* 3.4 12.7 + - + +
424N ILE 3.4 0.4 - - - -
425N ARG* 1.3 78.7 - - + +
427N TYR* 1.3 63.1 + - - +
429N ARG* 3.2 44.7 + - - +
430N THR* 3.0 28.8 + - - +
793N GLN* 2.7 46.5 + - - +
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Residues in contact with TYR 427 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I GLU* 3.5 20.6 + - - -
387N LEU* 2.8 46.0 - - + -
389N PRO* 2.9 31.7 - - - +
396N ILE* 3.5 33.2 - - + -
423N PRO 2.9 18.6 + - - +
424N ILE 3.7 3.6 - - - +
426N ARG* 1.3 78.0 - - - +
428N LEU* 1.3 63.7 + - + +
430N THR* 3.2 26.5 - - + +
431N ARG* 3.0 35.2 + - + +
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Residues in contact with LEU 428 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393N THR* 5.1 4.7 - - + -
396N ILE* 3.4 39.9 - - + -
397N ILE* 4.0 27.4 - - + -
400N TYR* 4.1 25.1 - - + -
424N ILE* 2.9 23.2 + - + +
425N ARG* 3.8 5.4 - - - +
427N TYR* 1.3 76.6 - - + +
429N ARG* 1.3 63.4 + - - +
430N THR 3.1 1.0 + - - -
431N ARG* 3.1 14.7 + - + +
432N GLU* 3.3 10.4 + - - -
434N THR* 3.8 20.4 + - + +
504N LEU* 5.7 1.1 - - + -
508N ILE* 3.9 24.7 - - + -
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Residues in contact with ARG 429 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425N ARG* 3.0 41.5 + - - +
426N ARG* 3.2 48.7 - - - +
428N LEU* 1.3 76.0 - - - +
430N THR* 1.3 63.8 + - - +
432N GLU* 3.7 15.0 - - - +
507N SER 3.3 21.5 + - - -
508N ILE* 3.9 29.4 + - + +
509N TYR* 3.7 21.8 + - + +
791N ASP* 5.6 6.5 + - - -
793N GLN* 4.1 4.6 + - - -
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Residues in contact with THR 430 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I GLU* 5.6 3.4 - - - +
426N ARG* 3.0 18.9 + - - +
427N TYR* 3.2 24.3 - - + +
428N LEU 3.0 0.2 - - - -
429N ARG* 1.3 80.8 - - - +
431N ARG* 1.3 70.2 + - + +
432N GLU* 3.8 8.0 - - - +
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Residues in contact with ARG 431 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I ARG* 4.3 6.3 - - - +
55I VAL* 5.7 1.4 - - - +
388N HIS 4.6 0.2 - - - -
389N PRO* 3.5 17.8 - - - +
390N GLY 4.1 1.8 - - - +
391N VAL 2.7 28.8 + - - +
393N THR* 3.2 38.1 - - - +
396N ILE* 3.2 22.3 - - - +
427N TYR* 3.0 42.4 + - + +
428N LEU* 3.1 14.7 + - - +
430N THR* 1.3 85.0 - - + +
432N GLU* 1.3 78.9 + - - +
433N ASP* 4.0 3.8 - - - +
434N THR* 4.3 5.4 - - + -
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Residues in contact with GLU 432 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393N THR* 4.7 2.6 + - - -
428N LEU 3.3 10.5 + - - -
429N ARG 3.7 10.1 - - - +
430N THR 3.8 5.4 - - - +
431N ARG* 1.3 89.1 - - - +
433N ASP* 1.3 76.5 + - - +
434N THR* 3.0 20.5 + - - +
435N VAL* 5.7 1.8 - - + -
509N TYR* 3.7 26.3 + - - +
514N LEU* 6.2 0.2 - - - +
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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