Contacts of the helix formed by residues 433 - 442 (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 ASP 433 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393N THR* 4.8 4.3 - - - +
431N ARG 4.0 3.4 - - - +
432N GLU* 1.3 85.5 - - - +
434N THR* 1.3 61.8 + - - +
435N VAL* 3.4 7.0 - - - +
436N ARG* 3.5 33.5 + - - +
437N GLN* 3.4 21.9 + - - +
518N GLU* 6.2 0.4 - - - -
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Residues in contact with THR 434 (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* 3.3 30.7 - - + -
397N ILE* 4.1 12.8 - - - -
428N LEU* 3.8 31.9 + - + +
431N ARG* 4.3 4.9 - - + -
432N GLU* 3.8 12.9 - - - +
433N ASP* 1.3 76.6 - - - +
435N VAL* 1.3 72.6 + - - +
437N GLN* 2.5 26.9 + - - +
438N ILE* 2.7 22.5 + - - +
508N ILE* 3.8 13.4 - - - +
509N TYR* 4.7 2.6 + - - -
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Residues in contact with VAL 435 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432N GLU* 6.0 0.9 - - + -
433N ASP* 5.0 6.1 - - - +
434N THR* 1.3 87.1 + - - +
436N ARG* 1.3 61.3 + - - +
438N ILE* 3.2 9.7 + - - +
439N VAL* 3.1 24.5 + - + +
509N TYR* 3.7 29.8 - - + +
514N LEU* 5.6 5.8 - - + -
515N PHE* 1.8 72.5 - - + -
518N GLU* 5.3 14.6 - - + -
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Residues in contact with ARG 436 (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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433N ASP* 3.5 32.6 + - - +
434N THR 3.1 0.4 - - - -
435N VAL* 1.3 75.8 - - - +
437N GLN* 1.3 60.2 + - + +
439N VAL* 3.3 9.1 + - - +
440N ALA* 2.9 28.4 + - - +
518N GLU* 3.7 41.7 + - + +
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Residues in contact with GLN 437 (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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392N ASN* 4.5 4.9 - - - +
393N THR* 3.9 12.4 - - + -
394N CYS* 2.8 57.8 - - - +
395N ASP* 5.2 2.1 - - - +
397N ILE* 4.7 9.9 - - + -
433N ASP 3.6 13.0 - - - +
434N THR* 2.5 21.0 + - - +
436N ARG* 1.3 77.0 - - + +
438N ILE* 1.3 56.6 + - - -
440N ALA* 3.8 8.3 - - + +
441N GLY* 3.1 23.0 + - - -
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Residues in contact with ILE 438 (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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397N ILE* 3.5 21.5 - - + -
401N ILE* 6.6 0.2 - - + -
434N THR* 2.7 25.9 + - - +
435N VAL* 3.6 26.9 - - - +
437N GLN* 1.3 70.1 - - - +
439N VAL* 1.3 68.1 + - + +
441N GLY* 3.5 2.5 + - - -
442N LEU* 3.1 33.9 + - + +
504N LEU* 4.2 26.2 - - + -
505N LEU* 5.1 13.0 - - + -
508N ILE* 4.2 19.3 - - + -
515N PHE* 4.5 14.1 - - + -
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Residues in contact with VAL 439 (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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435N VAL* 3.1 14.6 + - + +
436N ARG* 3.5 9.6 - - - +
438N ILE* 1.3 77.7 - - + +
440N ALA* 1.3 57.4 + - - +
442N LEU* 2.8 34.1 + - + +
515N PHE* 5.0 14.1 - - + +
518N GLU* 6.6 0.2 - - + -
519N TYR* 5.3 13.5 - - + +
522N LEU* 5.2 17.7 - - + -
541N ASN* 4.7 17.9 - - - +
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Residues in contact with ALA 440 (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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436N ARG 2.9 17.0 + - - +
437N GLN* 3.8 10.8 - - + +
438N ILE 3.4 0.2 - - - -
439N VAL* 1.3 77.4 - - - +
441N GLY* 1.3 61.1 + - - +
442N LEU 3.1 8.3 - - - +
537N ARG* 5.2 3.1 + - - -
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Residues in contact with GLY 441 (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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437N GLN 3.1 14.5 + - - -
438N ILE* 3.5 4.5 + - - -
439N VAL 3.3 0.2 - - - -
440N ALA* 1.3 76.7 - - - +
442N LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 442 (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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438N ILE* 3.1 28.3 + - + +
439N VAL* 2.8 24.5 + - + +
440N ALA 3.1 10.2 - - - +
441N GLY* 1.3 78.7 - - - +
501N ILE* 4.5 31.2 - - + -
505N LEU* 5.4 7.2 - - + -
537N ARG* 4.1 22.0 + - - -
541N ASN* 5.6 8.5 - - - +
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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