Contacts of the helix formed by residues 422 - 432 (chain A) in PDB entry 5SUY
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 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A HIS 3.8 2.2 + - - -
421A THR* 1.3 77.3 - - - +
423A MET* 1.3 63.5 + - - +
424A ALA* 3.6 10.2 + - - +
425A SER* 2.9 42.4 + - - -
426A VAL* 3.2 18.2 + - - +
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Residues in contact with MET 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A THR 3.4 2.0 + - - +
422A ASP* 1.3 73.7 - - - +
424A ALA* 1.3 62.7 + - - +
426A VAL* 3.4 2.4 + - - +
427A THR* 3.1 26.4 + - - -
478B TYR* 3.2 39.0 - - + +
481B GLY* 4.0 17.0 - - - +
482B LEU* 3.9 12.2 - - + +
485B ALA* 3.9 18.6 - - + -
487B LEU* 3.5 24.5 - - + -
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ASP* 3.3 9.2 + - - +
423A MET* 1.3 77.6 - - - +
425A SER* 1.3 59.4 - - - +
427A THR* 3.3 4.0 + - - -
428A LYS* 3.0 46.8 + - - +
487B LEU* 4.1 24.7 - - + +
508B LEU* 5.5 0.2 - - - +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LEU* 5.3 2.0 - - - +
421A THR* 4.4 9.6 - - - -
422A ASP* 2.9 34.6 + - - -
423A MET 3.2 0.2 - - - -
424A ALA* 1.3 74.0 - - - +
426A VAL* 1.3 63.8 + - - +
428A LYS* 3.4 9.6 + - - +
429A ALA* 2.9 24.6 + - - +
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LEU* 4.5 10.8 - - + -
418A SER 4.5 4.9 - - - +
421A THR* 3.7 24.7 - - + -
422A ASP 3.2 12.7 + - - +
423A MET 3.8 3.4 - - - +
425A SER* 1.3 74.1 - - - +
427A THR* 1.3 58.3 + - - +
429A ALA* 3.2 8.1 + - - +
430A MET* 2.9 27.3 + - + +
461B TRP* 4.2 5.1 - - + -
462B LEU* 3.8 27.8 - - + -
466B VAL* 4.0 17.3 - - + -
478B TYR* 3.6 29.2 - - + +
482B LEU* 5.8 0.9 - - + -
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A MET 3.1 14.6 + - - -
424A ALA 3.3 8.3 + - - -
426A VAL* 1.3 77.6 - - - +
428A LYS* 1.3 56.9 + - - +
430A MET* 3.1 14.5 + - + +
431A ALA* 2.9 27.0 + - - +
482B LEU* 3.3 24.0 - - - +
487B LEU* 3.7 34.0 - - + +
488B ILE* 4.7 2.0 - - + -
505B PHE* 3.8 19.3 - - + -
508B LEU* 4.0 12.3 - - + -
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Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ALA* 3.0 36.0 + - - +
425A SER* 3.8 8.7 - - - +
427A THR* 1.3 73.7 - - - +
429A ALA* 1.3 61.5 + - - +
431A ALA* 3.3 8.3 + - - +
432A ALA* 3.2 21.3 + - - +
487B LEU* 6.3 0.2 - - - -
508B LEU* 4.0 45.9 + - + +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LEU* 4.1 26.7 - - + -
425A SER 2.9 14.8 + - - +
426A VAL 3.5 8.5 - - - +
427A THR 3.2 0.2 - - - -
428A LYS* 1.3 76.5 - - - +
430A MET* 1.4 61.1 + - - +
432A ALA* 3.1 18.4 + - - +
435A SER* 3.3 13.3 - - - -
461B TRP* 4.3 5.1 - - + -
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Residues in contact with MET 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A VAL* 2.9 13.6 + - - +
427A THR* 3.4 10.5 - - + +
429A ALA* 1.4 75.3 - - - +
431A ALA* 1.3 57.4 + - - +
432A ALA 4.1 0.3 - - - +
435A SER* 2.8 21.2 + - - -
437A LEU* 3.8 30.9 - - + +
453B PHE* 5.1 0.2 - - + -
458B VAL* 4.0 36.6 - - + +
461B TRP* 3.7 45.0 - - + -
462B LEU* 4.6 6.5 - - - -
482B LEU* 4.6 9.0 - - + -
488B ILE* 4.4 10.8 - - + -
505B PHE* 3.5 27.4 - - + -
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A THR 2.9 14.8 + - - +
428A LYS* 3.7 6.1 - - - +
429A ALA 3.2 0.2 - - - -
430A MET* 1.3 74.3 - - - +
432A ALA* 1.3 65.3 + - - +
433A PRO* 3.8 2.4 - - - +
505B PHE* 3.5 35.7 - - + -
508B LEU* 3.9 17.9 - - + -
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A LYS 3.2 9.6 + - - +
429A ALA* 3.1 17.5 + - - +
430A MET 4.1 0.2 - - - +
431A ALA* 1.3 81.0 - - - +
433A PRO* 1.3 82.2 - - + +
434A GLU 3.5 0.2 + - - -
435A SER* 3.3 18.7 + - - -
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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