Contacts of the helix formed by residues 524 - 534 (chain N) in PDB entry 6AH0
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 ALA 524 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517N GLY* 5.6 13.0 - - - -
518N SER* 5.8 1.6 - - - +
523N GLN* 1.3 76.8 - - - +
525N VAL* 1.3 62.4 + - - +
527N ARG* 4.5 0.3 - - - -
528N ALA* 3.6 15.6 + - - -
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Residues in contact with VAL 525 (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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523N GLN 3.5 0.8 - - - +
524N ALA* 1.3 74.8 - - - +
526N MET* 1.3 59.7 + - - +
528N ALA* 3.3 3.6 + - - +
529N VAL* 2.9 25.6 + - - -
556N LEU 5.3 8.1 - - - -
560N ARG* 6.5 1.1 - - - +
567N LEU 6.0 5.2 - - - -
568N GLN* 6.5 1.1 - - - +
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Residues in contact with MET 526 (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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497N ASN* 4.3 22.2 - - - +
498N GLY* 5.0 1.4 - - - +
523N GLN* 4.3 3.4 + - - +
524N ALA 3.5 0.2 - - - -
525N VAL* 1.3 76.3 - - - +
527N ARG* 1.3 50.9 + - - +
529N VAL* 3.0 2.4 + - - +
530N ILE* 2.5 37.1 + - - -
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Residues in contact with ARG 527 (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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497N ASN 4.0 5.0 + - - -
500N GLU 5.0 0.9 - - - -
501N ILE* 3.4 33.3 - - - +
523N GLN 4.0 12.6 + - - -
524N ALA 4.5 1.8 - - - -
525N VAL 3.5 0.2 - - - -
526N MET* 1.3 73.7 - - - +
528N ALA* 1.3 55.5 + - - +
531N GLY* 2.9 26.9 + - - -
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Residues in contact with ALA 528 (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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514N ASP* 5.9 7.0 - - - +
524N ALA 3.6 10.9 + - - -
525N VAL 3.3 6.8 + - - -
526N MET 3.1 0.4 - - - -
527N ARG* 1.3 77.1 - - - +
529N VAL* 1.3 55.9 + - - +
531N GLY* 3.5 1.4 + - - -
532N ILE* 2.9 24.4 + - - -
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Residues in contact with VAL 529 (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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525N VAL 2.9 13.7 + - - -
526N MET* 3.5 2.7 - - - +
528N ALA* 1.3 73.0 - - - +
530N ILE* 1.3 56.3 + - - +
532N ILE* 4.3 2.0 - - - +
533N GLY* 2.6 34.3 + - - -
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Residues in contact with ILE 530 (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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498N GLY* 6.0 4.5 - - - -
501N ILE* 5.2 8.1 - - - +
526N MET 2.5 21.9 + - - -
527N ARG* 3.8 2.0 - - - +
529N VAL* 1.3 72.8 - - - +
531N GLY* 1.3 56.4 + - - +
533N GLY* 4.2 0.7 - - - -
534N ILE* 3.3 21.8 + - - -
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Residues in contact with GLY 531 (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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501N ILE 4.6 7.2 + - - -
510N ALA* 6.1 3.1 - - - -
527N ARG 2.9 16.5 + - - -
528N ALA 3.7 1.6 - - - -
530N ILE* 1.3 74.2 - - - +
532N ILE* 1.3 61.5 + - - +
534N ILE* 3.8 2.7 + - - -
535N GLU* 3.8 11.8 + - - -
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Residues in contact with ILE 532 (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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528N ALA 2.9 16.2 + - - -
529N VAL* 3.1 3.6 + - - +
531N GLY* 1.3 75.4 - - - +
533N GLY* 1.3 63.5 + - - +
534N ILE 3.2 0.2 - - - -
535N GLU* 3.1 17.2 + - - +
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Residues in contact with GLY 533 (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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529N VAL 2.6 19.4 + - - -
530N ILE* 4.2 1.3 - - - -
532N ILE* 1.3 72.5 - - - +
534N ILE* 1.3 60.3 + - - +
535N GLU 3.1 9.4 + - - +
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Residues in contact with ILE 534 (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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530N ILE 3.3 16.2 + - - -
531N GLY* 3.8 5.3 + - - -
532N ILE 3.2 1.2 - - - -
533N GLY* 1.3 75.6 - - - +
535N GLU* 1.3 59.2 + - - +
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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