Contacts of the helix formed by residues 521 - 525 (chain N) in PDB entry 5X22
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 PRO 521 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090M LYS* 4.5 2.7 - - + -
50N PHE* 4.4 0.7 - - + -
86N ARG 3.2 18.2 - - - +
87N ARG* 3.7 14.8 - - - +
88N TYR 3.2 29.2 - - - +
89N ARG 3.3 13.0 - - - +
90N MET* 3.6 14.6 - - - -
519N VAL 3.6 0.9 - - - +
520N LEU* 1.3 102.8 - - + +
522N PRO* 1.3 66.9 - - + +
523N ASP 3.2 0.2 - - - -
524N LEU* 3.1 26.9 + - + +
525N ARG* 3.4 8.0 - - - +
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Residues in contact with PRO 522 (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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44N LEU 4.2 2.0 - - - +
45N PHE* 3.6 20.6 - - + -
50N PHE* 3.5 34.5 - - + -
86N ARG* 3.3 49.8 - - + +
520N LEU 3.6 0.6 - - - +
521N PRO* 1.3 84.2 - - + +
523N ASP* 1.3 58.3 + - - +
525N ARG* 3.1 44.3 - - - +
526N PRO* 3.3 5.9 - - - +
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Residues in contact with ASP 523 (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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1015M LEU 4.9 1.7 - - - +
1016M ILE* 4.2 8.1 - - - +
83N SER 4.7 2.9 - - - +
84N ILE* 5.5 0.2 - - - -
86N ARG* 3.1 49.4 + - - +
87N ARG* 3.3 35.3 + - + +
522N PRO* 1.3 76.9 - - - +
524N LEU* 1.3 60.9 + - - +
525N ARG 3.3 1.6 - - - -
526N PRO* 3.4 20.3 - - - +
337P HIS* 5.5 6.8 - - - -
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Residues in contact with LEU 524 (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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1016M ILE* 3.3 41.8 - - + +
1087M VAL* 3.9 29.6 - - + +
1090M LYS* 3.8 28.5 - - + -
1091M GLU* 4.8 4.8 - - + +
87N ARG* 3.8 36.3 - - + +
520N LEU* 3.9 29.2 - - + +
521N PRO* 3.1 14.8 + - + +
523N ASP* 1.3 81.9 - - - +
525N ARG* 1.3 58.9 + - - +
526N PRO* 3.6 3.8 - - - -
538N SER* 5.0 0.7 + - - -
540N LEU* 4.7 3.6 - - - +
606N ILE* 5.8 0.9 - - - +
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Residues in contact with ARG 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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44N LEU* 3.0 35.6 + - - +
45N PHE* 3.6 15.7 - - - -
50N PHE* 3.9 5.3 - - - -
519N VAL* 3.5 16.3 - - - +
520N LEU* 2.9 31.4 + - + +
521N PRO 3.4 10.1 - - - +
522N PRO* 3.1 23.4 - - - +
524N LEU* 1.3 80.0 - - - +
526N PRO* 1.3 64.2 - - - +
538N SER* 3.9 18.8 - - - -
540N LEU* 4.2 14.6 - - + -
541N ASN* 2.9 47.7 + - - +
544N TYR* 4.2 25.4 - - - -
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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