Contacts of the helix formed by residues 73 - 90 (chain Y) in PDB entry 5KHR
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 73 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72Y SER* 3.8 25.8 - - - -
74Y PRO* 3.8 28.3 - - - -
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Residues in contact with PRO 74 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73Y PRO* 3.8 25.1 - - - -
75Y GLN* 3.8 29.2 - - - -
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Residues in contact with GLN 75 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74Y PRO* 3.8 29.2 - - - -
76Y LYS* 3.8 26.7 - - - +
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Residues in contact with LYS 76 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75Y GLN* 3.8 30.1 - - - +
77Y TYR* 3.8 25.1 - - - +
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Residues in contact with TYR 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Y LYS* 3.8 26.2 - - - +
78Y GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Y TYR* 3.8 28.9 - - - +
79Y LEU* 3.8 25.8 - - - +
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Residues in contact with LEU 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Y GLN* 3.8 26.7 - - - +
80Y LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y LEU* 3.8 26.7 - - - +
81Y VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Y LEU* 3.8 28.9 - - - +
82Y TYR* 3.8 26.7 - - - +
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Residues in contact with TYR 82 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81Y VAL* 3.8 26.2 - - - +
83Y HIS* 3.8 28.9 - - - +
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Residues in contact with HIS 83 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82Y TYR* 3.8 29.6 - - - +
84Y ALA* 3.8 26.0 - - - +
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Residues in contact with ALA 84 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83Y HIS* 3.8 29.2 - - - +
85Y ASP* 3.8 25.6 - - - +
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Residues in contact with ASP 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Y ALA* 3.8 24.7 - - - +
86Y SER* 3.8 29.4 - - - +
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Residues in contact with SER 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50Y HIS* 4.6 20.9 - - - +
85Y ASP* 3.8 29.2 - - - +
87Y LEU* 3.8 26.5 - - - +
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Residues in contact with LEU 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y SER* 3.8 25.6 - - - +
88Y PHE* 3.8 29.4 - - - +
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Residues in contact with PHE 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y LEU* 3.8 29.2 - - - +
89Y HIS* 3.8 26.2 - - - +
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Residues in contact with HIS 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Y PHE* 3.8 29.6 - - - +
90Y ASP* 3.8 25.6 - - - +
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Residues in contact with ASP 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Y HIS* 3.8 28.7 - - - +
91Y LYS* 3.8 24.7 - - - +
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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