Contacts of the helix formed by residues 72 - 80 (chain A) in PDB entry 4HJ5
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 TRP 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LYS* 3.5 34.1 - - + -
32A ASN* 3.2 27.6 - - + -
70A ILE* 3.3 22.4 - - + +
71A LEU* 1.3 73.9 - - - +
73A ASP* 1.3 71.8 + - - +
75A HIS* 3.1 24.8 + - - +
76A ASP* 3.8 1.3 - - - -
107A ILE* 3.8 23.0 - - + +
108A LEU 2.9 22.0 + - - +
109A HIS* 3.9 2.0 - - - -
1B G 3.2 97.0 + + - +
2B G 3.9 24.1 + + - -
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Residues in contact with ASP 73 (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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31A LYS 5.4 1.2 + - - -
72A TRP* 1.3 71.0 - - - +
74A GLU* 1.3 74.5 + - - +
76A ASP* 2.9 13.3 + - - +
77A PHE* 2.8 47.1 + - + -
110A GLY* 3.4 15.9 + - - -
1B G 2.8 48.6 + - - +
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Residues in contact with GLU 74 (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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73A ASP* 1.3 89.1 - - - +
75A HIS* 1.3 78.0 + - + +
77A PHE* 3.3 15.2 + - + +
78A TYR* 2.8 36.3 + - - +
110A GLY* 4.0 5.8 - - - -
111A ASP* 3.2 39.8 - - - +
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Residues in contact with HIS 75 (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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71A LEU* 4.0 23.3 - - + -
72A TRP 3.1 18.8 + - - +
74A GLU* 1.3 94.7 + - + +
76A ASP* 1.3 65.1 + - - +
78A TYR* 3.8 4.8 - - - +
79A CYS* 3.0 32.1 + - - +
108A LEU* 3.3 25.3 - - + +
109A HIS 2.6 30.4 + - - -
111A ASP 5.0 2.4 + - - -
112A SER* 5.6 1.1 - - - -
118A MET* 3.5 29.2 - - + +
119A SER* 5.9 1.8 - - - -
120A ILE* 5.3 6.3 - - + +
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Residues in contact with ASP 76 (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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28A TYR* 6.0 0.2 - - - +
29A SER 4.6 1.9 - - - +
30A ASP 5.6 0.2 - - - -
31A LYS 3.9 4.9 - - - +
32A ASN* 3.2 22.7 + - - +
33A PHE* 3.4 28.1 + - - +
71A LEU* 3.6 16.7 - - - +
72A TRP 3.4 2.2 + - - -
73A ASP* 2.9 17.2 + - - +
75A HIS* 1.3 75.9 - - - +
77A PHE* 1.3 69.6 + - - +
78A TYR 2.9 1.4 + - - -
79A CYS 3.0 0.9 + - - -
80A ARG* 3.0 58.1 + - - +
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Residues in contact with PHE 77 (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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73A ASP* 2.8 43.9 + - + -
74A GLU* 3.7 10.3 - - + +
76A ASP* 1.3 74.9 - - - +
78A TYR* 1.3 63.4 + - - +
80A ARG* 2.9 51.4 - - - +
81A ASN 5.1 0.2 + - - -
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Residues in contact with TYR 78 (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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74A GLU 2.8 21.5 + - - +
75A HIS* 3.8 4.7 - - - +
77A PHE* 1.3 76.6 - - - +
79A CYS* 1.3 75.5 + - - +
80A ARG 3.7 0.2 + - - -
81A ASN 4.7 0.5 + - - -
82A TYR* 3.2 49.8 + + - +
83A ILE* 5.8 0.7 - - + -
120A ILE* 3.7 16.4 - - + -
121A GLU* 2.7 36.0 + - - -
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Residues in contact with CYS 79 (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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33A PHE* 3.6 22.7 - - + -
71A LEU* 3.7 16.6 - - + -
75A HIS 3.0 20.2 + - - +
78A TYR* 1.3 89.7 - - - +
80A ARG* 1.3 63.9 + - - +
81A ASN 3.3 0.4 - - - -
82A TYR* 2.9 1.9 + - - -
83A ILE* 2.8 51.5 + - + -
120A ILE* 3.7 24.5 - - - -
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Residues in contact with ARG 80 (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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28A TYR* 4.9 17.0 - - + +
29A SER 4.6 10.9 + - - -
30A ASP* 5.8 2.4 - - - +
33A PHE* 3.5 33.2 - - + -
76A ASP* 3.0 50.7 + - - +
77A PHE* 2.9 54.3 - - - +
78A TYR 3.5 0.2 - - - -
79A CYS* 1.3 77.3 - - - +
81A ASN* 1.3 89.5 + - + +
82A TYR 3.7 0.9 + - - -
83A ILE 4.7 2.1 - - - +
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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