Contacts of the helix formed by residues 75 - 82 (chain A) in PDB entry 4YON
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 PHE 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.0 22.7 - + - -
71A LEU* 3.3 22.9 + - + +
74A ALA* 1.3 88.2 - - + +
76A LEU* 1.3 62.6 + - - +
77A HIS 3.4 1.1 - - - -
78A ARG* 3.3 2.3 + - - +
79A ILE* 2.9 40.4 + - + +
100A PHE* 3.5 32.8 - + + -
171A PHE* 5.8 0.2 - + - -
172A LEU* 3.9 26.2 - - + -
175A CYS* 3.3 32.1 - - + -
176A MET* 3.8 17.7 - - + -
188A LEU* 3.7 30.3 - - + -
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Residues in contact with LEU 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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71A LEU 3.5 5.8 + - - +
72A GLN* 3.1 15.8 + - - +
75A PHE* 1.3 78.7 - - - +
77A HIS* 1.3 59.4 + - - +
79A ILE* 3.8 4.4 - - + +
80A ARG* 2.9 48.8 + - - +
96A VAL* 3.7 29.8 - - + -
100A PHE* 3.8 24.0 - - + -
101A SER 6.0 0.7 - - - +
103A ILE* 3.8 20.4 - - + -
104A GLU* 3.4 37.7 - - + +
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Residues in contact with HIS 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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72A GLN* 2.7 53.8 + - + +
73A SER* 3.6 22.2 - - - +
76A LEU* 1.3 73.3 - - - +
78A ARG* 1.3 63.1 + - - +
80A ARG* 3.3 31.4 + - - +
81A GLN* 3.0 33.8 + - + +
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Residues in contact with ARG 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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73A SER 3.6 5.6 + - - +
74A ALA* 3.6 19.5 - - - +
75A PHE 3.3 3.0 + - - +
77A HIS* 1.3 79.3 - - - +
79A ILE* 1.3 63.6 + - - +
81A GLN* 3.4 14.1 + - - +
82A ASN* 3.5 11.6 + - - +
85A ASP* 5.1 5.7 + - - -
89A LYS* 5.6 2.6 - - - +
171A PHE* 3.9 35.0 - - + -
174A SER* 2.7 40.9 + - - -
175A CYS* 3.7 13.6 - - - +
178A LEU* 3.1 25.0 - - - +
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Residues in contact with ILE 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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75A PHE* 2.9 30.6 + - + +
76A LEU* 3.8 5.4 - - - +
78A ARG* 1.3 75.3 - - - +
80A ARG* 1.3 63.8 + - - +
82A ASN 3.2 4.7 - - - -
83A VAL* 3.1 30.6 + - + -
86A SER* 3.7 22.7 - - - +
91A LEU* 3.8 22.4 - - + -
96A VAL* 3.9 31.6 - - + -
100A PHE* 4.7 9.6 - - + -
171A PHE* 4.0 23.3 - - + -
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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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76A LEU* 2.9 34.4 + - - +
77A HIS* 3.4 30.6 + - - +
79A ILE* 1.3 79.5 - - - +
81A GLN* 1.3 69.2 + - - +
82A ASN 3.4 0.3 + - - -
83A VAL* 3.9 16.9 - - + +
104A GLU* 2.8 41.8 + - - -
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Residues in contact with GLN 81 (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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77A HIS* 3.0 23.5 + - + +
78A ARG* 3.9 7.2 - - - +
79A ILE 3.2 0.4 - - - -
80A ARG* 1.3 88.3 - - - +
82A ASN* 1.3 62.2 + - + +
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Residues in contact with ASN 82 (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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78A ARG 3.5 7.6 + - - +
79A ILE* 3.2 8.1 + - - +
81A GLN* 1.3 82.7 - - + +
83A VAL* 1.3 63.3 + - - +
84A ALA* 3.8 8.0 + - - +
85A ASP* 3.3 38.2 + - + +
86A SER* 3.5 9.4 + - - -
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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