Contacts of the helix formed by residues 72 - 83 (chain B) in PDB entry 4RN1
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 THR 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE 4.9 1.3 - - - +
71B HIS* 1.3 75.2 - - - +
73B ASP* 1.3 66.0 + - - +
74B ALA* 3.9 7.4 + - - +
75B TYR* 3.4 22.5 + - - +
76B LEU* 3.2 19.9 + - - +
96B TYR* 5.2 0.2 - - - -
146B LYS* 3.0 29.8 + - + +
147B ASP* 3.7 17.3 - - + +
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 6.1 1.0 - - - +
68B ALA* 4.7 15.9 - - - +
71B HIS 3.8 0.2 + - - -
72B THR* 1.3 72.6 - - - +
74B ALA* 1.3 58.3 + - - +
76B LEU* 3.3 9.8 + - - +
77B GLN* 2.8 53.5 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 3.3 7.7 - - - +
73B ASP* 1.3 79.7 - - - +
75B TYR* 1.3 57.3 + - - +
77B GLN* 4.0 8.8 - - - +
78B HIS* 3.0 28.1 + - - +
96B TYR* 3.4 24.1 + - + +
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 3.9 31.2 - + + -
72B THR* 3.4 19.3 + - - +
73B ASP 3.3 0.2 - - - -
74B ALA* 1.3 76.2 - - - +
76B LEU* 1.3 66.4 + - + +
78B HIS* 3.2 3.7 + - - +
79B LEU* 2.8 47.0 + - + +
96B TYR* 3.6 51.9 - + + -
98B LEU* 4.0 10.3 - - + +
146B LYS 3.9 1.8 - - - +
147B ASP* 3.7 16.8 - - - -
148B GLU 4.0 2.9 - - - -
149B ALA* 3.3 27.1 + - - +
154B TYR* 2.7 30.6 + - - -
155B LEU* 5.0 0.4 - - + -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 3.8 31.9 - - + +
67B MET* 3.9 23.1 - - + -
68B ALA* 3.9 24.5 - - + +
71B HIS* 3.8 29.8 - - + +
72B THR 3.2 18.9 + - - +
73B ASP* 3.7 7.2 - - - +
75B TYR* 1.3 80.3 - - + +
77B GLN* 1.3 62.6 + - + +
79B LEU* 3.1 13.3 + - + +
80B GLN* 3.1 24.9 + - - +
109B PHE* 4.1 2.5 - - + -
155B LEU* 4.1 15.3 - - + -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 5.1 5.6 - - + -
73B ASP* 2.8 39.6 + - - +
74B ALA* 4.0 7.2 - - - +
76B LEU* 1.3 76.1 - - + +
78B HIS* 1.3 61.1 + - - +
80B GLN* 3.4 21.1 + - - +
81B LYS* 3.3 20.6 + - - +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA 3.0 19.9 + - - +
75B TYR 3.5 5.2 - - - +
76B LEU 3.2 0.2 - - - -
77B GLN* 1.3 74.7 - - - +
79B LEU* 1.3 64.5 + - - +
81B LYS* 3.4 6.3 + - + +
82B VAL* 3.2 27.0 + - + +
90B HIS* 3.2 37.1 + + - -
92B ASP* 3.6 20.9 - - + +
93B SER* 2.9 25.8 + - - -
96B TYR* 3.5 25.7 - + + -
98B LEU* 3.6 22.0 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 2.8 45.1 + - + +
76B LEU* 3.3 14.4 - - + +
78B HIS* 1.3 78.6 - - - +
80B GLN* 1.3 61.2 + - - +
82B VAL* 3.4 5.6 - - + +
83B SER* 3.2 23.7 + - - -
98B LEU* 4.0 22.2 - - + +
108B ILE* 3.8 28.9 - - + -
109B PHE* 3.6 21.1 - - + +
112B ALA* 4.5 14.6 - - + -
154B TYR* 3.9 11.9 - - + +
155B LEU* 4.6 7.4 - - + -
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 3.2 27.3 - - - +
76B LEU 3.1 9.8 + - - +
77B GLN* 3.6 19.1 + - - +
78B HIS 3.2 0.2 - - - -
79B LEU* 1.3 75.2 - - - +
81B LYS* 1.3 65.2 + - - +
83B SER* 3.1 12.8 + - - -
84B GLN* 3.2 15.3 + - - +
109B PHE* 3.6 40.1 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLN 3.3 13.3 + - - +
78B HIS* 3.4 9.4 + - + +
80B GLN* 1.3 78.7 - - - +
82B VAL* 1.3 64.0 + - + +
83B SER 3.1 0.2 - - - -
84B GLN* 3.1 22.7 + - - +
90B HIS* 5.4 12.3 - - + +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B HIS* 3.2 41.5 + - + +
79B LEU* 3.4 9.2 - - - +
81B LYS* 1.3 77.8 - - + +
83B SER* 1.3 61.7 + - - +
84B GLN 3.3 3.1 - - - +
89B ASP* 6.4 0.9 - - + -
90B HIS* 4.6 9.4 - - + +
93B SER* 3.8 10.5 - - - +
98B LEU* 3.6 24.7 - - + +
108B ILE* 4.4 12.0 - - + +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU 3.2 17.5 + - - -
80B GLN 3.1 5.4 + - - -
81B LYS 3.1 1.0 - - - -
82B VAL* 1.3 79.4 - - - +
84B GLN* 1.3 61.0 + - - +
107B GLY* 3.2 14.4 - - - -
108B ILE* 3.1 28.5 + - - +
109B PHE* 3.2 21.3 + - - +
110B ASP* 4.5 3.1 + - - -
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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