Contacts of the helix formed by residues 83 - 94 (chain B) in PDB entry 5ICN
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 ASN 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B SER* 3.9 14.3 + - - -
79B ILE* 4.1 0.3 - - - +
80B ARG* 2.8 36.9 + - - +
82B ASP* 1.3 74.1 + - + +
84B MET* 1.3 60.9 + - - +
85B SER 3.5 2.5 - - - -
86B GLU* 3.6 27.5 + - - +
87B TYR* 3.1 43.0 + - + +
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Residues in contact with MET 84 (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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79B ILE* 4.4 4.5 - - + -
80B ARG 3.6 12.3 + - - +
81B PRO* 3.6 24.5 - - - +
82B ASP 2.8 5.4 + - - +
83B ASN* 1.3 78.8 - - - +
85B SER* 1.3 56.9 + - - +
87B TYR 3.7 0.2 + - - -
88B SER* 3.1 17.3 + - - -
91B MET* 3.4 38.5 - - + +
97B GLY* 6.3 2.0 - - - -
102B VAL* 3.7 36.1 - - + +
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Residues in contact with SER 85 (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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82B ASP 4.3 6.1 + - - -
83B ASN 3.5 0.2 - - - -
84B MET* 1.3 77.0 - - - +
86B GLU* 1.3 60.9 + - - +
88B SER* 3.0 18.3 + - - -
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Residues in contact with GLU 86 (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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83B ASN* 3.5 29.3 + - + +
84B MET 3.3 0.6 - - - -
85B SER* 1.3 80.1 + - - +
87B TYR* 1.3 74.3 + - - +
88B SER 3.5 0.4 + - - -
89B LYS* 5.0 2.8 + - - +
90B GLN* 5.8 0.2 + - - -
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Residues in contact with TYR 87 (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 PHE* 3.8 20.4 - + + -
78B SER* 3.4 26.8 - - - -
79B ILE* 3.9 22.7 - - + -
83B ASN* 3.1 52.4 + - + +
84B MET 3.7 2.0 + - - +
86B GLU* 1.3 92.7 - - + +
88B SER* 1.3 51.2 + - - +
89B LYS* 2.5 21.4 + - - +
90B GLN* 2.6 59.0 + - - +
91B MET* 3.3 5.2 + - + -
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Residues in contact with SER 88 (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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84B MET 3.1 12.6 + - - -
85B SER* 3.0 22.4 + - - -
86B GLU 3.5 1.8 + - - -
87B TYR* 1.3 71.6 - - - +
89B LYS* 1.3 63.0 + - - +
91B MET* 3.5 19.8 - - - +
92B GLN* 3.3 19.4 + - - +
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Residues in contact with LYS 89 (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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86B GLU 5.0 2.9 + - - +
87B TYR 2.5 6.3 + - - +
88B SER* 1.3 77.5 - - - +
90B GLN* 1.3 69.5 + - + +
92B GLN* 3.4 10.4 + - - +
93B ARG* 3.7 9.5 + - - +
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Residues in contact with GLN 90 (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 PHE* 3.6 25.9 - - + +
87B TYR* 2.6 47.2 + - - +
89B LYS* 1.3 80.1 - - + +
91B MET* 1.3 65.6 + - - +
93B ARG* 3.4 6.0 + - - -
94B PHE* 2.7 43.6 + - + -
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Residues in contact with MET 91 (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 PHE* 3.9 20.4 - - + -
79B ILE* 4.5 9.6 - - + -
84B MET* 3.4 59.0 - - + +
87B TYR 3.3 3.4 + - - +
88B SER* 3.5 23.1 - - - +
89B LYS 3.3 0.6 - - - -
90B GLN* 1.3 78.1 - - - +
92B GLN* 1.3 56.5 + - - +
94B PHE* 3.3 1.7 + - - +
95B ASN* 3.1 23.4 + - - -
96B VAL* 3.2 39.1 + - + +
97B GLY* 5.3 2.2 - - - -
102B VAL* 4.4 3.1 - - + -
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Residues in contact with GLN 92 (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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88B SER 3.3 8.6 + - - +
89B LYS 3.4 7.6 + - - +
90B GLN 3.2 0.6 - - - -
91B MET* 1.3 73.6 - - - +
93B ARG* 1.3 65.0 + - - +
94B PHE 3.1 2.5 + - - -
95B ASN* 3.6 9.5 + - - +
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Residues in contact with ARG 93 (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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89B LYS 3.7 8.4 + - - +
90B GLN* 3.4 11.4 + - + +
92B GLN* 1.3 79.3 - - - +
94B PHE* 1.3 80.8 + - + +
95B ASN 3.7 0.2 - - - -
145B SER* 3.1 40.5 + - - +
146B GLU* 4.4 9.1 - - - +
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Residues in contact with PHE 94 (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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69B SER* 5.7 0.7 - - - -
71B ASP* 3.7 23.1 - - + -
72B TYR* 3.0 42.3 - + + -
75B PHE* 3.7 31.4 - + + -
90B GLN* 2.7 47.3 + - + +
91B MET 3.3 1.1 + - - +
92B GLN 3.1 0.6 - - - -
93B ARG* 1.3 104.1 - - - +
95B ASN* 1.3 69.5 + - - +
96B VAL* 3.4 3.8 + - + +
145B SER* 3.2 21.1 - - - -
146B GLU* 4.0 5.6 - - - -
147B ALA* 3.0 20.8 + - - +
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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