Contacts of the helix formed by residues 85 - 93 (chain N) in PDB entry 2X86
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 ASP 85 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83N GLU* 2.9 22.9 + - - +
84N TRP* 1.3 73.8 - - - +
86N GLY* 1.3 57.9 + - - +
87N LYS* 2.9 12.3 + - - +
88N TYR* 2.7 34.0 + - + +
89N MET* 2.9 28.2 + - - +
139N VAL* 5.1 0.4 - - - -
34O LYS* 3.2 39.2 + - + +
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Residues in contact with GLY 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N TRP 3.0 8.7 + - - -
85N ASP* 1.3 70.0 + - - +
87N LYS* 1.3 61.6 + - - +
89N MET* 4.1 1.3 - - - -
90N MET* 2.8 36.0 + - - +
139N VAL* 4.1 16.2 - - - -
33O LEU* 2.9 26.0 + - - -
34O LYS 3.3 0.6 + - - -
36O GLY* 4.0 9.2 - - - -
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Residues in contact with LYS 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N ASP* 2.9 8.7 + - - +
86N GLY* 1.3 76.4 - - - +
88N TYR* 1.3 63.1 + - - +
90N MET* 4.0 2.6 - - - +
91N ASP* 3.0 44.9 + - - +
32O ASN* 4.3 9.0 - - - +
33O LEU* 3.2 11.2 + - - +
34O LYS* 3.9 23.8 - - + +
50O TYR* 6.4 0.9 - - - -
52O ASP* 3.7 37.7 + - + +
54O GLU* 5.5 4.4 - - - +
55O ASP* 5.5 1.0 + - - -
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Residues in contact with TYR 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N LYS* 3.0 25.7 + - - -
78N CYS* 3.6 30.3 - - + -
83N GLU* 4.6 14.1 - - + -
85N ASP* 2.7 30.2 + - + +
87N LYS* 1.3 75.1 - - - +
89N MET* 1.3 67.4 + - - +
91N ASP* 3.1 6.7 + - + +
92N ASN* 2.8 54.3 + - + +
400N NAP 3.6 14.6 + - - -
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Residues in contact with MET 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N CYS* 3.9 16.2 - - - +
80N SER 3.9 9.9 - - - +
83N GLU* 3.4 49.1 - - + +
85N ASP 2.9 15.5 + - - +
86N GLY* 3.3 8.7 + - - +
88N TYR* 1.3 79.4 - - - +
90N MET* 1.3 58.2 + - - +
92N ASN* 5.0 0.9 - - - -
93N ASN* 2.9 60.4 + - - +
139N VAL* 3.8 14.4 - - + +
140N PHE* 3.9 16.4 - - - +
143N SER* 3.6 20.6 - - - +
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Residues in contact with MET 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N GLY* 2.8 23.8 + - - +
87N LYS* 4.1 2.9 - - - +
89N MET* 1.3 72.1 - - + +
91N ASP* 1.3 58.4 + - - +
94N TYR* 3.2 29.4 + - + +
95N GLN* 2.8 28.6 + - - +
139N VAL* 5.0 3.8 - - - -
142N TYR* 4.1 20.6 - - + -
143N SER* 3.9 22.9 - - - -
146N LEU* 3.7 32.3 - - + -
33O LEU* 3.7 20.0 - - + -
50O TYR* 4.3 29.4 - - + -
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Residues in contact with ASP 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N LYS* 3.0 41.5 + - - +
88N TYR* 3.7 6.5 - - + +
90N MET* 1.3 76.8 - - - +
92N ASN* 1.3 60.0 + - + +
95N GLN* 3.3 18.5 - - - +
96N TYR* 2.9 31.9 + - - +
52O ASP* 5.2 3.9 - - - +
55O ASP* 4.3 13.8 - - - +
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Residues in contact with ASN 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N LYS* 2.8 30.1 + - - +
74N HIS* 5.7 0.3 + - - -
76N GLY 5.0 0.9 - - - +
77N ALA* 4.9 1.0 - - - -
78N CYS* 3.2 7.3 - - - +
88N TYR* 2.8 47.4 + - + +
89N MET* 4.4 0.4 - - - +
91N ASP* 1.3 76.7 - - + +
93N ASN* 1.3 73.0 + - - +
96N TYR* 3.1 24.2 - - - +
400N NAP 2.8 36.7 + - - -
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Residues in contact with ASN 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N HIS* 6.2 0.2 - - - -
77N ALA* 3.4 12.4 - - + +
78N CYS* 2.8 46.5 + - - +
89N MET* 2.9 29.2 + - - +
92N ASN* 1.3 84.3 + - - +
94N TYR* 1.3 65.4 + - - +
97N SER* 2.8 32.7 + - - -
140N PHE* 4.0 7.9 - - - -
143N SER* 3.2 28.2 + - - +
144N LYS* 4.6 6.9 - - + +
147N PHE* 6.0 0.4 - - - -
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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