Contacts of the helix formed by residues 85 - 93 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F GLU* 2.9 22.8 + - - +
84F TRP* 1.3 74.4 - - - +
86F GLY* 1.3 57.6 + - - +
87F LYS* 2.9 12.1 + - - +
88F TYR* 2.7 34.4 + - + +
89F MET* 2.9 28.4 + - - +
139F VAL* 5.1 0.4 - - - -
34G LYS* 3.4 36.6 + - + +
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Residues in contact with GLY 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F TRP 3.0 8.5 + - - -
85F ASP* 1.3 70.6 + - - +
87F LYS* 1.3 60.9 + - - +
89F MET* 4.1 1.3 - - - -
90F MET* 2.8 36.0 + - - +
139F VAL* 4.1 16.6 - - - -
33G LEU* 2.8 26.2 + - - -
34G LYS 3.2 0.6 + - - -
36G GLY* 4.0 9.4 - - - -
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Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ASP* 2.9 8.8 + - - +
86F GLY* 1.3 76.8 - - - +
88F TYR* 1.3 63.6 + - - +
90F MET* 3.9 2.3 - - - +
91F ASP* 3.0 44.7 + - - +
32G ASN* 4.3 9.9 - - - +
33G LEU* 3.2 11.1 + - - +
34G LYS* 3.9 23.1 - - + +
50G TYR* 6.0 0.7 - - - -
52G ASP* 3.6 35.9 + - + +
54G GLU* 5.5 4.8 - - - +
55G ASP* 5.6 1.0 + - - -
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Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LYS* 3.0 25.6 + - - -
78F CYS* 3.6 29.4 - - + -
83F GLU* 4.6 14.6 - - + -
85F ASP* 2.7 30.0 + - - +
87F LYS* 1.3 73.9 - - - +
89F MET* 1.3 67.8 + - - +
91F ASP* 3.1 6.3 + - + +
92F ASN* 2.8 54.5 + - + +
400F NAP 3.4 16.5 + - - -
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Residues in contact with MET 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F CYS* 3.9 16.6 - - - +
80F SER 3.9 10.3 - - - +
83F GLU* 3.4 48.9 - - + +
85F ASP 2.9 15.3 + - - +
86F GLY* 3.7 8.3 - - - +
88F TYR* 1.3 80.8 - - - +
90F MET* 1.3 56.6 + - - +
92F ASN* 5.0 0.7 - - - -
93F ASN* 2.9 60.8 + - - +
139F VAL* 3.8 13.9 - - + +
140F PHE* 3.9 16.8 - - - +
143F SER* 3.6 20.6 - - - +
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Residues in contact with MET 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F GLY* 2.8 23.8 + - - +
87F LYS* 4.1 2.2 - - - +
89F MET* 1.3 73.6 - - + +
91F ASP* 1.3 57.2 + - - +
94F TYR* 3.2 29.3 + - + +
95F GLN* 2.8 29.3 + - - +
139F VAL* 5.0 3.6 - - - -
142F TYR* 4.1 21.3 - - + -
143F SER* 3.9 23.6 - - - -
146F LEU* 3.7 32.5 - - + -
33G LEU* 3.6 20.4 - - + -
50G TYR* 4.2 28.3 - - + -
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Residues in contact with ASP 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F LEU* 6.1 0.2 - - - +
87F LYS* 3.0 42.1 + - - +
88F TYR* 3.7 6.9 - - + +
90F MET* 1.3 77.9 - - - +
92F ASN* 1.3 60.3 + - + +
95F GLN* 3.3 19.3 - - - +
96F TYR* 2.9 31.5 + - - +
52G ASP* 5.2 4.7 - - - +
55G ASP* 4.2 14.3 - - - +
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Residues in contact with ASN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LYS* 2.8 30.3 + - - +
74F HIS* 5.7 0.5 + - - -
76F GLY 5.0 1.2 - - - +
77F ALA* 4.9 1.4 - - - -
78F CYS* 3.2 8.9 - - + +
88F TYR* 2.8 45.4 + - + +
89F MET 4.9 0.2 - - - -
91F ASP* 1.3 76.3 - - + +
93F ASN* 1.3 72.1 + - - +
96F TYR* 3.1 24.3 - - - +
400F NAP 2.9 35.5 + - - -
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Residues in contact with ASN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F HIS* 4.9 0.2 + - - -
77F ALA* 3.4 11.5 - - + +
78F CYS* 2.8 47.2 + - - +
89F MET* 2.9 29.2 + - - +
92F ASN* 1.3 84.0 + - - +
94F TYR* 1.3 63.6 + - - +
95F GLN 3.7 0.2 - - - -
97F SER* 2.8 33.1 + - - -
140F PHE* 4.0 8.5 - - - -
143F SER* 3.2 28.2 + - - +
144F LYS* 4.6 7.1 - - - +
147F PHE* 6.0 0.2 - - - -
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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