Contacts of the helix formed by residues 85 - 93 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83H GLU* 2.9 22.3 + - - +
84H TRP* 1.3 74.2 - - - +
86H GLY* 1.3 56.9 + - - +
87H LYS* 2.9 11.8 + - - +
88H TYR* 2.7 35.1 + - + +
89H MET* 2.9 26.0 + - - +
139H VAL* 5.0 0.7 - - - -
34I LYS* 3.0 40.4 + - + +
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Residues in contact with GLY 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H TRP 3.0 6.9 + - - -
85H ASP* 1.3 70.0 - - - +
87H LYS* 1.3 60.9 + - - +
89H MET* 4.1 1.3 - - - -
90H MET* 2.8 36.0 + - - +
139H VAL* 4.1 16.8 - - - -
33I LEU* 2.8 28.2 + - - -
34I LYS 3.2 0.8 + - - -
36I GLY* 4.0 8.3 - - - -
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Residues in contact with LYS 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H ASP* 2.9 9.1 + - - +
86H GLY* 1.3 76.3 - - - +
88H TYR* 1.3 62.5 + - - +
90H MET* 3.9 2.9 - - - +
91H ASP* 3.0 44.3 + - - +
32I ASN* 4.3 9.4 - - - +
33I LEU* 3.3 10.4 + - - +
34I LYS* 3.9 23.1 - - + +
50I TYR* 6.5 0.4 - - - -
52I ASP* 3.5 37.2 + - + +
54I GLU* 5.3 5.6 - - - +
55I ASP* 5.6 0.8 + - - -
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Residues in contact with TYR 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LYS* 3.0 25.2 + - - -
78H CYS* 3.6 29.2 - - + -
83H GLU* 4.6 13.9 - - + -
85H ASP* 2.7 30.6 + - - +
87H LYS* 1.3 72.7 - - - +
89H MET* 1.3 68.4 + - - +
91H ASP* 3.1 7.5 + - + +
92H ASN* 2.8 53.6 + - + +
400H NAP 3.6 15.2 + - - -
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Residues in contact with MET 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H CYS* 3.9 16.2 - - - +
80H SER 3.9 10.1 - - - +
83H GLU* 3.4 48.9 - - + +
85H ASP 2.9 15.8 + - - +
86H GLY* 3.3 8.0 + - - +
88H TYR* 1.3 80.4 - - - +
90H MET* 1.3 57.8 + - - +
92H ASN* 5.0 0.7 - - - -
93H ASN* 2.9 60.9 + - - +
139H VAL* 3.8 14.1 - - + +
140H PHE* 3.9 16.4 - - - +
143H SER* 3.6 20.6 - - - +
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Residues in contact with MET 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H GLY* 2.8 24.5 + - - +
87H LYS* 4.1 2.9 - - - +
89H MET* 1.3 73.9 - - + +
91H ASP* 1.3 58.1 - - - +
94H TYR* 3.2 28.6 + - + +
95H GLN* 2.8 28.6 + - - +
139H VAL* 5.0 3.8 - - + -
142H TYR* 4.1 21.1 - - + -
143H SER* 3.9 23.1 - - - -
146H LEU* 3.6 33.0 - - + -
33I LEU* 3.7 20.6 - - + -
50I TYR* 4.1 28.7 - - + -
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Residues in contact with ASP 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H LYS* 3.0 41.6 + - - +
88H TYR* 3.7 6.6 - - + +
90H MET* 1.3 77.6 - - - +
92H ASN* 1.3 60.3 + - + +
95H GLN* 3.3 17.3 - - - +
96H TYR* 2.9 31.4 + - - +
52I ASP* 5.2 4.5 - - - +
55I ASP* 4.1 16.6 - - - +
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Residues in contact with ASN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LYS* 2.8 29.8 + - - +
74H HIS* 5.7 0.5 + - - -
76H GLY 5.0 0.9 - - - +
77H ALA* 4.9 1.0 - - - -
78H CYS* 3.2 9.3 - - - +
88H TYR* 2.8 47.1 + - + +
89H MET* 4.4 0.7 - - - +
91H ASP* 1.3 76.0 - - + +
93H ASN* 1.3 72.5 + - - +
96H TYR* 3.1 24.2 - - - +
400H NAP 3.0 33.6 + - - -
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Residues in contact with ASN 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H HIS* 4.9 0.4 + - - -
77H ALA* 3.4 12.8 - - + +
78H CYS* 2.8 46.7 + - - +
89H MET* 2.9 30.5 + - - +
92H ASN* 1.3 82.7 + - - +
94H TYR* 1.3 63.9 + - - +
95H GLN 3.7 0.2 - - - -
97H SER* 2.8 32.8 + - - -
140H PHE* 4.0 7.9 - - - -
143H SER* 3.2 28.2 + - - +
144H LYS* 4.6 7.8 - - + +
147H 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