Contacts of the helix formed by residues 85 - 93 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLU* 2.9 21.7 + - - +
84A TRP* 1.3 74.4 - - - +
86A GLY* 1.3 57.8 + - - +
87A LYS* 2.9 12.3 + - - +
88A TYR* 2.7 33.6 + - + +
89A MET* 2.9 25.8 + - - +
139A VAL* 5.1 0.4 - - - -
34B LYS* 3.3 37.4 + - + +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TRP 3.0 8.7 + - - -
85A ASP* 1.3 70.6 + - - +
87A LYS* 1.3 60.9 + - - +
89A MET* 4.1 1.1 - - - -
90A MET* 2.8 36.0 + - - +
139A VAL* 4.1 25.1 - - - -
33B LEU* 2.8 26.2 + - - -
34B LYS 3.2 0.6 + - - -
36B GLY* 4.1 0.9 - - - -
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 2.9 8.6 + - - +
86A GLY* 1.3 76.6 - - - +
88A TYR* 1.3 64.2 + - - +
90A MET* 3.9 2.5 - - - +
91A ASP* 3.0 44.9 + - - +
32B ASN* 4.3 9.4 - - - +
33B LEU* 3.3 10.5 + - - +
34B LYS* 4.0 22.7 - - + +
50B TYR* 6.5 0.4 - - - -
52B ASP* 3.9 35.3 + - + +
54B GLU* 5.6 4.6 - - - +
55B ASP* 5.8 0.2 + - - -
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 3.0 25.5 + - - -
78A CYS* 3.6 29.2 - - + -
83A GLU* 4.6 14.1 - - + -
85A ASP* 2.7 29.3 + - - +
87A LYS* 1.3 73.9 - - - +
89A MET* 1.3 66.8 + - - +
91A ASP* 3.1 5.5 + - + -
92A ASN* 2.8 55.2 + - + +
400A NAP 3.5 16.7 + - - -
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A CYS* 3.9 17.3 - - - +
80A SER 3.9 10.3 - - - +
83A GLU* 3.4 48.9 - - + +
85A ASP 2.9 14.9 + - - +
86A GLY* 3.3 8.7 + - - +
88A TYR* 1.3 80.6 - - - +
90A MET* 1.3 57.9 + - - +
92A ASN* 5.0 0.4 - - - -
93A ASN* 2.9 60.0 + - - +
139A VAL* 3.8 14.4 - - + +
140A PHE* 3.9 16.6 - - - +
143A SER* 3.6 20.2 - - - +
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY* 2.8 24.1 + - - +
87A LYS* 4.1 2.5 - - - +
89A MET* 1.3 73.6 - - + +
91A ASP* 1.3 57.5 + - - +
94A TYR* 3.2 28.7 + - + +
95A GLN* 2.8 29.4 + - - +
139A VAL* 5.0 3.8 - - - -
142A TYR* 4.1 21.1 - - + -
143A SER* 3.9 23.3 - - - -
146A LEU* 3.7 33.0 - - + -
33B LEU* 3.7 20.0 - - + -
50B TYR* 4.2 28.0 - - + -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 6.2 0.2 - - - +
87A LYS* 3.0 42.6 + - - +
88A TYR* 3.7 6.9 - - + +
90A MET* 1.3 77.4 - - - +
92A ASN* 1.3 59.7 + - + +
95A GLN* 3.3 19.1 - - - +
96A TYR* 2.9 32.1 + - - +
52B ASP* 5.2 4.6 - - - +
55B ASP* 4.2 14.9 - - - +
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 2.7 28.8 + - - +
74A HIS* 5.7 0.5 + - - -
76A GLY 5.0 0.7 - - - +
77A ALA* 4.9 1.2 - - - -
78A CYS* 3.2 8.5 - - - +
88A TYR* 2.8 45.9 + - + +
89A MET* 4.4 0.4 - - - +
91A ASP* 1.3 75.2 - - + +
93A ASN* 1.3 73.5 + - - +
96A TYR* 3.1 23.4 - - - +
400A NAP 2.8 38.6 + - - -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 3.4 11.3 - - + +
78A CYS* 2.8 46.8 + - - +
89A MET* 2.9 29.0 + - - +
92A ASN* 1.3 83.9 + - - +
94A TYR* 1.3 64.0 + - - +
95A GLN 3.7 0.2 - - - -
97A SER* 2.8 33.2 + - - -
140A PHE* 4.0 8.3 - - - -
143A SER* 3.2 28.0 + - - +
144A LYS* 4.6 7.4 - - + +
147A 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