Contacts of the helix formed by residues 85 - 93 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F LYS* 3.2 38.7 + - + +
83J GLU* 2.9 21.6 + - - +
84J TRP* 1.3 75.5 - - - +
86J GLY* 1.3 56.6 + - - +
87J LYS* 2.9 12.1 + - - +
88J TYR* 2.7 34.1 + - + +
89J MET* 2.9 27.9 + - - +
139J VAL* 5.1 0.7 - - - -
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Residues in contact with GLY 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 2.8 28.4 + - - -
34F LYS 3.2 0.6 + - - -
36F GLY* 4.0 9.2 - - - -
84J TRP 3.0 6.9 + - - -
85J ASP* 1.3 71.1 + - - +
87J LYS* 1.3 59.9 + - - +
89J MET* 4.1 1.6 - - - -
90J MET* 2.8 36.2 + - - +
139J VAL* 4.1 16.6 - - - -
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Residues in contact with LYS 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ASN* 4.2 9.9 - - - +
33F LEU* 3.2 10.8 + - - +
34F LYS* 3.8 24.0 - - + +
50F TYR* 6.4 0.7 - - - -
52F ASP* 3.6 36.8 + - + +
54F GLU* 5.4 5.0 - - - +
55F ASP* 5.6 1.0 + - - -
85J ASP* 2.9 8.7 + - - +
86J GLY* 1.3 77.1 - - - +
88J TYR* 1.3 63.3 + - - +
90J MET* 3.9 2.7 - - - +
91J ASP* 3.0 44.4 + - - +
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Residues in contact with TYR 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J LYS* 3.0 25.5 + - - -
78J CYS* 3.6 31.0 - - + -
83J GLU* 4.6 14.8 - - + -
85J ASP* 2.7 29.4 + - + +
87J LYS* 1.3 75.0 - - - +
89J MET* 1.3 66.2 + - - +
91J ASP* 3.1 6.9 + - + -
92J ASN* 2.8 54.5 + - + +
400J NAP 3.5 15.8 + - - -
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Residues in contact with MET 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J CYS* 3.9 16.2 - - - +
80J SER 3.9 11.4 - - - +
83J GLU* 3.4 48.5 - - + +
85J ASP 2.9 15.1 + - - +
86J GLY* 3.7 8.5 - - - +
88J TYR* 1.3 80.6 - - - +
90J MET* 1.3 56.7 + - + +
92J ASN* 5.0 0.4 - - - -
93J ASN* 2.9 61.8 + - - +
139J VAL* 3.8 14.8 - - + +
140J PHE* 3.9 16.2 - - - +
143J SER* 3.6 20.2 - - - +
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Residues in contact with MET 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.6 20.2 - - + -
50F TYR* 4.1 28.5 - - + -
86J GLY* 2.8 23.8 + - - +
87J LYS* 4.1 2.9 - - - +
89J MET* 1.3 72.7 - - - +
91J ASP* 1.3 58.1 + - - +
94J TYR* 3.2 29.3 + - + +
95J GLN* 2.8 29.7 + - - +
139J VAL* 5.0 4.3 - - - -
142J TYR* 4.1 20.9 - - + -
143J SER* 3.9 23.1 - - - -
146J LEU* 3.7 33.0 - - + -
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Residues in contact with ASP 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ASP* 5.1 4.9 - - - +
55F ASP* 4.1 15.9 - - - +
87J LYS* 3.0 40.8 + - - +
88J TYR* 3.1 7.1 + - + +
90J MET* 1.3 77.2 - - - +
92J ASN* 1.3 60.0 - - + +
95J GLN* 3.3 16.7 - - - +
96J TYR* 2.9 31.9 + - - +
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Residues in contact with ASN 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J LYS* 2.8 28.1 + - - +
74J HIS* 5.7 0.7 + - - -
76J GLY 5.0 0.9 - - - +
77J ALA* 4.9 1.0 - - - -
78J CYS* 3.2 8.7 - - - +
88J TYR* 2.8 48.1 + - + +
89J MET* 4.4 0.4 - - - +
91J ASP* 1.3 76.1 - - + +
93J ASN* 1.3 71.1 + - - +
96J TYR* 3.1 24.1 - - - +
400J NAP 3.0 36.7 + - - -
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Residues in contact with ASN 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74J HIS* 4.9 0.2 + - - -
77J ALA* 3.4 12.8 - - + +
78J CYS* 2.8 45.9 + - - +
89J MET* 2.9 28.6 + - - +
92J ASN* 1.3 83.6 + - - +
94J TYR* 1.3 64.0 + - - +
95J GLN 3.7 0.2 - - - -
97J SER* 2.8 32.4 + - - -
140J PHE* 4.0 8.7 - - - -
143J SER* 3.2 28.8 + - - +
144J LYS* 4.6 6.9 - - + +
147J 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