Contacts of the helix formed by residues 81 - 92 (chain C) in PDB entry 3BDW
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 THR 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C LYS* 1.3 72.7 - - - +
82C TRP* 1.3 56.1 + - - +
83C ASN* 3.2 13.2 - - + +
84C GLU* 3.0 46.4 + - + +
85C SER* 2.7 34.3 + - - -
166C CYS 4.2 2.0 - - - +
167C GLU* 3.5 43.5 + - - +
168C ASP 3.6 8.7 - - - -
169C LYS* 4.4 6.6 - - - +
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Residues in contact with TRP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C THR* 1.3 74.2 - - - +
83C ASN* 1.3 88.8 + - - +
85C SER* 3.4 4.0 + - - -
86C ARG* 2.9 53.7 + - - +
96C LEU* 3.7 16.4 - - + +
116C TRP* 3.5 31.7 - + + +
117C ILE 3.1 24.0 + - - -
118C GLY 4.7 5.6 - - - -
119C LEU 4.3 7.5 + - - -
120C SER* 3.8 31.4 - - - -
131C GLU* 4.9 4.9 - - + -
152C CYS* 3.3 41.1 - - + +
153C ILE 4.9 0.4 + - - -
166C CYS* 3.1 21.0 + - + +
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Residues in contact with ASN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C THR* 3.2 10.5 - - + +
82C TRP* 1.3 103.5 - - - +
84C GLU* 1.3 60.4 + - + +
86C ARG* 3.0 31.1 + - - +
87C HIS* 2.9 51.0 + - + -
166C CYS* 5.8 0.4 - - - +
167C GLU* 5.7 2.7 - - - +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LYS* 3.7 26.9 - - + +
81C THR* 3.0 40.2 + - + +
83C ASN* 1.3 77.3 - - + +
85C SER* 1.3 57.2 + - - +
87C HIS* 3.4 8.2 + - + +
88C LEU* 3.0 36.4 + - + +
169C LYS* 3.8 18.8 + - - -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LYS* 3.5 10.8 + - - +
81C THR 2.7 23.9 + - - -
82C TRP* 3.4 7.2 - - - -
84C GLU* 1.3 75.0 - - - +
86C ARG* 1.3 64.4 + - - +
88C LEU* 3.3 7.2 + - - +
89C CYS* 3.0 31.3 + - - -
96C LEU* 4.0 9.2 - - - -
116C TRP* 3.6 4.7 - - - -
172C TYR* 3.4 42.7 - - - +
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TRP* 2.9 41.7 + - + +
83C ASN* 3.0 40.5 + - - +
85C SER* 1.3 78.1 - - - +
87C HIS* 1.3 80.2 + - - +
89C CYS* 3.9 2.6 + - - +
90C ALA* 3.2 24.8 + - - +
94C SER 5.2 0.2 - - - +
95C SER* 6.0 0.2 - - - -
96C LEU* 4.1 13.9 - - + -
131C GLU* 3.1 37.0 + - - +
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ASN* 2.9 48.2 + - + +
84C GLU* 3.9 7.2 - - + +
85C SER 3.2 0.2 - - - -
86C ARG* 1.3 101.9 + - - +
88C LEU* 1.3 53.8 + - + +
90C ALA* 3.1 10.4 + - - +
91C SER* 2.6 35.7 + - - -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLU* 4.2 5.6 - - - +
80C LYS* 3.7 38.4 - - + -
84C GLU* 3.0 23.5 + - + +
85C SER* 3.3 4.2 + - - +
87C HIS* 1.3 72.8 - - + +
89C CYS* 1.3 64.3 + - - +
91C SER* 2.6 28.3 + - - +
92C GLN* 3.0 14.4 + - + +
172C TYR* 3.4 32.3 - - + +
174C CYS* 4.7 0.7 - - - -
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Residues in contact with CYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER 3.0 20.9 + - - +
86C ARG 4.0 3.6 - - - +
88C LEU* 1.3 75.2 - - - +
90C ALA* 1.3 61.0 + - - +
92C GLN* 3.0 8.4 + - - +
94C SER* 2.8 41.4 + - - +
95C SER* 3.8 7.9 - - - -
96C LEU* 3.9 23.3 - - - +
172C TYR* 3.9 2.9 - - - -
174C CYS* 2.1 55.2 - - + -
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ARG 3.2 14.4 + - - +
87C HIS* 3.1 16.7 + - - +
89C CYS* 1.3 80.8 - - - +
91C SER* 1.3 55.6 + - - +
93C LYS* 3.0 19.8 + - - +
94C SER 3.3 10.7 + - - +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS 2.6 16.5 + - - -
88C LEU* 2.6 29.8 + - - +
90C ALA* 1.3 72.3 - - - +
92C GLN* 1.3 73.6 + - - +
93C LYS* 3.2 7.4 + - - +
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Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN* 4.5 9.2 + - - +
65C TRP* 3.8 35.1 + - + -
74C PHE* 6.0 6.2 - - + -
88C LEU* 3.0 14.9 + - + +
89C CYS* 3.0 9.5 + - - +
91C SER* 1.3 91.1 + - - +
93C LYS* 1.3 74.8 + - - +
94C SER* 3.3 2.6 - - - +
174C CYS* 5.3 2.7 - - - -
176C GLN* 3.3 14.0 + - - -
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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