Contacts of the helix formed by residues 80 - 93 (chain C) in PDB entry 3N6J
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 ILE 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ARG* 6.1 0.7 - - + -
77C PRO* 3.5 32.5 + - + +
78C ILE 3.1 1.0 - - - -
79C SER* 1.3 92.1 - - - +
81C LEU* 1.3 58.5 + - - +
82C ASN* 3.1 4.3 - - - -
83C LYS* 2.9 56.2 + - + +
84C ILE* 3.1 16.5 + - + +
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Residues in contact with LEU 81 (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 ILE* 3.2 20.1 + - + +
79C SER 4.4 5.6 - - - +
80C ILE* 1.3 77.0 - - - +
82C ASN* 1.3 79.8 + - - +
84C ILE* 3.5 14.3 - - - +
85C VAL* 3.3 29.9 + - + +
118C GLU* 6.0 1.8 - - + -
121C LEU* 3.7 43.2 - - + +
122C LEU* 3.8 33.7 - - + +
125C MSE 4.0 23.6 - - + -
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Residues in contact with ASN 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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79C SER 5.9 0.7 - - - +
80C ILE* 3.0 2.4 + - - +
81C LEU* 1.3 92.8 - - + +
83C LYS* 1.3 61.6 + - - +
85C VAL* 3.4 19.3 - - - +
86C ASN* 3.5 11.3 - - - +
118C GLU* 5.4 2.4 - - - +
321C THR* 5.2 6.9 + - - +
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Residues in contact with LYS 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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80C ILE* 2.9 32.3 + - + +
82C ASN* 1.3 76.5 - - - +
84C ILE* 1.3 66.0 + - + +
86C ASN* 3.0 18.7 + - - +
87C ASP* 3.1 34.6 + - - +
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Residues in contact with ILE 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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11C ILE* 6.0 2.9 - - + -
72C HIS* 4.8 10.5 - - + +
73C VAL* 5.1 12.3 - - + -
76C ARG* 4.8 25.6 - - + -
77C PRO 4.3 10.8 - - - +
80C ILE* 3.1 38.3 + - + +
81C LEU* 3.5 13.0 + - + +
83C LYS* 1.3 79.7 - - + +
85C VAL* 1.3 63.0 + - + +
87C ASP* 3.2 16.3 + - - +
88C MSE 3.2 14.5 + - + +
117C LEU* 4.2 24.9 - - + -
121C LEU* 4.8 15.0 - - + -
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Residues in contact with VAL 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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81C LEU* 3.3 18.8 + - + +
82C ASN* 3.4 14.6 - - - +
84C ILE* 1.3 82.1 - - + +
86C ASN* 1.3 60.3 + - + +
88C MSE 3.3 7.0 + - - +
89C HIS* 2.9 32.0 + - - +
114C VAL* 3.9 15.6 - - + +
117C LEU* 5.0 4.3 - - + -
118C GLU* 3.8 46.7 - - + +
121C LEU* 3.8 17.0 - - + -
319C THR* 6.2 0.9 - - + -
321C THR* 5.7 2.5 - - + -
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Residues in contact with ASN 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 ASN 3.5 11.0 - - - +
83C LYS* 3.0 11.7 + - - +
85C VAL* 1.3 82.8 - - + +
87C ASP* 1.3 63.6 + - - +
89C HIS* 3.9 6.8 - - - +
90C ASN* 3.0 41.0 + - - +
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Residues in contact with ASP 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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72C HIS* 6.5 1.3 - - + -
83C LYS* 3.1 33.8 + - - +
84C ILE* 3.6 9.2 - - - +
86C ASN* 1.3 84.7 - - - +
88C MSE 1.3 63.8 + - - +
89C HIS 3.6 0.2 + - - -
90C ASN* 3.8 22.9 + - - +
91C GLY* 3.9 5.5 + - - -
92C TYR* 5.4 1.0 - - - -
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Residues in contact with MSE 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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65C ALA 3.7 23.1 - - - +
66C LEU* 4.7 3.6 - - + -
69C ALA* 4.0 21.8 - - + -
84C ILE* 3.2 11.4 + - + +
85C VAL* 3.3 9.2 + - - +
87C ASP* 1.3 78.4 - - - +
89C HIS* 1.3 61.2 + - - +
91C GLY 4.5 0.2 - - - -
92C TYR* 3.1 55.1 + - + +
113C ALA* 3.9 28.9 - - + +
114C VAL* 3.9 28.6 - - + +
117C LEU* 4.0 21.5 - - - -
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Residues in contact with HIS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL 2.9 18.0 + - - +
86C ASN* 3.9 7.9 - - - +
88C MSE 1.3 78.9 - - - +
90C ASN* 1.3 68.3 + - + +
91C GLY 3.4 0.9 + - - -
92C TYR* 4.7 1.5 - - - +
93C LEU* 3.7 26.4 + - + +
111C VAL* 4.2 29.1 - - + +
114C VAL* 4.2 21.9 - - + +
296C TRP* 6.3 1.0 - - - -
317C PHE 5.8 0.2 - - - -
318C TRP 5.3 4.0 - - - -
319C THR* 4.3 12.4 - - + +
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Residues in contact with ASN 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 ASN* 3.0 35.4 + - - +
87C ASP* 3.8 20.1 + - - +
89C HIS* 1.3 81.2 - - + +
91C GLY* 1.3 63.9 + - - +
93C LEU* 3.1 24.9 - - - +
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Residues in contact with GLY 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 ASP 3.9 7.6 + - - -
88C MSE 4.2 0.4 + - - -
89C HIS 3.3 1.0 - - - -
90C ASN* 1.3 87.5 + - - +
92C TYR* 1.3 59.6 + - - +
93C LEU* 2.7 22.8 + - - +
94C ASP* 4.0 2.4 + - - +
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Residues in contact with TYR 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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65C ALA* 3.4 39.7 + - + -
68C GLU* 4.3 21.5 + - - +
69C ALA* 4.7 1.2 + - - +
87C ASP 5.4 0.7 - - - -
88C MSE 3.1 49.9 - - + +
89C HIS* 4.7 1.8 - - - +
91C GLY* 1.3 73.6 - - - +
93C LEU* 1.3 53.1 + - - +
94C ASP 2.9 14.4 + - - -
95C ALA* 3.1 19.5 + - - +
96C ASP* 3.4 6.2 - - - +
110C ARG* 3.9 39.5 - - + +
111C VAL* 6.4 0.9 - - + -
114C VAL* 5.3 3.4 - - + -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C HIS* 3.7 23.1 + - + +
90C ASN* 3.1 26.5 - - - +
91C GLY 2.7 13.9 + - - +
92C TYR* 1.3 71.4 - - - +
94C ASP* 1.3 90.0 + - - +
95C ALA 3.4 0.2 - - - -
96C ASP* 3.1 28.7 + - - +
97C TYR* 3.2 46.4 + - + +
111C VAL* 5.8 4.7 - - + -
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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