Contacts of the helix formed by residues 65 - 88 (chain C) in PDB entry 5NJ8
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 65 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LYS 3.8 3.2 + - - -
64C LEU* 1.3 77.6 - - - +
66C LYS* 1.3 66.1 + - - +
67C LEU* 4.0 20.3 - - + +
68C SER* 2.1 59.2 + - - -
69C VAL* 3.0 9.1 + - - +
101D ARG* 6.0 1.8 - - - +
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Residues in contact with LYS 66 (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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44C ASN* 3.6 42.2 + - - +
47C LEU* 3.7 36.7 - - + +
48C ASP* 6.0 1.8 - - - +
64C LEU 5.3 2.0 - - - +
65C ASP* 1.3 75.0 - - - +
67C LEU* 1.3 59.6 + - + +
69C VAL* 2.6 29.5 + - + +
70C LEU* 3.0 13.8 + - - +
101D ARG* 5.1 4.7 - - - +
105D MET* 3.8 20.4 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP* 4.0 15.7 - - + +
66C LYS* 1.3 79.5 - - + +
68C SER* 1.3 57.5 + - - +
70C LEU* 3.3 12.5 + - + -
71C ARG* 2.9 23.9 + - - +
101D ARG* 3.5 48.5 - - + +
104D LYS* 4.5 26.9 - - + +
105D MET* 3.9 15.5 - - + +
108D TYR* 3.3 27.4 - - + +
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.7 9.3 - - - +
65C ASP* 2.1 56.2 + - - -
67C LEU* 1.3 76.3 - - - +
69C VAL* 1.3 63.6 + - - +
71C ARG* 3.4 31.8 - - - +
72C LEU* 2.9 37.7 + - - +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.7 26.2 - - + +
50C LEU* 4.5 8.7 - - + -
51C ALA* 3.5 43.5 - - + +
54C LEU* 4.4 9.3 - - + +
61C ILE 5.6 0.2 - - - +
64C LEU* 3.8 24.5 - - + +
65C ASP 3.0 18.8 + - - +
66C LYS* 2.6 16.4 + - + +
68C SER* 1.3 71.6 + - - +
70C LEU* 1.3 55.2 + - - +
72C LEU* 3.8 1.7 - - - +
73C SER* 2.8 30.5 + - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.3 16.6 - - + -
50C LEU* 4.1 11.7 - - + -
66C LYS 3.0 10.9 + - - +
67C LEU* 3.6 15.3 - - - +
68C SER 3.2 0.2 - - - -
69C VAL* 1.3 77.5 - - - +
71C ARG* 1.3 63.3 + - - +
73C SER* 2.8 17.1 + - - -
74C VAL* 2.9 16.1 + - - +
105D MET* 3.5 45.8 - - + +
108D TYR* 3.7 17.0 - - + -
109D ILE* 4.8 7.6 - - + +
112D LEU* 4.4 13.3 - - + +
132D LEU* 4.1 25.8 - - + -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 5.9 0.4 - - - +
67C LEU 2.9 10.3 + - - +
68C SER* 3.4 32.7 - - - +
70C LEU* 1.3 76.1 - - - +
72C LEU* 1.3 67.7 + - - +
74C VAL* 3.2 10.3 - - - +
75C SER* 2.5 38.7 + - - -
151C SER 3.0 29.0 + - - -
152C ASP* 3.8 21.7 + - - +
154C ILE* 3.9 11.3 - - - +
155C HIS* 4.0 23.6 - - + +
156C GLN* 4.1 27.8 - - - +
108D TYR* 3.4 37.2 - - + +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 4.1 14.4 - - + +
56C PHE* 3.6 27.1 - - + -
64C LEU* 3.5 41.1 - - + -
68C SER* 2.9 28.5 + - - +
69C VAL 3.8 2.9 - - - +
71C ARG* 1.3 81.5 - - + +
73C SER* 1.3 60.4 + - - +
75C SER* 3.2 4.5 + - - -
76C TYR* 2.9 30.0 + - - +
151C SER* 3.5 17.9 - - - +
154C ILE* 3.4 32.1 - - + -
158D PHE* 4.6 4.4 - - + -
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.9 22.1 - - - +
54C LEU* 3.7 14.3 - - - +
69C VAL 2.8 15.3 + - - -
70C LEU* 2.8 20.4 + - - -
72C LEU* 1.3 76.3 - - - +
74C VAL* 1.3 55.0 + - - +
76C TYR* 3.5 5.3 - - - +
77C LEU* 2.9 34.9 + - - +
112D LEU* 4.4 5.4 - - - +
139D MET* 3.9 23.5 - - - +
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU 2.9 17.2 + - - +
71C ARG* 3.2 20.2 - - + +
73C SER* 1.3 74.8 + - - +
75C SER* 1.3 65.3 + - - +
77C LEU* 3.4 8.4 + - - +
78C ARG* 2.9 33.8 + - - +
155C HIS* 4.9 4.9 - - + -
108D TYR* 4.6 6.3 - - + +
111D GLU* 3.8 42.2 - - + +
112D LEU* 3.8 31.1 - - + +
115D MET* 4.8 4.7 - - + -
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Residues in contact with SER 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG 2.5 24.5 + - - -
72C LEU* 3.2 7.8 + - - -
74C VAL* 1.3 74.7 - - - +
76C TYR* 1.3 67.4 + - - +
78C ARG* 2.8 21.8 + - - +
79C ALA* 2.9 14.3 + - - +
136C PHE* 5.3 4.4 - - - +
154C ILE* 4.8 11.4 - - - -
155C HIS* 3.1 32.4 + - - +
158D PHE* 4.6 10.3 - - - -
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Residues in contact with TYR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 5.3 0.4 - - + -
55C PRO* 3.6 30.1 - - + -
72C LEU 2.9 13.2 + - - +
73C SER* 3.5 10.5 - - - +
75C SER* 1.3 76.1 - - - +
77C LEU* 1.3 65.6 + - - +
79C ALA* 3.1 2.6 + - + +
80C LYS* 3.0 27.8 + - + +
139D MET* 3.9 20.6 - - + -
142D LEU* 3.6 31.2 + - + +
143D ARG* 3.4 39.7 + - + +
157D SER 5.0 0.7 - - - -
158D PHE* 3.4 46.9 - + + -
159D LEU* 6.0 0.4 - - + -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER* 2.9 23.4 + - - +
74C VAL* 3.6 6.7 - - - +
76C TYR* 1.3 76.2 - - + +
78C ARG* 1.3 58.7 + - - +
80C LYS* 3.9 3.2 - - - +
81C SER* 2.9 33.5 + - - -
112D LEU* 4.2 27.4 - - + -
115D MET* 3.7 17.0 - - + -
116D VAL* 4.3 14.6 - - + -
135D ALA* 5.2 4.7 - - + +
138D HIS* 3.3 36.6 - - + +
139D MET* 4.4 21.1 - - + -
142D LEU* 4.4 11.2 - - + -
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 2.9 19.3 + - - +
75C SER* 2.8 18.3 + - - +
77C LEU* 1.3 72.8 - - - +
79C ALA* 1.3 62.3 + - - +
81C SER* 3.4 9.4 + - - -
82C PHE* 3.7 7.1 + - - +
136C PHE* 3.7 31.5 - - + -
155C HIS* 5.0 10.0 - - - -
247C HIS 5.1 1.6 - - - +
249C GLN* 4.1 21.5 + - + +
250C LYS 5.5 0.4 + - - -
251C LYS* 4.1 25.7 - - - +
111D GLU* 2.9 45.5 + - - +
115D MET* 3.8 21.9 - - + -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER 2.9 11.3 + - - +
76C TYR* 3.1 10.5 + - + +
78C ARG* 1.3 78.9 - - - +
80C LYS* 1.3 64.8 + - - +
81C SER 3.1 0.3 + - - -
82C PHE* 3.3 6.2 - - - -
83C PHE* 2.9 27.8 + - + +
136C PHE* 3.7 27.5 - - + +
137C TYR* 5.7 2.0 - - + -
158D PHE* 4.8 5.6 - - + -
159D LEU* 4.3 24.2 - - + -
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Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 3.0 21.0 + - + +
77C LEU 4.2 1.8 - - - +
79C ALA* 1.3 76.0 - - - +
81C SER* 1.3 64.3 + - - +
83C PHE* 4.0 8.7 - - - -
84C ASP* 3.0 27.4 + - - +
142D LEU* 4.0 31.0 - - + -
159D LEU* 5.9 0.2 - - - +
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU 2.9 20.6 + - - -
78C ARG 3.7 6.3 - - - -
79C ALA 3.1 0.4 + - - -
80C LYS* 1.3 76.9 - - - +
82C PHE* 1.3 53.2 + - - +
84C ASP* 2.5 24.2 - - - +
85C VAL* 4.3 3.1 - - - +
248C GLY* 3.6 17.3 - - - -
115D MET* 3.1 30.1 - - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ARG 3.7 7.8 + - - +
79C ALA 3.3 17.7 + - - -
81C SER* 1.3 76.9 - - - +
83C PHE* 1.3 95.6 + + - +
84C ASP* 3.1 2.2 - - - -
85C VAL* 2.9 10.2 + - - +
86C ALA* 2.9 39.5 + - + -
136C PHE* 3.6 27.1 - + - -
245C TYR 5.0 6.3 - - - -
246C LEU* 4.1 7.2 - - + -
247C HIS* 3.2 49.4 - - + +
248C GLY* 3.6 2.7 - - - +
266C PHE* 3.9 28.7 - + - -
166D HIS* 6.1 0.7 - + - -
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 2.9 21.8 + - + +
80C LYS* 3.1 8.9 + - - +
82C PHE* 1.3 118.0 - + - +
84C ASP* 1.3 62.3 + - - +
86C ALA* 4.4 3.6 - - + +
87C LEU* 2.9 37.6 + - + +
136C PHE* 5.6 1.3 - + - -
266C PHE* 5.0 6.1 - + - -
159D LEU* 3.5 24.5 - - + -
163D GLU* 3.2 51.8 - - + -
166D HIS* 4.6 12.6 - + + -
167D LEU* 4.0 19.1 - - + -
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LYS 3.0 11.0 + - - +
81C SER* 2.5 30.7 - - - +
83C PHE* 1.3 77.1 - - - +
85C VAL* 1.3 81.2 + - - +
87C LEU* 4.5 7.1 - - - +
88C LYS* 3.1 28.6 - - - +
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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
----------------------------------------------------------
81C SER 4.3 4.7 - - - +
82C PHE* 2.9 10.0 + - + +
84C ASP* 1.3 98.2 + - - +
86C ALA* 1.3 68.6 + - - +
87C LEU 3.3 0.6 + - - -
88C LYS* 3.4 16.4 + - - -
247C HIS* 5.3 13.2 - - + -
248C GLY* 5.9 2.2 - - - +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PHE* 2.9 32.9 + - + +
83C PHE* 3.5 5.8 + - + +
85C VAL* 1.3 80.5 - - - +
87C LEU* 1.3 60.7 + - - +
88C LYS 4.7 1.0 - - - -
166D HIS* 3.4 37.6 + - + +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 2.9 42.8 + - + +
84C ASP* 4.4 5.8 - - - +
86C ALA* 1.3 78.9 - - - +
88C LYS* 1.3 86.8 + - + +
160D THR* 6.4 0.7 - - - -
162D GLN* 5.0 14.1 - - + +
163D GLU* 4.8 14.1 - - + +
166D HIS* 4.4 20.6 - - + +
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASP 3.1 21.3 + - - +
85C VAL* 3.4 13.8 + - - +
86C ALA 4.7 1.1 - - - -
87C LEU* 1.3 94.7 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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