Contacts of the helix formed by residues 79 - 102 (chain C) in PDB entry 5LN3
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 79 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 6.2 3.8 - - + -
152B SER* 6.1 3.4 - - - -
154B ALA* 5.6 4.9 - - + -
78C GLY* 1.3 75.2 - - - +
80C THR* 1.3 77.2 + - - +
81C SER* 3.8 22.7 - - - +
82C ASP* 3.1 34.0 - - + +
83C ALA* 3.7 14.4 + - - +
131C GLY 5.5 3.4 - - - +
132C VAL* 5.4 1.3 - - + +
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLY 5.9 0.2 - - - +
154B ALA* 4.9 13.9 - - - +
155B TYR* 4.8 17.0 - - + +
156B PHE* 5.6 4.7 - - - -
66C TYR* 5.6 6.1 - - - +
78C GLY 3.8 2.8 + - - -
79C ILE* 1.3 82.4 - - - +
81C SER* 1.3 65.7 + - - +
83C ALA* 3.2 15.2 + - + +
84C ASN* 3.4 29.8 + - - +
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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
----------------------------------------------------------
119B GLN* 3.5 23.1 - - - +
152B SER* 2.9 29.1 + - - -
153B GLY* 3.5 24.8 - - - +
154B ALA* 3.8 4.2 + - - +
79C ILE* 3.3 19.4 - - - +
80C THR* 1.3 78.0 - - - +
82C ASP* 1.4 61.3 + - - +
84C ASN* 4.1 5.8 + - - +
85C VAL* 3.6 17.2 + - - +
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Residues in contact with ASP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 6.0 2.4 - - - -
119B GLN* 3.6 20.9 + - - +
123B GLN* 5.2 3.4 + - - +
79C ILE* 3.1 28.8 + - + +
80C THR 3.4 0.4 - - - -
81C SER* 1.4 77.2 - - - +
83C ALA* 1.4 63.1 + - - +
84C ASN 3.5 0.2 - - - -
85C VAL* 3.3 17.4 - - - +
86C LEU* 3.3 28.4 - - + +
128C ARG* 3.8 15.6 + - - -
130C PHE* 4.0 23.6 - - + +
131C GLY 5.2 3.8 + - - +
132C VAL* 4.7 6.5 - - + -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 6.4 0.7 - - + -
76C VAL* 3.9 27.8 - - + -
79C ILE 3.7 11.6 + - - +
80C THR* 3.2 13.2 + - + +
82C ASP* 1.4 60.9 - - - +
84C ASN* 1.3 59.6 + - - +
86C LEU* 3.1 15.3 + - - +
87C THR* 2.8 37.0 + - - +
132C VAL* 4.7 4.9 - - + -
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Residues in contact with ASN 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR* 4.1 24.6 + - - -
66C TYR* 6.2 0.3 - - - -
80C THR* 3.4 33.5 + - - +
81C SER* 4.3 5.6 - - - +
83C ALA* 1.3 79.3 - - - +
85C VAL* 1.4 55.1 + - + +
87C THR* 3.5 12.6 + - - -
88C ASN* 2.6 38.3 + - - +
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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
----------------------------------------------------------
116B SER* 5.7 6.3 - - - +
119B GLN* 3.8 22.2 - - + -
123B GLN* 4.3 22.7 - - - +
81C SER 3.6 19.3 - - - +
82C ASP* 3.3 8.5 - - - +
83C ALA 3.3 0.2 - - - -
84C ASN* 1.4 75.5 - - + +
86C LEU* 1.4 63.4 + - + +
88C ASN* 3.2 21.9 + - - +
89C GLU* 3.8 15.8 - - - +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLN* 5.6 4.5 - - - +
82C ASP* 3.3 24.2 - - + +
83C ALA* 3.1 6.6 + - - +
85C VAL* 1.4 63.5 - - + +
87C THR* 1.4 63.7 + - - +
89C GLU* 3.3 27.6 + - - +
90C LEU* 3.4 20.2 + - + +
114C LEU* 5.2 13.7 - - + -
117C ILE* 5.7 5.2 - - + -
118C LYS* 5.0 9.0 - - - +
121C TYR* 5.1 7.9 - - - +
130C PHE* 4.8 24.5 - - + -
132C VAL* 3.8 42.0 - - + -
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 5.2 15.3 - - + -
67C LYS 6.0 0.2 - - - +
68C LEU* 3.7 20.6 - - + -
76C VAL* 5.3 7.8 - - - +
83C ALA* 2.8 23.7 + - - +
84C ASN* 3.5 12.9 - - - -
86C LEU* 1.4 72.7 - - - +
88C ASN* 1.3 61.4 + - - +
90C LEU* 3.1 12.9 + - - +
91C ARG* 3.0 42.7 + - - +
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Residues in contact with ASN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773 LYS* 5.8 4.0 - - - +
112B GLN* 6.1 3.2 - - - +
84C ASN* 2.6 28.6 + - - +
85C VAL* 3.2 13.8 - - - +
87C THR* 1.3 80.0 - - - +
89C GLU* 1.4 58.0 + - + +
91C ARG* 3.2 35.2 + - - +
92C LEU* 3.1 37.5 + - + +
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.8 21.3 - - - +
86C LEU* 3.3 22.8 + - - +
87C THR 3.3 0.8 - - - -
88C ASN* 1.4 74.5 - - + +
90C LEU* 1.3 72.1 + - + +
92C LEU* 3.2 13.6 + - + +
93C ILE* 3.1 31.0 + - + +
117C ILE* 4.5 22.7 - - + +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.2 14.1 - - + -
86C LEU* 3.4 16.8 - - + +
87C THR* 3.1 12.7 + - - +
89C GLU* 1.3 85.5 - - + +
91C ARG* 1.3 65.1 + - - +
92C LEU 3.2 0.3 + - - -
93C ILE* 3.6 25.3 + - + +
94C ALA* 3.7 3.1 + - - +
110C LEU* 3.6 28.0 - - + +
113C ALA* 5.2 0.9 - - + -
114C LEU* 4.4 46.0 - - + +
117C ILE* 4.9 6.7 - - + -
134C LEU* 4.4 24.5 - - + -
136C TYR* 4.9 4.3 - - + +
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733 LEU* 4.8 15.3 - - + +
763 LEU* 3.5 48.0 + - + +
773 LYS* 4.2 23.3 - - - +
67C LYS 4.0 18.3 + - - -
68C LEU* 3.7 29.0 - - + +
87C THR* 3.0 26.7 + - - +
88C ASN* 3.2 39.9 - - - +
89C GLU 3.3 0.2 - - - -
90C LEU* 1.3 78.2 - - - +
92C LEU* 1.4 63.3 + - - +
94C ALA* 3.5 16.2 + - - +
95C GLN* 3.6 11.4 + - - +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693 PHE* 4.0 15.0 - - + -
733 LEU* 3.7 34.3 - - + -
88C ASN* 3.1 23.6 + - + +
89C GLU* 3.4 19.1 - - + +
90C LEU 3.2 0.4 - - - -
91C ARG* 1.4 73.2 - - - +
93C ILE* 1.4 62.8 - - + +
95C GLN* 3.1 26.8 + - - +
96C ARG* 3.3 31.5 + - - +
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLU* 3.1 15.2 + - + +
90C LEU* 3.6 16.8 - - + +
92C LEU* 1.4 73.3 - - + +
94C ALA* 1.3 66.2 + - - +
96C ARG* 3.3 25.0 + - + +
97C TYR* 3.3 14.2 + - - +
105C ILE* 4.3 6.6 - - + +
109C GLN 5.5 0.4 - - - +
110C LEU* 4.3 17.3 - - + +
113C ALA* 3.2 35.2 - - + -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU 4.9 10.5 - - - +
69C ASN* 5.4 7.0 - - + +
90C LEU 3.7 6.0 + - - +
91C ARG 3.5 12.4 + - - +
92C LEU 3.3 0.6 - - - -
93C ILE* 1.3 79.9 - - - +
95C GLN* 1.4 57.8 + - + +
97C TYR* 3.2 5.2 + - - +
98C LEU* 3.0 36.9 + - + +
105C ILE* 3.8 34.1 - - + +
110C LEU* 4.8 4.9 - - + -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683 LYS* 4.0 9.8 + - - +
693 PHE* 3.5 44.0 + - + +
723 ASN* 3.2 40.9 + - - +
733 LEU* 4.3 19.5 - - + -
763 LEU* 5.3 5.8 - - + +
69C ASN* 5.7 0.7 + - - -
70C GLU* 5.2 4.9 - - - +
91C ARG 3.6 14.4 - - - +
92C LEU* 3.1 11.5 + - - +
94C ALA* 1.4 79.3 - - + +
96C ARG* 1.4 58.5 + - - +
98C LEU* 3.4 20.3 + - - +
99C LEU* 3.0 21.7 + - - +
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Residues in contact with ARG 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663 ARG* 5.3 3.8 - - - +
693 PHE* 4.2 25.3 - - - -
92C LEU* 3.4 40.6 + - - +
93C ILE* 3.3 20.8 + - + +
95C GLN* 1.4 71.9 - - - +
97C TYR* 1.3 65.0 + - + +
99C LEU* 3.1 21.2 + - - +
100C GLN* 3.2 16.3 + - + +
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Residues in contact with TYR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714 ASN* 5.4 2.3 + - - -
754 LEU* 4.2 8.7 - - - +
93C ILE 3.3 8.7 + - - +
94C ALA 3.2 8.9 + - - +
96C ARG* 1.3 79.4 - - + +
98C LEU* 1.3 55.8 + - - +
100C GLN* 5.0 0.4 - - - -
101C TYR* 2.8 95.8 + + + +
103C GLU* 3.6 27.4 + - - -
104C PRO 3.7 4.0 - - - -
105C ILE* 3.4 40.2 - - + -
106C PRO* 3.6 22.7 - - + +
109C GLN* 5.4 7.9 - - + -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653 GLN* 4.1 2.6 - - - +
683 LYS* 4.3 16.6 - - + +
723 ASN* 4.7 6.1 - - - +
69C ASN* 4.9 16.4 - - - +
70C GLU* 5.3 6.1 - - - +
94C ALA* 3.0 23.4 + - + +
95C GLN* 3.4 40.2 - - - +
97C TYR* 1.3 75.3 - - - +
99C LEU* 1.4 61.4 + - - +
102C GLN* 3.2 24.9 + - - +
103C GLU* 4.1 9.0 - - - +
104C PRO* 3.8 39.5 - - + -
105C ILE* 5.4 1.6 - - + +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 THR 5.9 0.2 - - - +
653 GLN* 3.7 40.1 - - + +
663 ARG* 4.5 17.3 - - + +
683 LYS* 3.9 19.5 - - - +
693 PHE* 4.3 20.2 - - + -
854 ARG* 5.1 0.3 + - - -
864 ARG* 3.7 25.9 - - - +
95C GLN 3.0 9.8 + - - +
96C ARG* 3.1 13.0 + - - +
98C LEU* 1.4 77.6 - - - +
100C GLN* 1.4 76.5 + - - +
102C GLN* 3.4 17.0 - - - +
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824 ASN* 4.0 5.0 - - - +
834 PHE* 3.8 51.8 + - + -
854 ARG* 5.3 0.2 + - - -
864 ARG* 3.7 30.4 + - + +
874 ASN* 5.6 4.2 - - - +
96C ARG* 3.2 16.5 + - + +
97C TYR* 5.0 0.2 - - - -
99C LEU* 1.4 95.3 - - - +
101C TYR* 1.4 75.9 - - + +
102C GLN* 3.5 5.1 + - - +
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Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674 TYR* 3.1 38.2 + + - -
754 LEU* 3.8 33.0 - - + -
794 ALA* 4.0 22.6 - - + +
824 ASN* 4.1 4.4 - - - +
834 PHE* 3.6 26.1 - + + -
97C TYR* 2.8 82.8 + + + +
100C GLN* 1.4 83.6 - - + +
102C GLN* 1.3 67.7 + - - +
103C GLU* 3.5 12.7 - - - +
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Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653 GLN* 3.9 25.0 - - - +
824 ASN* 3.4 33.1 + - - +
854 ARG* 3.2 29.0 + - - +
98C LEU 3.2 14.0 + - - +
99C LEU 3.4 21.2 - - - +
100C GLN 4.1 2.2 - - - +
101C TYR* 1.3 76.9 - - - +
103C GLU* 1.3 65.8 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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