Contacts of the helix formed by residues 76 - 99 (chain C) in PDB entry 5LF4
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 LEU 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.8 29.2 - - + -
16B GLY 5.0 6.1 - - - +
18B LEU* 4.0 23.1 - - + -
155B ASN* 6.2 2.2 - - - +
25C ALA* 4.3 13.5 - - + +
73C PHE* 4.6 0.4 - - - -
75C GLY* 1.3 70.2 - - - -
77C THR* 1.3 65.2 + - - +
78C ALA* 3.3 2.2 - - + +
79C ASP* 3.2 29.9 + - + +
80C ALA 3.0 18.0 + - - -
125C ARG* 4.4 0.4 - - - +
128C GLY* 2.9 17.0 + - - +
129C ILE* 3.2 7.2 - - - +
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Residues in contact with THR 77 (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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155B ASN* 2.3 38.0 + - - +
61C LYS* 3.9 20.4 - - - +
73C PHE* 3.7 33.1 - - + -
75C GLY 3.3 6.7 + - - +
76C LEU* 1.3 72.4 - - - +
78C ALA* 1.3 59.4 + - - +
80C ALA* 3.2 3.6 + - - +
81C ARG* 3.1 23.8 + - - +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 3.7 16.6 - - + +
153B SER* 3.5 25.4 - - - +
154B GLY 3.8 16.8 - - - +
155B ASN* 3.4 7.7 + - - +
76C LEU* 3.3 2.1 - - + +
77C THR* 1.3 77.3 + - - +
79C ASP* 1.3 68.3 + - - +
81C ARG* 3.2 24.2 + - - +
82C ILE* 3.3 15.6 + - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 2.9 21.4 + - - +
122B THR* 4.6 0.2 + - - -
76C LEU* 3.2 23.5 + - + +
78C ALA* 1.3 76.8 - - - +
80C ALA* 1.3 64.9 + - - +
82C ILE* 3.1 14.0 + - - +
83C VAL* 3.1 16.8 + - - +
125C ARG* 2.8 45.6 + - - -
127C PHE* 3.5 13.3 - - + -
128C GLY* 2.9 19.6 + - - +
129C ILE* 4.1 9.0 - - + -
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C PHE* 3.5 50.3 - - + -
76C LEU 3.0 9.0 + - - +
77C THR 3.2 9.8 + - - +
79C ASP* 1.3 76.0 - - - +
81C ARG* 1.3 52.6 + - - +
83C VAL* 3.1 2.8 + - - +
84C ILE* 2.8 41.4 + - + +
129C ILE* 3.7 18.1 - - + +
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Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 3.7 22.9 - - - +
115B CYS* 3.3 24.3 + - - -
116B ASP* 2.6 27.4 + - - +
119B GLN* 4.2 8.7 - - - +
154B GLY 2.9 30.4 + - - -
155B ASN* 4.5 5.3 + - - +
156B TYR* 4.3 20.0 - - - -
63C YCM 5.4 7.4 - - - +
77C THR 3.1 11.5 + - - +
78C ALA* 3.5 20.9 + - - +
79C ASP 3.2 0.4 - - - -
80C ALA* 1.3 75.3 - - - +
82C ILE* 1.3 62.0 + - - +
84C ILE* 3.7 10.3 - - + +
85C ASN* 3.1 43.6 + - - +
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Residues in contact with ILE 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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116B ASP* 3.6 38.4 - - + +
119B GLN* 3.4 37.2 - - + +
123B GLN* 5.1 0.9 - - - +
78C ALA 3.3 6.7 + - - +
79C ASP 3.1 8.6 + - - +
81C ARG* 1.3 78.6 - - - +
83C VAL* 1.3 61.5 + - - +
85C ASN* 3.5 3.7 + - + +
86C ARG* 3.0 35.3 + - + +
118C TYR* 5.8 1.8 - - - +
127C PHE* 4.1 21.5 - - + -
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Residues in contact with VAL 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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71C MET* 5.0 6.1 - - + -
79C ASP 3.1 11.1 + - - +
80C ALA 3.1 6.8 + - - +
82C ILE* 1.3 75.5 - - - +
84C ILE* 1.3 65.7 + - - +
86C ARG* 3.2 7.0 + - - +
87C ALA* 2.9 23.0 + - - +
111C ILE* 3.8 35.4 - - + -
114C LEU* 4.5 9.7 - - + +
115C LYS* 4.7 3.6 - - + -
127C PHE* 3.7 37.7 - - + -
129C ILE* 4.1 22.9 - - + -
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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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63C YCM 3.6 35.2 - - + +
65C LEU* 3.8 12.9 - - + +
71C MET* 3.6 34.1 - - + -
73C PHE* 4.4 6.3 - - + -
80C ALA* 2.8 31.6 + - + +
81C ARG* 3.7 7.6 - - + +
83C VAL* 1.3 76.9 - - - +
85C ASN* 1.3 57.8 + - - +
87C ALA* 3.2 3.9 + - - +
88C ARG* 2.9 64.5 + - - +
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Residues in contact with ASN 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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112B THR* 5.1 5.3 - - - +
116B ASP* 4.7 11.0 + - - +
81C ARG* 3.1 38.5 + - - +
82C ILE* 4.2 3.6 - - - +
84C ILE* 1.3 75.8 - - - +
86C ARG* 1.3 64.1 + - - +
88C ARG* 3.1 36.6 + - - +
89C VAL* 3.0 30.5 + - + +
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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
----------------------------------------------------------
82C ILE* 3.0 32.7 + - + +
83C VAL 3.2 4.5 + - - +
85C ASN* 1.3 76.0 - - - +
87C ALA* 1.3 61.5 + - - +
89C VAL* 3.3 9.8 + - - +
90C GLU* 3.0 22.5 + - - +
110C TYR* 3.5 28.5 + - - +
114C LEU* 3.5 41.8 - - + +
117C ARG* 4.1 10.1 - - - +
118C TYR* 4.3 13.3 + - - -
127C PHE* 5.9 0.6 - - - -
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Residues in contact with ALA 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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65C LEU* 4.0 14.8 - - + -
83C VAL 2.9 16.8 + - - +
84C ILE* 3.6 4.9 - - - +
86C ARG* 1.3 75.9 - - - +
88C ARG* 1.3 59.2 + - - +
90C GLU* 3.3 2.6 + - - +
91C CYS* 2.9 34.5 + - - -
107C ILE* 3.7 6.9 - - + +
110C TYR* 4.2 10.7 - - - -
111C ILE* 3.8 32.1 - - + -
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Residues in contact with ARG 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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63C YCM 3.9 22.4 - - - +
64C ALA* 2.7 36.5 + - - +
65C LEU* 3.4 29.3 + - - +
84C ILE* 2.9 30.0 + - - +
85C ASN* 3.1 34.8 + - - +
87C ALA* 1.3 74.0 - - - +
89C VAL* 1.3 65.4 + - + +
91C CYS* 3.4 10.1 + - - +
92C GLN* 3.4 18.1 + - - +
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Residues in contact with VAL 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 ASN* 3.0 19.8 + - + +
86C ARG* 3.6 13.2 - - - +
88C ARG* 1.3 74.0 - - + +
90C GLU* 1.3 65.3 + - - +
92C GLN* 3.1 11.5 + - - +
93C SER* 3.1 24.4 + - - +
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Residues in contact with GLU 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 3.0 14.2 + - - +
87C ALA 3.6 7.4 - - - +
89C VAL* 1.3 78.3 - - - +
91C CYS* 1.3 57.6 + - - +
93C SER* 3.1 16.9 + - - +
94C HIS* 2.9 29.5 + - - +
106C TYR* 2.8 30.9 + - + -
107C ILE* 4.0 7.6 - - + -
110C TYR* 3.5 47.0 + - + +
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Residues in contact with CYS 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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65C LEU* 4.1 15.7 - - - +
66C ASP* 3.3 34.7 - - + +
69C VAL* 5.4 0.4 - - - -
87C ALA 2.9 21.1 + - - +
88C ARG 3.7 5.8 - - - +
89C VAL 3.3 0.4 - - - -
90C GLU* 1.3 75.5 - - - +
92C GLN* 1.3 58.9 + - - +
94C HIS* 3.6 2.3 + - - +
95C ARG* 3.1 32.2 + - - +
102C VAL* 3.9 29.1 - - + +
107C ILE* 3.8 20.4 - - - -
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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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65C LEU 5.5 1.6 + - - -
66C ASP* 3.8 24.5 + - - -
88C ARG 3.6 12.0 + - - +
89C VAL* 3.1 9.7 + - - +
91C CYS* 1.3 75.8 - - - +
93C SER* 1.3 65.1 + - - +
95C ARG* 3.5 19.5 + - - +
96C LEU* 2.9 24.7 + - - +
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Residues in contact with SER 93 (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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89C VAL* 3.1 18.7 + - - +
90C GLU* 3.5 23.5 + - - -
92C GLN* 1.3 73.6 - - - +
94C HIS* 1.3 64.7 + - - +
96C LEU* 3.0 14.4 + - - +
97C THR* 2.9 30.9 + - - +
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Residues in contact with HIS 94 (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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90C GLU* 2.9 17.5 + - - +
91C CYS 3.7 0.4 - - - +
93C SER* 1.3 73.2 - - - +
95C ARG* 1.3 58.8 + - - +
97C THR* 4.3 4.5 - - - -
98C VAL* 2.8 68.3 + - + +
100C ASP* 3.1 21.5 + - + -
101C PRO 3.4 20.6 - - - -
102C VAL* 3.4 34.4 - - + +
103C THR 4.8 1.1 + - - -
106C TYR* 4.0 38.8 - + + +
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Residues in contact with ARG 95 (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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66C ASP* 3.1 38.7 + - - +
67C ASP* 3.6 24.9 + - - +
68C ASN* 4.1 2.8 + - - +
91C CYS 3.1 14.2 + - - +
92C GLN* 3.9 23.8 - - - +
94C HIS* 1.3 77.6 + - - +
96C LEU* 1.3 60.4 + - - +
99C GLU* 2.9 29.1 + - - +
100C ASP 3.5 21.1 - - - +
101C PRO* 4.0 33.5 - - + +
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Residues in contact with LEU 96 (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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92C GLN 2.9 15.9 + - - +
93C SER* 3.2 17.0 - - - +
95C ARG* 1.3 79.7 - - - +
97C THR* 1.3 68.5 + - + +
99C GLU* 4.4 8.8 - - - +
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Residues in contact with THR 97 (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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93C SER* 2.9 22.5 + - - +
94C HIS* 3.8 3.6 + - - -
96C LEU* 1.3 88.6 - - + +
98C VAL* 1.3 69.2 + - - +
99C GLU* 5.1 1.6 - - - -
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Residues in contact with VAL 98 (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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94C HIS* 2.8 54.6 + - + +
97C THR* 1.3 89.0 - - - +
99C GLU* 1.3 68.8 + - - +
100C ASP* 4.2 16.1 - - + +
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Residues in contact with GLU 99 (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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95C ARG* 2.9 24.2 + - - +
96C LEU 4.4 9.0 - - - +
97C THR 5.1 1.3 - - - +
98C VAL* 1.3 80.9 - - - +
100C ASP* 1.3 66.7 + - - +
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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