Contacts of the helix formed by residues 79 - 100 (chain C) in PDB entry 4J4L
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 ASN 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C GLY* 2.8 12.4 + - - +
77C GLY 4.2 5.2 - - - +
78C PHE* 1.3 79.5 + - - +
80C GLU* 1.3 55.4 + - - +
81C GLU* 3.1 9.7 + - - +
82C THR* 3.2 37.2 + - - +
83C CYS* 2.9 34.4 + - - +
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Residues in contact with GLU 80 (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 PHE* 3.9 27.6 - - + -
79C ASN* 1.3 71.1 + - - +
81C GLU* 1.3 68.2 + - - +
83C CYS* 3.9 1.2 - - - +
84C LEU* 3.0 33.1 + - - +
129C LYS* 5.7 0.5 + - - -
183C GLN 4.4 2.3 - - - +
184C MET* 3.6 49.0 - - + +
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASN* 3.2 9.0 + - - +
80C GLU* 1.3 88.2 - - - +
82C THR* 1.3 68.7 + - + +
84C LEU* 4.2 4.4 - - - +
85C VAL* 3.3 28.3 + - + +
131C LYS* 5.7 12.9 + - + +
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Residues in contact with THR 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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70C LYS 4.5 3.7 + - - -
71C ASP* 3.0 23.8 + - - +
72C GLY* 3.9 0.5 - - - -
79C ASN* 3.2 27.8 + - - +
81C GLU* 1.3 79.5 - - + +
83C CYS* 1.3 66.1 + - - +
85C VAL* 3.4 6.2 + - - +
86C LYS* 3.1 20.6 + - - +
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Residues in contact with CYS 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 ASP 3.0 11.1 + - - -
72C GLY 3.6 10.1 - - - +
73C CYS* 2.1 47.8 - - - -
78C PHE* 4.6 3.6 - - + -
79C ASN 2.9 18.3 + - - +
80C GLU* 3.9 4.7 - - - +
82C THR* 1.3 75.8 - - - +
84C LEU* 1.3 65.5 + - - +
86C LYS* 3.0 5.4 + - - +
87C ILE* 2.9 40.6 + - - +
180C ALA* 3.7 13.7 - - - -
184C MET* 5.1 4.3 - - - -
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Residues in contact with LEU 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 GLU 3.0 20.5 + - - +
81C GLU* 4.2 4.7 - - - +
83C CYS* 1.3 78.5 - - - +
85C VAL* 1.3 63.8 + - + +
87C ILE* 3.3 8.8 + - + -
88C ILE* 3.1 40.9 + - + +
126C LEU* 4.2 26.2 - - + +
129C LYS* 4.2 15.5 - - + +
130C ALA* 3.9 25.6 - - + -
181C LEU* 4.5 7.0 - - + -
184C MET* 3.5 28.0 - - + -
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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 GLU* 3.3 20.3 + - + +
82C THR* 3.9 6.1 - - - +
83C CYS 3.2 0.6 - - - -
84C LEU* 1.3 78.4 - - + +
86C LYS* 1.3 54.6 + - - +
88C ILE* 3.5 8.4 + - + +
89C THR* 2.7 43.8 + - - +
131C LYS 6.0 1.6 - - - +
132C ASN* 5.4 19.1 - - + +
137C THR* 5.4 8.7 - - - +
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Residues in contact with LYS 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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65C PRO* 4.8 4.6 - - - +
66C LYS 3.4 34.5 + - - +
67C MET* 4.0 12.8 - - - -
71C ASP* 3.4 43.7 - - + +
73C CYS* 4.9 0.4 - - - -
82C THR 3.1 12.9 + - - +
83C CYS* 3.0 9.3 + - - +
85C VAL* 1.3 75.4 - - - +
87C ILE* 1.3 60.1 + - - +
89C THR* 4.2 7.7 - - - +
90C GLY* 2.8 35.1 + - - +
93C GLU* 4.7 12.5 + - - -
173C PHE* 3.8 8.4 - - + -
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Residues in contact with ILE 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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29C ILE* 6.4 0.2 - - + -
67C MET* 3.9 10.3 - - + -
83C CYS* 2.9 39.7 + - - +
84C LEU* 3.7 10.3 - - + +
86C LYS* 1.3 75.3 - - - +
88C ILE* 1.3 66.9 + - - +
91C LEU* 2.9 31.1 + - + +
126C LEU* 3.7 29.8 - - + -
173C PHE* 3.8 7.8 - - - -
177C SER* 3.5 41.5 - - - +
180C ALA* 4.9 0.2 - - + -
181C LEU* 4.1 24.2 - - + -
184C MET* 5.4 0.2 - - - -
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Residues in contact with ILE 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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84C LEU* 3.1 34.1 + - + +
85C VAL* 3.9 7.4 - - + +
87C ILE* 1.3 78.1 - - - +
89C THR* 1.3 55.0 + - - +
91C LEU* 3.6 6.3 + - - +
92C LEU* 3.1 36.1 + - + +
123C ILE* 4.7 7.5 - - + +
126C LEU* 3.6 37.9 - - + +
127C GLN* 3.8 29.2 - - + +
130C ALA* 4.1 14.6 - - + -
137C THR 6.3 1.3 - - - +
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Residues in contact with THR 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 VAL* 2.7 34.7 + - - +
86C LYS* 3.8 9.6 - - - +
88C ILE* 1.3 72.1 - - - +
90C GLY* 1.3 67.3 + - - +
92C LEU* 3.2 8.1 + - - +
93C GLU* 3.0 44.7 + - + +
137C THR* 3.8 34.5 + - - +
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Residues in contact with GLY 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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65C PRO* 3.9 6.7 - - - -
86C LYS* 2.8 24.0 + - - +
89C THR* 1.3 70.9 - - - +
91C LEU* 1.3 66.2 + - - -
93C GLU* 2.8 18.2 + - - +
94C PHE* 2.8 30.2 + - - -
173C PHE* 3.8 15.3 - - - -
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Residues in contact with LEU 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 ILE* 2.9 25.9 + - + +
88C ILE* 4.0 2.9 - - - +
90C GLY* 1.3 76.4 - - - +
92C LEU* 1.3 63.5 + - - +
94C PHE* 3.0 13.4 + - - +
95C GLU* 3.4 14.0 + - - +
119C THR* 4.8 6.8 - - + +
122C LEU* 3.7 18.8 - - + -
123C ILE* 3.8 27.4 - - + +
126C LEU* 3.6 31.6 - - + -
170C PHE* 3.9 26.9 - - + -
173C PHE* 4.0 13.7 - - + -
174C LEU* 4.1 15.9 - - + -
177C SER* 5.6 0.2 - - - +
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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
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88C ILE* 3.1 30.8 + - + +
89C THR* 3.6 7.2 - - + +
90C GLY 3.1 0.2 - - - -
91C LEU* 1.3 78.3 - - - +
93C GLU* 1.3 58.8 + - - +
95C GLU* 3.2 45.3 - - - +
96C VAL 4.9 0.3 + - - -
123C ILE* 4.0 20.8 - - + +
127C GLN* 4.8 9.2 - - - +
137C THR 5.1 6.7 - - - +
138C THR* 4.3 30.1 - - + +
139C PRO* 3.6 24.3 - - + +
144C ASN* 5.6 1.6 + - - -
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Residues in contact with GLU 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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65C PRO* 3.4 30.2 - - + +
86C LYS* 4.7 6.9 + - - -
89C THR* 3.2 29.4 - - + +
90C GLY* 2.8 10.7 + - - +
92C LEU* 1.3 73.2 - - - +
94C PHE* 1.3 66.3 + - - +
95C GLU 3.2 2.7 + - - -
96C VAL* 3.9 10.0 - - - +
97C TYR* 3.5 19.2 - - + -
139C PRO* 4.3 18.8 - - + -
144C ASN* 5.6 1.1 + - - +
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Residues in contact with PHE 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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64C LEU* 4.4 6.1 - - + -
65C PRO* 3.6 46.4 - - + -
90C GLY 2.8 25.6 + - - -
91C LEU* 3.0 9.5 + - - +
93C GLU* 1.3 75.0 - - - +
95C GLU* 1.3 66.7 + - - +
97C TYR* 2.8 30.6 + + + +
98C LEU* 3.0 16.0 + - + +
119C THR* 5.8 0.2 - - + -
166C ILE* 4.6 4.7 - - + -
169C SER* 3.6 22.7 - - - -
170C PHE* 3.6 54.1 - + + -
173C PHE* 3.7 24.5 - + + -
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Residues in contact with GLU 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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91C LEU 3.4 10.8 - - - +
92C LEU* 3.2 42.6 - - - +
93C GLU 3.2 1.2 - - - -
94C PHE* 1.3 77.1 - - - +
96C VAL* 1.3 58.3 + - - +
98C LEU* 2.9 15.9 + - - +
99C GLU* 2.9 26.9 + - - +
116C GLN* 5.0 1.7 - - - +
119C THR* 5.1 6.8 - - + +
120C LYS* 3.0 42.1 + - - +
123C ILE* 3.8 14.7 - - + +
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Residues in contact with VAL 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 LEU 4.9 0.4 + - - -
93C GLU 3.9 13.8 + - - +
95C GLU* 1.3 77.3 - - - +
97C TYR* 1.3 68.9 + - + +
99C GLU* 3.3 8.5 + - + +
100C TYR* 3.1 23.2 + - - +
144C ASN* 3.6 60.7 - - + +
147C LEU* 3.9 18.4 - - + -
148C LEU* 3.9 20.9 - - + +
151C LEU* 5.8 0.6 - - + +
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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
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62C LEU* 3.5 26.4 + - + +
63C ASN 4.7 2.8 + - - -
64C LEU* 3.6 32.1 - - + -
65C PRO* 4.8 7.2 - - + -
93C GLU* 3.5 23.3 - - + -
94C PHE* 2.8 22.0 + + + +
96C VAL* 1.3 76.5 - - + +
98C LEU* 1.3 62.9 + - - +
100C TYR* 3.3 17.0 - - - +
101C LEU* 3.3 15.9 - - - +
147C LEU* 3.7 27.6 - - + +
151C LEU* 4.0 25.1 - - + -
166C ILE* 3.6 33.5 - - + +
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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
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94C PHE* 3.0 18.1 + - + +
95C GLU* 2.9 17.0 + - + +
97C TYR* 1.3 77.1 - - - +
99C GLU* 1.3 62.0 + - - +
100C TYR 3.3 0.4 - - - -
101C LEU* 3.2 26.3 + - + +
102C GLN* 3.0 26.5 + - - -
115C VAL* 4.2 6.7 - - + +
116C GLN* 3.9 25.1 - - + +
119C THR* 3.5 41.5 - - + +
166C ILE* 4.6 5.2 - - + -
170C PHE* 3.9 30.1 - - + -
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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 GLU 2.9 10.8 + - - +
96C VAL* 3.4 15.0 - - + +
98C LEU* 1.3 73.3 - - - +
100C TYR* 1.3 61.6 + - - +
101C LEU 3.0 5.8 + - - -
102C GLN* 3.2 23.0 + - - +
116C GLN* 3.1 26.1 + - - +
148C LEU* 3.8 24.3 - - + +
152C GLN* 5.5 1.9 + - - -
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Residues in contact with TYR 100 (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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96C VAL 3.1 13.1 + - - +
97C TYR* 3.3 12.1 - - - +
99C GLU* 1.3 77.7 - - - +
101C LEU* 1.3 65.1 + - + +
102C GLN 3.5 1.7 + - - +
104C ARG* 2.7 65.1 + - - +
148C LEU* 3.9 13.7 - - + +
151C LEU* 3.9 39.6 + - + -
152C GLN* 4.2 10.7 + - + +
159C GLN* 2.7 36.7 + - - +
162C THR* 3.6 19.1 - - + -
163C THR* 3.5 19.7 - - - -
166C ILE* 3.6 20.2 - - + -
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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