Contacts of the helix formed by residues 70 - 91 (chain C) in PDB entry 3J9X
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 GLY 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 A 3.4 26.9 + - - +
288 T 4.1 2.3 + - - -
69C THR* 1.3 75.7 - - - +
71C PRO* 1.3 68.7 - - - +
73C ARG* 2.9 31.8 + - - +
90E ILE* 5.5 0.6 - - - +
99E MET* 5.3 0.4 - - - +
111F PHE* 3.6 18.6 - - - -
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Residues in contact with PRO 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 A 3.7 30.1 - - + +
288 T 3.6 26.5 - - - +
69C THR 4.4 0.7 - - - +
70C GLY* 1.3 82.0 - - - +
72C ASN* 1.3 64.9 + - - +
73C ARG 3.1 0.4 - - - -
74C ALA* 3.0 6.0 + - + +
75C ILE* 3.0 24.1 + - - +
71F PRO* 3.6 18.7 - - + +
74F ALA 4.8 0.4 - - - -
75F ILE* 3.6 38.4 - - + +
107F TYR* 6.5 0.9 - - + -
111F PHE* 4.6 6.1 - - + -
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Residues in contact with ASN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 3.5 15.7 - - + -
69C THR 3.3 13.3 + - - +
70C GLY 3.0 1.2 - - - -
71C PRO* 1.3 74.8 - - - +
73C ARG* 1.3 64.6 + - - +
75C ILE* 3.3 17.8 + - + +
76C TYR* 3.1 26.3 - - + -
72F ASN* 3.1 24.8 - - - +
75F ILE* 3.5 10.9 - - - +
111F PHE 3.2 25.9 + - - -
112F ASN* 4.6 11.1 + - - +
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 A 2.9 39.8 + - - +
60C SER* 2.7 45.3 + - - +
63C LEU* 3.5 17.5 - - + +
64C THR* 3.0 31.7 + - - +
68C ILE* 2.8 55.6 + - + +
69C THR* 3.9 8.3 - - - +
70C GLY 2.9 13.7 + - - +
72C ASN* 1.3 77.7 - - - +
74C ALA* 1.3 57.8 + - - +
76C TYR 3.1 3.1 + - - -
77C GLN* 2.8 32.5 + - - +
89E ARG 4.6 0.6 + - - -
90E ILE* 3.7 27.5 + - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3237 A 4.1 26.1 - - + +
268 T 4.3 5.5 - - - +
278 A 3.8 38.3 + - + +
70C GLY 3.7 1.0 + - - -
71C PRO 3.0 11.5 + - - +
73C ARG* 1.3 79.8 - - - +
75C ILE* 1.3 62.0 + - - +
77C GLN* 3.6 8.5 - - - +
78C GLY* 2.9 21.0 + - - -
71F PRO* 4.8 4.3 - - + -
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO 3.0 14.2 + - - +
72C ASN* 3.4 22.9 - - + +
74C ALA* 1.3 77.9 - - - +
76C TYR* 1.3 70.3 + - + +
78C GLY* 3.3 0.7 + - - -
79C PHE* 3.2 17.0 + - - +
107C TYR* 3.5 31.2 - - + -
111C PHE* 4.8 9.9 - - + +
113C ALA* 4.2 19.7 - - + -
71F PRO* 3.5 27.6 - - + -
72F ASN* 3.5 35.7 - - - +
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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
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59C VAL* 4.3 6.0 - - - +
63C LEU* 3.6 34.1 - - + -
68C ILE* 4.0 18.5 - - + +
72C ASN* 3.1 27.1 + - + -
73C ARG 3.1 2.8 + - - +
75C ILE* 1.3 79.9 - - + +
77C GLN* 1.3 60.6 + - - +
79C PHE* 3.2 7.7 + - - +
80C GLY* 2.9 25.5 + - - -
113C ALA* 4.0 7.8 - - + -
114C ASN* 2.9 37.8 + - - +
117C VAL* 3.7 29.0 - - + +
118C LEU* 3.6 31.2 - - + -
121C VAL* 4.4 9.1 - - + +
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Residues in contact with GLN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268 T 3.2 33.9 + - + +
278 A 3.2 20.2 + - - +
55C VAL* 5.2 0.5 - - - +
56C ASN* 3.1 41.8 + - - +
59C VAL* 3.3 23.1 - - - +
60C SER* 3.4 12.3 - - - +
63C LEU* 4.0 3.7 - - + +
73C ARG 2.8 22.4 + - - +
74C ALA* 3.6 7.9 - - - +
76C TYR* 1.3 76.3 - - - +
78C GLY* 1.3 56.2 + - - +
80C GLY* 3.2 1.6 + - - -
81C LEU* 2.9 38.3 + - + +
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3237 A 5.6 1.1 - - - -
3247 T 3.7 30.7 + - - +
268 T 5.3 0.2 + - - -
74C ALA 2.9 14.3 + - - -
75C ILE 3.8 3.8 - - - -
76C TYR 3.2 0.2 - - - -
77C GLN* 1.3 77.6 - - - +
79C PHE* 1.3 60.4 + - - +
81C LEU* 3.3 6.2 + - - +
82C LYS* 3.0 24.1 + - - +
107C TYR* 3.5 11.6 + - - -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE 3.2 13.3 + - - +
76C TYR 3.4 7.4 - - - +
78C GLY* 1.3 74.9 - - - +
80C GLY* 1.3 64.9 + - - +
82C LYS* 3.2 6.2 + - - +
83C VAL* 3.1 29.2 + - + +
100C ILE* 5.0 1.1 - - + -
103C LEU* 3.6 30.7 - - + -
104C LYS* 3.8 29.2 - - + -
107C TYR* 3.5 27.9 + + + -
118C LEU* 3.3 49.6 - - + -
121C VAL* 3.8 16.6 - - + -
122C VAL* 3.6 24.7 - - + -
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Residues in contact with GLY 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 4.1 6.5 - - - -
59C VAL* 4.7 2.2 - - - -
76C TYR 2.9 12.2 + - - -
77C GLN 3.2 3.1 + - - -
79C PHE* 1.3 77.1 - - - +
81C LEU* 1.3 62.2 - - - +
83C VAL* 3.1 2.9 + - - -
84C ALA* 3.1 19.2 + - - +
121C VAL* 3.6 13.9 - - - -
125C ILE* 3.2 30.1 - - - +
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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
----------------------------------------------------------
3247 T 3.6 24.5 - - + +
3257 A 3.4 30.7 - - + +
258 A 4.9 6.1 - - + -
268 T 5.2 2.5 - - - +
52C PHE* 3.7 37.6 - - + +
55C VAL* 4.3 6.1 - - + -
56C ASN* 3.3 29.6 - - - +
77C GLN* 2.9 26.7 + - + +
78C GLY* 3.6 4.5 - - - +
80C GLY* 1.3 74.7 - - - +
82C LYS* 1.3 58.1 + - - +
84C ALA* 3.3 6.7 + - - +
85C ARG* 2.9 27.5 + - - +
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Residues in contact with LYS 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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3247 T 4.0 13.9 + - - +
3257 A 2.9 31.7 + - - +
168 T 5.6 1.3 - - - -
178 A 3.8 13.0 + - - -
78C GLY 3.0 13.0 + - - +
79C PHE* 3.2 10.5 + - - +
81C LEU* 1.3 74.3 - - - +
83C VAL* 1.3 66.0 + - - +
85C ARG* 3.2 10.2 + - - +
86C ALA* 3.1 24.5 + - + +
99C MET* 4.7 16.6 - - + -
103C LEU* 3.5 28.9 - - + +
106C TYR* 5.5 4.0 - - - -
107C TYR* 5.2 1.1 - - + -
106D TYR* 2.7 38.2 + - - -
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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
----------------------------------------------------------
79C PHE* 3.1 35.0 + - + +
80C GLY* 3.3 9.0 - - - +
82C LYS* 1.3 77.6 - - - +
84C ALA* 1.3 61.8 + - - +
86C ALA* 3.4 6.7 + - - +
87C LEU* 3.0 21.1 + - + +
96C LEU* 4.3 4.4 - - + +
99C MET* 6.3 0.4 - - - -
100C ILE* 4.3 19.7 - - + -
103C LEU* 3.6 17.9 - - + -
122C VAL* 4.5 7.9 - - + -
125C ILE* 3.7 26.9 - - + -
126C THR* 4.3 15.9 - - + -
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Residues in contact with ALA 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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51C LYS 5.5 0.9 - - - +
52C PHE* 3.6 20.9 - - + -
55C VAL* 4.0 20.9 - - + -
80C GLY 3.1 10.8 + - - +
81C LEU* 3.5 8.1 - - - +
83C VAL* 1.3 78.2 - - - +
85C ARG* 1.3 63.6 + - - +
87C LEU* 3.1 12.8 + - + +
88C ASN* 2.9 26.6 + - - +
125C ILE* 4.5 6.7 - - + -
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Residues in contact with ARG 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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3257 A 3.0 35.7 + - - +
3267 T 3.1 34.5 + - - +
168 T 3.8 34.8 + - - +
178 A 3.9 21.2 + - - -
52C PHE* 3.6 10.0 - - - -
81C LEU 2.9 14.0 + - - +
82C LYS* 3.2 15.5 + - - +
84C ALA* 1.3 75.9 - - - +
86C ALA* 1.3 64.0 - - - +
88C ASN* 3.1 5.9 + - - +
89C ARG* 3.0 50.9 + - - +
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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
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168 T 5.4 2.7 - - - -
82C LYS* 3.1 11.8 + - - +
83C VAL* 3.7 8.7 - - - +
85C ARG* 1.3 77.6 - - - +
87C LEU* 1.3 58.1 + - - +
89C ARG* 4.5 3.1 - - - +
90C ILE* 2.7 50.8 + - + +
96C LEU* 3.9 10.3 - - + -
99C MET* 3.8 33.9 - - + -
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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
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83C VAL* 3.0 15.2 + - + +
84C ALA* 3.3 12.3 - - + +
86C ALA* 1.3 76.3 - - - +
88C ASN* 1.3 64.6 + - - +
91C GLY* 2.7 30.7 + - - +
92C SER* 3.6 32.8 - - - +
96C LEU* 3.8 23.5 - - + +
125C ILE* 4.8 22.0 - - + +
126C THR* 6.1 2.5 - - + -
57h GLU* 5.8 3.6 - - - +
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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
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3267 T 5.9 1.1 - - - +
7B SER* 3.8 17.8 + - - +
48C ASN* 4.9 5.4 + - - -
51C LYS* 3.9 31.1 + - - +
52C PHE* 3.3 34.5 - - + -
84C ALA* 2.9 12.6 + - - +
85C ARG* 3.6 8.1 - - - +
87C LEU* 1.3 86.9 - - - +
89C ARG* 1.3 61.6 + - + +
90C ILE 3.7 0.5 + - - -
91C GLY 4.8 0.5 + - - -
57h GLU* 5.2 4.3 - - - +
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3267 T 3.8 18.9 + - - +
3277 A 4.3 14.3 + - - -
148 T 4.7 4.0 + - - -
158 A 3.6 26.5 + - - +
168 T 3.5 37.2 + - - +
60A SER* 4.7 2.6 + - - -
73A ARG* 4.6 3.6 + - - -
7B SER* 3.6 36.2 - - - +
8B ARG* 5.5 3.4 - - - +
85C ARG* 3.0 53.8 + - - +
86C ALA* 4.2 1.8 - - - +
88C ASN* 1.3 81.3 - - + +
90C ILE* 1.3 62.3 + - + +
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158 A 5.4 0.9 - - - +
168 T 4.4 11.0 - - - +
60A SER* 4.7 2.6 + - - -
64A THR* 2.6 35.5 + - - +
69A THR* 4.4 17.5 - - + -
70A GLY 5.5 0.4 - - - +
73A ARG* 3.7 20.9 + - - +
86C ALA* 2.7 27.6 + - + +
88C ASN 5.0 0.7 - - - -
89C ARG* 1.3 79.6 - - + +
91C GLY* 1.3 69.1 + - - +
95C ALA* 3.5 26.9 - - + +
96C LEU* 4.2 3.4 - - - +
99C MET* 3.7 31.0 - - + -
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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
----------------------------------------------------------
64A THR* 3.8 1.1 - - - +
86C ALA 3.6 0.4 + - - -
87C LEU* 2.7 30.9 + - - -
88C ASN 4.6 0.4 - - - -
90C ILE* 1.3 89.1 - - - +
92C SER* 1.3 67.3 + - - +
96C LEU* 3.6 10.6 - - - +
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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