Contacts of the helix formed by residues 82 - 108 (chain C) in PDB entry 3J41
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 SER 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 5.5 0.9 - - - -
76C LEU* 3.9 1.1 - - - -
81C MET* 1.3 77.6 - - - +
83C LEU* 1.3 64.6 + - - +
84C LEU* 3.1 12.3 + - - +
85C ARG* 3.1 26.8 + - - +
86C ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 3.8 31.8 - - + +
82C SER* 1.3 74.1 - - - +
84C LEU* 1.3 58.8 + - - +
86C ALA* 3.8 0.5 + - - +
87C ILE* 3.0 55.9 + - + +
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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
----------------------------------------------------------
9C PHE* 4.5 16.2 - - + -
82C SER* 3.0 9.8 - - - +
83C LEU* 1.3 78.6 - - - +
85C ARG* 1.3 66.2 + - - +
87C ILE* 3.6 5.9 + - + +
88C CYS* 3.1 43.9 + - - -
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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
----------------------------------------------------------
9C PHE* 3.5 54.3 - - + +
12C ALA* 4.5 8.5 - - - +
62C ILE 5.6 0.8 + - - -
63C SER* 6.3 0.2 - - - +
81C MET* 3.8 21.1 - - + +
82C SER* 3.1 24.5 + - - +
84C LEU* 1.3 72.4 - - - +
86C ALA* 1.3 57.4 + - - +
88C CYS* 3.0 2.3 + - - -
89C TYR* 2.6 76.3 + - + +
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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
----------------------------------------------------------
72C THR* 3.5 24.2 - - + -
73C PHE* 6.0 0.4 - - - -
76C LEU* 3.9 27.6 - - + -
81C MET* 3.5 7.3 - - + +
82C SER 3.1 15.1 + - - +
83C LEU 3.9 4.7 - - - +
85C ARG* 1.3 78.1 - - - +
87C ILE* 1.3 59.8 + - + +
89C TYR* 3.1 2.9 + - - +
90C MET* 2.8 38.7 + - - +
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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
----------------------------------------------------------
83C LEU* 3.0 43.2 + - + +
84C LEU* 4.0 5.8 - - + +
85C ARG 3.3 0.6 - - - -
86C ALA* 1.3 75.3 - - + +
88C CYS* 1.3 60.9 + - - +
90C MET* 3.8 9.4 - - + +
91C VAL* 2.9 45.8 + - + +
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Residues in contact with CYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 3.9 19.1 - - + -
10C TRP* 5.5 5.4 - - - -
13C ILE* 3.8 27.6 - - + +
84C LEU* 3.1 38.4 + - - +
85C ARG 3.0 4.5 + - - +
87C ILE* 1.3 78.9 - - - +
89C TYR* 1.3 58.3 + - - +
91C VAL* 3.5 7.8 - - - +
92C ALA* 2.9 31.0 + - - +
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Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE 5.3 0.4 - - - -
12C ALA* 3.6 15.9 - - + +
13C ILE* 4.6 10.5 - - + -
16C GLU* 3.7 29.8 - - + -
63C SER* 2.9 39.8 + - - -
66C HIS* 3.5 32.5 - + - -
72C THR* 3.7 5.8 - - + +
81C MET* 3.7 8.5 - - + -
85C ARG* 2.6 58.7 + - + +
86C ALA 3.2 10.1 - - - +
88C CYS* 1.3 75.1 - - - +
90C MET* 1.3 51.5 + - - +
92C ALA* 3.2 6.5 + - - +
93C GLN* 2.8 45.9 + - - +
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Residues in contact with MET 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 3.5 35.7 - - + +
72C THR* 4.0 10.1 - - + -
73C PHE* 5.2 7.9 - - + -
86C ALA* 2.8 24.4 + - - +
87C ILE* 3.8 9.2 - - - +
89C TYR* 1.3 73.4 - - - +
91C VAL* 1.3 60.8 + - + +
93C GLN* 3.3 18.5 - - - +
94C LEU* 2.8 42.1 + - + +
205C TRP* 4.4 16.8 - - + -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 2.9 39.6 + - + +
88C CYS* 3.5 7.9 - - - +
90C MET* 1.3 75.9 - - + +
92C ALA* 1.3 65.1 + - - +
94C LEU* 3.3 6.6 + - + +
95C LEU* 3.0 47.4 + - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 3.5 35.7 - - + +
16C GLU* 4.2 4.3 - - + -
17C PHE* 3.5 23.9 - - + +
88C CYS 2.9 17.9 + - - +
89C TYR* 3.5 5.2 - - - +
91C VAL* 1.3 78.9 - - - +
93C GLN* 1.3 52.1 + - - +
95C LEU* 4.9 1.6 - - - -
96C GLY* 2.7 32.4 + - - -
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Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU* 3.1 25.9 - - + +
20C SER* 3.3 24.9 - - - +
66C HIS* 3.6 2.6 - - - +
67C VAL* 4.0 3.8 - - - -
68C ASN 3.6 8.3 - - - +
69C PRO* 3.0 46.4 - - + +
72C THR* 2.9 20.6 + - - -
89C TYR* 2.8 29.7 + - - +
90C MET* 3.3 12.4 - - - +
92C ALA* 1.3 72.1 - - - +
94C LEU* 1.3 58.8 + - - +
97C ALA* 2.8 30.8 + - - +
186C ALA* 3.8 5.8 - - + +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 4.5 4.5 - - + -
90C MET* 2.8 32.7 + - + +
91C VAL* 3.8 6.3 - - + +
93C GLN* 1.3 74.3 - - - +
95C LEU* 1.3 70.9 + - + +
97C ALA* 3.5 2.3 + - - +
98C VAL* 3.0 32.0 + - - +
186C ALA* 3.9 24.2 - - + -
189C PHE* 3.8 31.7 - - + -
205C TRP* 3.9 28.9 - - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 3.8 18.1 - - + -
91C VAL* 3.0 39.7 + - + +
92C ALA* 4.2 1.8 - - - +
94C LEU* 1.3 81.8 - - + +
96C GLY* 1.3 66.4 + - - +
98C VAL* 3.4 6.9 + - + +
99C ALA* 2.9 26.0 + - - +
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Residues in contact with GLY 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 3.5 29.3 - - - -
20C SER* 4.0 1.6 - - - -
21C LEU* 3.0 17.5 - - - +
92C ALA 2.7 21.2 + - - -
93C GLN 3.7 0.9 - - - -
94C LEU 3.2 0.2 - - - -
95C LEU* 1.3 77.6 - - - +
97C ALA* 1.3 60.9 + - - +
99C ALA* 3.3 0.7 + - - +
100C GLY 3.0 18.0 + - - -
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C SER* 3.8 2.8 - - - +
24C VAL* 3.4 30.1 - - + +
93C GLN 2.8 18.1 + - - +
94C LEU* 3.8 4.0 - - - +
95C LEU 3.3 0.2 - - - -
96C GLY* 1.3 75.2 - - - +
98C VAL* 1.3 64.7 + - - +
100C GLY* 2.9 3.3 + - - -
101C ALA* 2.8 23.0 + - - +
186C ALA* 3.3 31.2 - - + +
189C PHE* 6.0 0.2 - - + -
190C ALA* 3.6 5.6 - - + -
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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
----------------------------------------------------------
94C LEU 3.0 19.4 + - - +
95C LEU* 3.7 7.9 - - + +
97C ALA* 1.3 74.5 - - - +
99C ALA* 1.3 59.9 + - - +
101C ALA* 3.3 3.5 + - - +
102C ALA* 2.8 28.6 + - + +
189C PHE* 3.9 27.8 - - + -
190C ALA* 3.7 10.3 - - - +
193C ILE* 4.1 14.4 - - + -
194C LEU* 3.8 20.4 - - + +
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 4.4 11.0 - - + -
21C LEU* 4.0 16.8 - - + -
95C LEU 2.9 18.3 + - - +
96C GLY 3.6 4.7 - - - +
98C VAL* 1.3 77.7 - - - +
100C GLY* 1.3 53.2 + - - +
102C ALA* 2.9 8.9 + - - +
103C VAL* 2.7 42.9 + - + +
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 3.5 37.3 - - - +
25C PHE* 3.4 14.0 - - - -
96C GLY 3.0 8.2 + - - -
97C ALA 2.9 6.4 + - - -
99C ALA* 1.3 76.2 - - - +
101C ALA* 1.3 58.2 + - - +
103C VAL* 4.6 0.9 - - - -
104C LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 4.0 1.4 - - - +
28C LEU* 3.9 20.0 - - + -
97C ALA 2.8 14.5 + - - +
98C VAL 3.5 1.3 - - - +
100C GLY* 1.3 75.2 - - - +
102C ALA* 1.3 57.3 + - - +
104C LEU* 3.3 8.6 - - - +
105C TYR* 2.9 28.4 + - - +
116C LEU* 4.3 8.4 - - + +
190C ALA* 3.8 21.5 - - + +
194C LEU* 3.5 21.1 - - + +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 2.8 17.3 + - + +
99C ALA* 3.1 13.2 - - - +
101C ALA* 1.3 74.4 - - - +
103C VAL* 1.3 67.5 + - + +
105C TYR* 3.0 8.9 + - - +
106C SER* 2.9 22.8 + - - -
194C LEU* 3.6 13.7 - - + +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 4.6 2.7 - - + -
136B PHE* 3.5 37.7 - - + -
21C LEU* 4.9 5.6 - - + -
25C PHE* 3.9 13.4 - - + -
99C ALA* 2.7 30.1 + - + +
100C GLY* 4.0 4.9 - - - +
102C ALA* 1.3 73.4 - - + +
104C LEU* 1.3 60.1 + - - +
106C SER* 2.7 26.4 + - - +
107C VAL* 3.2 17.0 + - + +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 3.9 11.9 - - + -
178B TYR* 3.6 24.0 - - + +
25C PHE* 3.5 26.0 - - + +
28C LEU* 4.0 22.9 - - + -
29C GLY* 3.8 14.6 - - - +
32C LEU* 4.1 11.0 - - + -
100C GLY 2.9 19.4 + - - +
101C ALA* 3.3 6.5 - - - +
103C VAL* 1.3 75.5 - - - +
105C TYR* 1.3 55.6 + - - +
107C VAL* 3.2 3.3 + - + +
108C THR* 2.7 35.5 + - - +
116C LEU* 3.6 30.7 - - + -
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ALA 2.9 13.8 + - - +
102C ALA* 3.0 11.6 + - - +
104C LEU* 1.3 77.5 - - - +
106C SER* 1.3 67.9 + - - +
108C THR* 3.2 21.7 + - - +
113C ARG* 3.1 61.5 + - - -
116C LEU* 4.2 25.4 - - + -
194C LEU* 5.5 5.2 - - + -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLN* 2.6 29.2 + - - +
132B ILE* 5.5 2.1 - - - +
102C ALA 2.9 11.6 + - - -
103C VAL* 2.7 24.8 + - - +
105C TYR* 1.3 84.7 - - - +
107C VAL* 1.3 57.1 + - - +
108C THR 3.5 0.2 - - - -
113C ARG* 4.8 2.3 + - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.6 1.7 - - - +
129B GLN* 2.8 53.1 + - + +
132B ILE* 3.6 33.7 - - + -
133B VAL* 3.1 21.5 - - + -
178B TYR* 3.7 13.0 - - + -
25C PHE* 5.2 5.6 - - + -
103C VAL* 3.3 18.8 - - + +
104C LEU* 3.2 5.6 + - + +
106C SER* 1.3 83.8 - - - +
108C THR* 1.3 60.4 + - - +
109C PRO* 4.0 1.9 - - - +
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Residues in contact with THR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLN* 4.5 3.9 + - - -
178B TYR* 3.5 22.0 + - - -
32C LEU* 3.6 16.0 - - + +
104C LEU* 2.7 29.7 + - + +
105C TYR* 3.2 17.0 - - - +
107C VAL* 1.3 79.9 - - - +
109C PRO* 1.3 74.0 + - - +
112C VAL* 4.0 4.5 - - - +
113C ARG* 2.8 48.3 + - + +
116C LEU* 4.8 0.9 - - + -
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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