Contacts of the helix formed by residues 96 - 116 (chain B) in PDB entry 1JPM
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 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASP* 3.3 23.1 + - - +
61B SER* 4.1 16.1 + - - +
62B ILE* 5.5 0.2 - - - -
65B ALA* 4.0 11.0 - - - +
93B LEU* 3.6 30.6 - - + +
94B THR 2.8 23.8 + - - -
95B GLY* 1.3 71.4 - - - +
97B MET* 1.3 65.6 + - - +
98B SER 3.2 2.9 - - - -
99B ALA* 3.2 11.7 + - + +
100B LYS* 3.2 20.6 + - - +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 5.4 4.9 - - + -
57B ASP* 3.7 4.8 + - - +
90B GLN* 4.2 8.5 - - - +
95B GLY* 2.9 22.8 + - - +
96B ASN* 1.3 76.1 - - - +
98B SER* 1.3 57.2 + - - +
100B LYS* 3.3 15.0 + - - -
101B ALA* 2.9 25.8 + - - +
248B PHE* 4.7 10.5 - - + -
249B THR* 4.1 22.0 - - + -
270B MET 3.0 18.6 - - - +
271B LYS* 3.2 23.6 - - - +
272B ALA 3.5 21.1 - - - +
273B GLY* 3.2 14.3 - - - +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 3.4 11.4 - - - +
49B PRO 4.2 0.5 + - - -
51B THR* 4.2 2.3 + - - -
55B THR* 3.6 18.0 + - - +
57B ASP* 2.7 33.0 + - - +
62B ILE* 3.9 8.7 - - - -
97B MET* 1.3 79.0 - - - +
99B ALA* 1.3 61.5 + - - +
101B ALA* 3.3 2.3 + - - +
102B ALA 3.0 19.1 + - - -
270B MET* 3.1 37.0 + - - +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 4.6 0.2 + - - -
62B ILE* 3.8 30.9 - - + +
65B ALA* 3.8 29.2 - - + -
66B ILE* 4.1 7.1 - - + +
70B LEU* 4.1 6.5 - - + -
93B LEU* 5.8 0.4 - - + -
96B ASN* 3.2 13.4 + - + +
98B SER* 1.3 78.3 - - - +
100B LYS* 1.3 62.7 + - - +
102B ALA* 3.4 3.0 + - - +
103B VAL* 3.2 26.3 + - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.1 6.7 - - + -
89B ILE* 3.4 40.1 - - + +
90B GLN* 3.1 28.1 + - - +
93B LEU* 2.8 39.9 + - + -
94B THR* 4.3 0.6 - - - +
95B GLY 2.8 33.3 + - - +
96B ASN 3.2 6.2 + - - +
97B MET* 3.5 20.2 - - - +
99B ALA* 1.3 77.8 - - + +
101B ALA* 1.3 56.8 + - - +
103B VAL* 3.3 4.0 + - - +
104B GLU* 2.9 31.2 + - - +
273B GLY* 3.5 11.7 - - - +
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET 2.9 15.2 + - - +
98B SER 3.6 5.2 - - - +
100B LYS* 1.3 74.3 - - - +
102B ALA* 1.3 65.8 + - - +
104B GLU* 3.1 1.7 + - - +
105B MET* 2.9 31.1 + - + +
269B LEU* 3.3 36.8 - - + +
270B MET* 3.9 11.7 - - - -
273B GLY 3.4 9.8 + - - -
274B GLY* 3.5 6.5 - - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.8 23.6 - - + +
46B GLY* 3.3 21.2 - - - -
47B GLU 3.7 19.7 + - - +
48B ALA* 3.4 28.5 - - + -
66B ILE* 4.6 3.6 - - + -
98B SER 3.0 7.8 + - - +
99B ALA 3.7 5.4 - - - +
101B ALA* 1.3 79.0 - - - +
103B VAL* 1.3 61.0 + - - +
105B MET* 3.5 1.1 + - - -
106B ALA* 3.4 8.0 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.9 3.1 - - + -
34B VAL* 5.0 7.4 - - + -
36B ILE* 4.4 9.0 - - + -
66B ILE* 4.2 20.4 - - + -
70B LEU* 3.5 25.6 - - + -
74B LEU* 3.4 32.3 - - + -
89B ILE* 3.8 8.7 - - + -
99B ALA 3.2 13.3 + - - +
100B LYS* 3.7 7.4 - - - +
101B ALA 3.2 0.6 - - - -
102B ALA* 1.3 76.4 - - - +
104B GLU* 1.3 64.5 + - - +
106B ALA* 3.3 5.2 + - - +
107B LEU* 3.0 30.1 + - + +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.5 24.8 - - + +
89B ILE* 4.6 8.5 - - + -
90B GLN* 3.0 19.2 + - - +
100B LYS 2.9 19.6 + - - +
101B ALA 3.1 5.4 + - - +
103B VAL* 1.3 73.5 - - - +
105B MET* 1.3 59.9 + - - +
107B LEU* 3.1 7.3 + - - +
108B TYR* 2.8 42.8 + - + -
273B GLY 3.6 10.3 - - - +
274B GLY* 3.8 7.9 - - - -
275B ILE* 2.8 22.8 + - - +
276B SER* 2.5 32.8 + - - -
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP 3.3 12.1 - - - +
46B GLY* 3.6 2.2 - - - -
47B GLU 3.4 38.8 - - - +
101B ALA 2.9 18.9 + - - +
102B ALA 3.6 6.3 - - - +
103B VAL 3.2 0.2 - - - -
104B GLU* 1.3 77.7 - - - +
106B ALA* 1.3 57.9 + - - +
108B TYR* 3.2 4.4 + - - +
109B ASP* 2.8 30.0 + - - +
269B LEU* 4.1 32.1 - - + -
270B MET* 4.9 5.6 - - + -
274B GLY* 6.2 0.4 - - - -
275B ILE* 5.1 5.6 - - + +
299B GLU* 4.2 8.1 - - - +
302B LEU* 4.9 2.0 - - - +
303B GLY* 4.1 22.0 - - - +
306B ALA* 3.6 28.9 - - + -
352B LEU* 4.3 4.1 - - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 4.5 3.8 - - + -
36B ILE* 3.4 26.9 - - + -
38B TYR* 2.9 13.5 + - - -
44B GLY* 3.4 25.8 - - - +
45B TRP 3.1 19.2 + - - +
46B GLY* 4.0 2.5 - - - +
102B ALA 3.4 5.9 + - - +
103B VAL 3.3 4.3 + - - +
105B MET* 1.3 79.5 - - - +
107B LEU* 1.3 58.9 + - - +
109B ASP* 3.5 1.9 - - - +
110B GLY 3.0 16.6 + - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 3.6 28.5 - - + -
36B ILE* 3.8 11.9 - - + -
38B TYR* 3.3 14.9 + - - +
74B LEU* 4.0 2.2 - - + -
79B LEU* 4.2 11.9 - - + +
82B TYR* 3.1 21.0 + - + +
85B ILE* 3.9 12.8 - - + -
86B LEU* 5.1 4.0 - - + -
89B ILE* 3.1 37.0 - - + -
103B VAL* 3.0 25.3 + - + +
104B GLU* 3.1 6.5 + - - +
106B ALA* 1.3 75.0 - - - +
108B TYR* 1.3 54.3 + - + +
110B GLY* 3.2 2.1 + - - -
111B TRP* 2.7 30.7 + - - +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 3.1 28.2 + + - -
86B LEU* 3.6 13.6 - - + +
104B GLU* 2.8 49.8 + - + +
105B MET 3.9 2.0 - - - +
107B LEU* 1.3 70.3 - - - +
109B ASP* 1.3 61.1 + - - +
111B TRP* 3.5 35.4 - + - +
112B ALA* 2.8 31.7 + - - +
119B LEU* 3.7 22.5 - - + +
123B LEU* 4.1 8.7 - - + -
275B ILE* 3.7 42.4 - - + -
276B SER* 3.5 22.9 - - - -
279B GLU* 4.2 8.0 + - - -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLY* 3.5 5.4 - - - -
45B TRP* 3.0 30.6 + - - +
105B MET 2.8 19.5 + - - +
106B ALA 3.5 6.3 - - - +
108B TYR* 1.3 77.6 - - - +
110B GLY* 1.3 62.9 + - - +
112B ALA 3.4 0.2 + - - -
113B GLN* 2.9 46.2 + - - +
119B LEU* 5.1 0.6 - - - +
351B GLY* 3.3 2.5 - - - -
352B LEU* 2.7 55.5 + - + +
353B GLY 4.6 0.7 + - - -
354B ILE* 5.1 0.9 + - - +
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.1 14.5 - - - +
38B TYR* 3.7 27.1 - - - -
79B LEU* 3.7 7.2 - - - -
106B ALA 3.0 11.5 + - - -
107B LEU 3.6 2.7 - - - -
109B ASP* 1.3 77.1 - - - +
111B TRP* 1.3 55.1 + - - +
113B GLN* 3.3 8.4 + - - +
114B MET* 2.9 25.6 + - - +
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Residues in contact with TRP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TRP* 5.5 3.8 - + - -
117A LEU* 5.1 1.8 - - - +
121A GLN 5.0 4.0 + - - -
122A MET* 3.5 46.7 - - + +
123A LEU 6.2 0.4 - - - -
124A GLY 5.7 0.9 - - - -
79B LEU* 3.5 19.8 + - + +
82B TYR* 3.7 41.3 - + + +
107B LEU 2.7 19.6 + - - +
108B TYR* 3.5 36.6 - + - +
110B GLY* 1.3 72.2 - - - +
112B ALA* 1.3 62.4 + - - +
114B MET* 3.3 35.0 + - + +
115B CYS* 3.3 25.8 + - - -
122B MET* 3.5 27.8 - - + -
123B LEU* 4.8 6.1 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B TYR 2.8 20.6 + - - +
111B TRP* 1.3 69.7 - - - +
113B GLN* 1.3 66.4 + - - +
115B CYS* 3.0 4.0 + - - +
116B GLY 3.0 17.5 + - - -
117B LEU 3.2 27.3 + - - +
119B LEU* 3.7 20.2 - - + -
122B MET* 3.4 18.8 - - + -
351B GLY* 3.5 14.6 - - - -
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.7 4.7 - - + -
42B ALA* 3.5 24.5 - - + +
43B VAL 3.1 27.7 + - - +
44B GLY* 4.4 0.4 - - - -
109B ASP* 2.9 41.8 + - - +
110B GLY* 3.3 6.9 + - - +
112B ALA* 1.3 75.5 - - - +
114B MET* 1.3 63.8 + - - +
116B GLY* 3.1 12.6 + - - -
350B PRO* 3.8 32.4 + - + +
351B GLY* 3.8 1.1 - - - -
4C ILE 5.6 0.2 - - - +
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Residues in contact with MET 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.5 34.5 - - + -
1B MET* 3.7 37.6 - - + +
79B LEU* 4.1 17.7 - - + +
80B ALA* 5.4 1.6 - - - -
110B GLY 2.9 13.5 + - - +
111B TRP* 3.4 38.8 - - + +
112B ALA 3.2 0.2 - - - -
113B GLN* 1.3 79.4 - - - +
115B CYS* 1.3 65.8 + - - +
116B GLY 3.2 0.9 + - - -
4C ILE 4.6 0.3 - - - +
5C ARG* 2.9 50.7 + - - +
7C GLU* 5.9 0.9 - - - +
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Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A MET 4.5 4.7 - - - +
115A CYS* 3.8 39.8 - - + -
122A MET* 4.1 11.4 - - - -
111B TRP* 3.3 8.3 + - - -
112B ALA 3.0 2.6 + - - +
114B MET* 1.3 94.9 - - - +
116B GLY* 1.3 61.7 + - - +
117B LEU* 3.4 9.4 + - + +
122B MET* 2.9 38.8 - - + -
4C ILE* 4.7 9.7 - - - +
5C ARG* 4.1 5.8 - - - +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.0 3.6 + - - -
113B GLN 3.1 13.4 + - - -
114B MET 3.2 1.8 + - - -
115B CYS* 1.3 78.8 - - - +
117B LEU* 1.3 64.0 + - - +
118B PRO* 4.7 0.9 - - - +
350B PRO* 4.0 21.3 - - - +
4C ILE* 4.3 13.5 - - - -
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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
------------------------------------------------------------
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