Contacts of the helix formed by residues 96 - 115 (chain B) in PDB entry 1SJB
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 HIS 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO* 4.6 3.8 - - + -
57A SER* 2.6 32.2 + - - -
59A TYR* 4.0 21.1 - + - -
96A HIS* 6.5 0.9 - + - -
58B GLU* 3.3 27.5 + - + +
62B GLY* 5.0 7.7 + - - -
63B ALA* 5.5 0.6 - - - -
66B VAL* 3.9 30.9 - - + +
71B LEU* 5.1 1.8 - - + -
93B PHE* 5.6 2.0 - - + -
94B LYS 2.9 26.2 - - - -
95B GLY* 1.3 69.7 - - - +
97B ARG* 1.3 63.9 + - - +
98B MET 3.3 3.1 - - - -
99B ALA* 3.2 10.0 + - + -
100B LYS* 3.1 27.6 + - + +
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Residues in contact with ARG 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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220A GLU* 3.0 37.8 + - - +
58B GLU* 3.5 6.7 + - - +
95B GLY* 4.0 20.3 - - - +
96B HIS* 1.3 74.0 - - - +
98B MET* 1.3 61.1 + - - +
100B LYS* 3.7 6.5 - - + +
101B GLY 2.8 25.3 + - - -
243B VAL* 3.0 49.1 + - - +
244B SER* 4.7 8.1 - - - -
265B GLY 3.4 1.7 - - - +
266B ARG 3.5 15.9 - - - +
267B VAL 4.1 5.5 + - - -
268B GLY* 3.2 25.6 - - - +
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Residues in contact with MET 98 (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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47B CYS* 3.7 6.4 - - - -
48B VAL* 3.7 23.5 + - + +
49B THR* 3.8 31.6 - - + -
55B TYR* 3.5 34.8 - - + -
56B SER* 3.6 18.2 - - - +
58B GLU* 3.1 25.5 + - - +
97B ARG* 1.3 75.4 - - + +
99B ALA* 1.3 63.1 + - - +
101B GLY* 3.9 0.7 - - - -
102B ALA* 3.1 23.6 + - - +
265B GLY* 3.1 20.4 - - - +
266B ARG* 4.3 14.6 - - + -
292B MET* 4.0 10.3 - - + -
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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
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47B CYS* 4.1 11.1 - - - -
58B GLU* 3.4 8.6 + - - +
63B ALA* 4.3 7.6 - - + +
66B VAL* 3.8 28.7 - - + -
67B LEU* 3.7 18.7 - - + +
71B LEU* 3.9 6.5 - - + -
96B HIS* 3.2 9.5 + - + +
98B MET* 1.3 77.6 - - - +
100B LYS* 1.3 61.9 + - - +
102B ALA* 3.2 6.2 + - - +
103B LEU* 3.1 22.2 + - - +
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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
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71B LEU* 4.0 20.4 - - + -
86B VAL* 4.8 3.8 - - + +
87B THR* 5.2 2.6 + - - +
90B LEU* 3.0 42.4 + - + -
91B ALA* 4.1 6.1 + - - +
93B PHE* 2.7 36.3 + - - -
95B GLY 3.4 18.6 + - - +
96B HIS* 3.1 15.4 + - - +
97B ARG* 3.7 7.6 - - + +
99B ALA* 1.3 78.1 - - - +
101B GLY* 1.3 59.1 + - - +
103B LEU* 3.3 5.5 + - - +
104B GLU* 2.8 30.5 + - - +
268B GLY* 3.9 7.4 - - - +
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Residues in contact with GLY 101 (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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97B ARG 2.8 17.6 + - - -
98B MET 3.9 1.3 - - - -
100B LYS* 1.3 73.1 - - - +
102B ALA* 1.3 53.5 + - - +
104B GLU* 3.4 3.2 - - - +
105B MET* 2.8 35.5 + - - +
265B GLY* 5.1 5.6 - - - -
268B GLY 3.0 27.8 + - - -
269B GLY* 3.6 10.5 - - - -
270B TYR* 5.1 1.7 + - - -
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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 LEU* 3.8 15.0 - - + +
45B GLY* 3.4 9.0 - - - -
46B GLU 3.5 27.8 - - - +
47B CYS* 3.8 17.3 - - + +
67B LEU* 5.3 1.1 - - + -
98B MET 3.1 14.0 + - - +
99B ALA* 3.2 11.2 + - - +
101B GLY* 1.3 76.3 - - - +
103B LEU* 1.3 57.4 + - - +
105B MET* 3.2 8.7 - - - +
106B ALA 3.1 22.0 + - - -
265B GLY* 5.7 0.6 - - - -
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Residues in contact with LEU 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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3B LEU* 5.6 0.7 - - + -
6B VAL* 4.1 23.6 - - + -
34B LEU* 3.5 19.0 - - + +
36B ALA* 5.4 0.2 - - + -
67B LEU* 3.8 9.9 - - + -
71B LEU* 3.8 32.8 - - + +
72B ILE* 4.2 8.3 - - + +
75B LEU* 3.5 35.7 - - + -
86B VAL* 5.3 0.4 - - + -
90B LEU* 4.1 8.7 - - + -
99B ALA 3.1 12.0 + - - +
100B LYS* 3.7 8.5 - - - +
102B ALA* 1.3 71.6 - - - +
104B GLU* 1.3 65.8 + - - +
106B ALA* 3.3 4.4 + - + +
107B VAL* 3.1 32.3 + - + +
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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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83B ALA* 4.3 21.5 - - + +
86B VAL* 4.3 16.4 - - + +
87B THR* 4.0 17.0 + - - -
100B LYS 2.8 17.7 + - - +
101B GLY* 3.4 6.5 - - - +
103B LEU* 1.3 78.6 - - - +
105B MET* 1.3 57.0 + - - +
107B VAL* 3.4 4.9 + - - +
108B LEU* 2.9 34.9 + - + +
268B GLY 4.3 6.0 - - - +
269B GLY* 4.2 5.7 - - - -
270B TYR* 3.4 12.1 + - - +
271B LEU* 3.1 52.3 + - - +
272B GLU* 4.9 1.2 + - - +
275B ARG* 5.2 0.5 + - - -
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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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44B TRP 3.6 7.6 - - - +
45B GLY* 3.7 4.7 - - - -
46B GLU* 3.2 49.8 - - + +
48B VAL* 6.3 1.8 - - + -
101B GLY 2.8 13.7 + - - +
102B ALA* 3.2 13.2 + - - +
104B GLU* 1.3 78.7 + - - +
106B ALA* 1.3 58.7 + - - +
108B LEU* 3.6 6.0 - - - +
109B ASP* 2.8 31.0 + - - +
119B PHE* 4.1 11.9 - - + -
270B TYR* 3.6 44.4 - - + +
297B LEU* 5.1 1.8 - - - -
298B GLY* 4.7 13.0 - - - -
301B ALA* 4.8 4.5 - - - -
347B LEU* 4.9 5.6 - - + -
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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 LEU* 4.0 13.2 - - + +
36B ALA* 3.6 23.8 - - + +
43B GLY* 3.3 15.4 - - - +
44B TRP 3.6 12.1 + - - -
45B GLY* 3.7 15.5 - - - +
102B ALA 3.1 7.7 + - - +
103B LEU* 3.6 9.2 - - + +
104B GLU 3.3 0.2 - - - -
105B MET* 1.3 79.7 - - - +
107B VAL* 1.3 64.8 + - - +
110B ALA* 3.1 18.9 + - - +
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Residues in contact with VAL 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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1B MET* 5.3 1.3 - - - +
3B LEU* 5.4 8.5 - - + -
36B ALA* 4.8 9.6 - - + -
38B THR* 5.9 4.4 - - + +
75B LEU* 4.4 12.8 - - + -
81B ILE* 4.6 9.6 - - + -
82B THR* 4.0 5.8 - - - -
83B ALA* 3.7 30.3 - - - +
86B VAL* 4.2 16.6 - - + -
103B LEU* 3.1 17.4 + - + +
104B GLU 3.5 7.4 - - - +
106B ALA* 1.3 76.4 - - - +
108B LEU* 1.3 65.5 + - - +
110B ALA* 3.1 7.9 + - - +
111B GLU* 2.9 25.6 + - + +
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Residues in contact with LEU 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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83B ALA* 3.5 25.6 - - + -
104B GLU* 2.9 21.4 + - - +
105B MET* 3.6 5.4 - - - +
107B VAL* 1.3 79.2 - - - +
109B ASP* 1.3 62.7 + - - +
111B GLU* 3.2 7.5 + - - +
112B LEU* 2.9 53.2 + - + +
119B PHE* 3.4 33.0 - - + -
122B GLU* 4.9 10.5 - - + +
123B LEU* 5.6 2.2 - - + -
270B TYR* 4.4 9.2 - - + -
271B LEU* 4.3 24.7 - - + -
117C ARG* 5.5 0.2 - - - +
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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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43B GLY* 3.4 4.3 - - - -
44B TRP 2.9 27.3 + - - +
105B MET 2.8 20.6 + - - +
106B ALA 3.7 4.3 - - - +
108B LEU* 1.3 73.5 - - - +
110B ALA* 1.3 58.8 + - - +
112B LEU* 3.4 0.7 + - - +
113B ARG* 2.8 54.4 + - - +
119B PHE* 3.6 13.0 - - + -
346B GLY* 3.0 8.5 - - - -
347B LEU* 2.7 40.6 + - + +
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Residues in contact with ALA 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* 4.2 3.6 - - - +
36B ALA* 4.8 1.8 - - + +
38B THR* 4.4 18.2 - - + +
40B ALA* 5.1 4.0 - - - +
41B GLY* 4.2 10.2 - - - +
42B GLU 3.3 30.5 - - - +
43B GLY* 3.7 1.9 - - - +
106B ALA 3.1 11.1 + - - +
107B VAL* 3.5 8.7 - - - +
109B ASP* 1.3 82.3 - - - +
111B GLU* 1.3 56.3 + - - +
113B ARG* 3.5 2.8 + - - +
114B ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 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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1B MET* 3.8 21.8 - - + +
81B ILE 4.8 0.6 - - - +
82B THR* 3.5 15.2 - - - +
83B ALA* 2.8 39.5 + - - +
84B ALA 5.4 0.2 + - - -
107B VAL* 2.9 17.6 + - + +
108B LEU* 3.5 7.3 - - - +
110B ALA* 1.3 74.2 - - - +
112B LEU* 1.3 66.4 + - + +
114B ALA* 3.3 2.4 + - - +
115B HIS* 2.9 36.9 + - + +
117C ARG* 2.8 42.4 + - - +
121C ALA* 5.2 1.0 - - - +
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Residues in contact with LEU 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 LEU* 2.9 37.1 + - + +
111B GLU* 1.3 76.2 - - + +
113B ARG* 1.3 59.2 + - - +
115B HIS* 3.2 2.2 + - + +
116B GLU 2.7 8.5 + - - -
117B ARG* 2.7 50.6 + - + +
118B SER 4.0 1.6 - - - +
119B PHE* 3.7 34.3 - - + +
122B GLU* 3.5 48.5 - - + +
346B GLY* 3.8 9.4 - - - -
117C ARG* 4.4 13.5 - - - +
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Residues in contact with ARG 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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42B GLU 4.1 12.5 + - - +
44B TRP* 4.4 11.7 - - - -
109B ASP* 2.8 57.2 + - - +
110B ALA* 3.6 6.3 - - - +
112B LEU* 1.3 77.6 - - - +
114B ALA* 1.3 57.3 + - - +
116B GLU* 2.8 24.8 + - - +
345B PRO* 3.6 25.3 + - + +
346B GLY 3.6 13.0 - - - +
347B LEU* 4.2 1.5 - - - +
348B GLY* 4.5 1.2 - - - -
349B VAL 3.2 41.0 + - - +
350B ALA* 4.0 8.4 - - - +
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Residues in contact with ALA 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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1B MET* 3.0 36.1 - - + -
40B ALA* 3.8 20.4 + - + +
110B ALA 3.0 9.7 + - - +
111B GLU 3.4 2.9 - - - +
112B LEU 3.2 0.2 - - - -
113B ARG* 1.3 78.0 - - - +
115B HIS* 1.3 62.2 + - + +
116B GLU* 3.2 5.1 + - - +
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Residues in contact with HIS 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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1B MET* 4.5 12.6 - - + -
111B GLU* 2.9 30.9 + - + +
112B LEU* 4.0 3.8 - - + +
114B ALA* 1.3 77.2 - - + +
116B GLU* 1.3 72.3 + - - +
117B ARG* 3.1 6.8 + - + -
115C HIS* 3.2 37.0 - - + +
116C GLU* 3.0 28.5 + - + -
117C ARG* 3.6 46.4 + - + +
121C ALA* 5.7 0.4 - - - +
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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