Contacts of the helix formed by residues 97 - 117 (chain B) in PDB entry 4J1O
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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLY* 4.9 2.0 - - - -
67B ALA* 4.0 17.7 - - + -
94B LEU* 3.7 32.1 - - + +
95B CYS 2.9 25.0 + - - -
96B GLY* 1.3 72.2 - - - +
98B ASN* 1.3 65.7 + - - +
99B TYR* 3.1 34.1 - + + -
100B ALA* 3.0 10.0 + - - +
101B LYS* 3.1 11.6 + - - +
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 6.2 0.3 - - - -
91B ASP* 5.7 0.2 - - - +
96B GLY* 3.3 8.1 - - - +
97B HIS* 1.3 75.5 - - - +
99B TYR* 1.3 58.6 + - - +
101B LYS* 3.2 16.3 + - - +
102B ALA* 2.8 28.8 + - - +
246B GLU 3.5 13.1 + - - -
247B ASP* 4.4 9.1 - - - +
268B THR 3.3 7.7 - - - +
269B ARG* 3.1 29.2 + - - +
270B ILE 3.6 10.1 + - - +
271B GLY* 3.7 15.5 - - - -
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 2.9 36.2 + - - +
51B PRO* 4.0 11.2 - - + -
58B PRO 4.8 4.7 - - - -
59B SER* 3.2 35.2 - - - -
60B HIS* 3.4 23.3 + - - -
63B GLY* 2.8 30.7 + - - -
64B ALA* 3.6 15.0 - - + -
97B HIS* 3.1 37.8 - + + -
98B ASN* 1.3 80.1 - - - +
100B ALA* 1.3 68.3 + - + +
102B ALA* 3.9 8.5 - - - +
103B ALA 4.0 0.3 + - - -
268B THR* 3.3 21.3 + - - +
269B ARG* 5.1 0.6 - - - +
406B IOD 4.4 14.1 - - + -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 4.6 7.9 - - - -
64B ALA* 4.1 13.0 - - - +
67B ALA* 3.5 32.5 - - + -
68B LEU* 3.6 16.3 - - + +
71B MET* 4.3 7.4 - - + -
97B HIS 3.0 7.2 + - - +
99B TYR* 1.3 85.8 - - + +
101B LYS* 1.3 66.2 + - - +
102B ALA 3.1 1.3 - - - -
103B ALA* 3.1 18.9 + - - +
104B ILE 3.7 1.0 + - - -
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Residues in contact with LYS 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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71B MET* 3.8 22.0 - - + +
87B ARG* 5.4 5.2 - - + +
90B MET* 3.5 40.5 - - + +
91B ASP* 2.8 30.4 + - - +
94B LEU* 2.8 29.1 + - - -
95B CYS* 4.3 0.4 - - - +
96B GLY* 2.9 31.5 + - - +
97B HIS 3.1 7.3 + - - +
98B ASN* 3.7 19.9 + - - +
100B ALA* 1.3 78.6 - - - +
102B ALA* 1.3 61.8 + - - +
104B ILE* 3.1 6.5 + - - +
105B ASP* 3.0 19.1 + - - +
271B GLY 4.2 7.2 - - - +
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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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98B ASN 2.8 19.7 + - - +
99B TYR 3.9 4.9 - - - +
100B ALA 3.1 0.2 - - - -
101B LYS* 1.3 73.7 - - - +
103B ALA* 1.3 56.8 + - - +
105B ASP* 3.3 1.1 + - - +
106B ILE* 2.9 39.2 + - + +
267B LEU 4.7 0.4 - - - -
268B THR* 3.6 28.7 - - + +
271B GLY 3.6 10.5 + - - -
272B GLY* 3.6 22.7 - - - +
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Residues in contact with ALA 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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35B VAL* 3.9 24.9 - - + +
47B GLY* 3.3 11.3 - - - -
48B GLU* 4.0 33.1 + - - +
49B THR* 4.2 13.2 - - + +
68B LEU* 4.7 0.9 - - + -
99B TYR 4.0 1.2 + - - -
100B ALA 3.1 12.7 + - - +
102B ALA* 1.3 80.0 - - - +
104B ILE* 1.3 62.0 + - - +
106B ILE* 4.7 0.4 - - - -
107B ALA* 3.2 19.2 + - - +
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Residues in contact with ILE 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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3B ILE* 5.8 0.7 - - + -
6B ILE* 4.4 13.2 - - + -
35B VAL* 3.8 24.2 - - + -
37B ILE* 3.8 16.6 - - + +
68B LEU* 3.9 22.0 - - + -
71B MET* 4.8 2.0 - - + -
72B ALA* 6.1 0.7 - - + -
75B LEU* 4.1 23.6 - - + -
86B LEU* 3.8 22.0 - - + -
90B MET* 3.6 25.6 - - + -
100B ALA 4.4 0.9 - - - +
101B LYS 3.1 8.4 + - - +
103B ALA* 1.3 75.1 - - - +
105B ASP* 1.3 66.1 + - - +
107B ALA* 3.3 3.6 + - - +
108B ALA* 2.9 22.0 + - - +
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Residues in contact with ASP 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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83B PRO* 4.8 6.8 - - - +
86B LEU* 5.2 2.2 - - - -
87B ARG* 5.7 4.0 - - + +
90B MET* 4.4 7.6 - - + +
101B LYS 3.0 12.2 + - - +
102B ALA 3.3 8.9 + - - +
104B ILE* 1.3 78.4 - - - +
106B ILE* 1.3 65.3 + - - +
108B ALA* 3.2 7.3 + - - +
109B TYR* 3.1 31.5 + - - -
271B GLY 4.1 9.1 - - - +
272B GLY* 3.6 5.2 - - - -
273B LEU* 2.7 34.9 + - - +
274B GLN* 3.2 29.6 + - - +
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Residues in contact with ILE 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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46B TRP 3.6 14.6 - - - +
47B GLY* 4.0 5.8 - - - -
48B GLU 4.3 9.6 - - - +
102B ALA* 2.9 28.6 + - + +
103B ALA 4.0 3.6 - - - +
104B ILE 3.3 0.2 - - - -
105B ASP* 1.3 83.6 - - - +
107B ALA* 1.3 57.8 + - - +
109B TYR* 3.2 4.0 + - - +
110B ASP* 3.0 26.2 + - - +
267B LEU* 4.1 9.9 - - + -
272B GLY* 5.1 0.2 - - - -
273B LEU* 4.3 13.5 - - + +
300B ILE* 4.5 3.6 - - + -
301B ILE* 3.6 30.5 - - + -
304B ALA* 3.8 26.9 - - + -
352B LEU* 3.8 14.2 - - + +
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Residues in contact with ALA 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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35B VAL* 4.2 3.8 - - + +
37B ILE* 3.6 25.6 - - + -
45B GLY* 3.5 15.6 - - - +
46B TRP 3.3 26.8 + - - -
47B GLY 3.6 2.0 - - - +
103B ALA 3.2 16.5 + - - +
104B ILE* 3.3 1.1 + - - +
106B ILE* 1.3 75.7 - - - +
108B ALA* 1.3 59.6 + - - +
110B ASP* 3.4 2.8 + - - +
111B LEU* 3.0 29.0 + - - +
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Residues in contact with ALA 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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37B ILE* 4.2 5.3 - - + +
80B PRO* 3.4 23.9 - - + +
83B PRO* 5.4 6.1 - - + -
86B LEU* 3.7 21.5 - - + -
104B ILE 2.9 14.0 + - - +
105B ASP* 3.5 9.4 - - - +
107B ALA* 1.3 76.8 - - - +
109B TYR* 1.3 57.3 - - + +
111B LEU* 3.2 6.6 + - - +
112B MET* 2.8 36.4 + - - +
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Residues in contact with TYR 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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125A GLY* 6.1 0.3 - - - -
83B PRO* 3.5 36.3 - - + +
105B ASP* 3.1 46.3 + - - -
106B ILE 3.2 6.5 + - - +
108B ALA* 1.3 71.5 - - - +
110B ASP* 1.3 61.5 + - - +
112B MET* 3.3 18.1 + - + +
113B GLY 2.9 24.6 + - - -
120B VAL* 3.5 19.7 - - + +
123B LEU* 4.2 20.7 - - + +
124B LEU* 3.6 29.2 - - + +
273B LEU* 3.7 26.0 - - + -
274B GLN* 3.5 21.0 - - - +
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Residues in contact with ASP 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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45B GLY* 3.5 4.2 - - - -
46B TRP* 2.9 31.9 + - - +
106B ILE 3.0 14.8 + - - +
107B ALA 3.5 9.4 - - - +
109B TYR* 1.3 76.9 - - - +
111B LEU* 1.3 62.7 + - - +
113B GLY 3.3 0.3 + - - -
114B LYS* 3.0 48.5 + - - +
120B VAL* 4.2 8.4 - - - +
350B PRO 4.8 0.2 - - - +
351B GLY* 3.7 3.3 - - - -
352B LEU* 2.9 42.3 + - + +
353B GLY 4.6 0.5 + - - -
354B ILE 4.8 6.2 - - - +
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Residues in contact with LEU 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* 4.6 8.7 - - - -
37B ILE* 4.1 26.5 - - + +
39B ALA* 4.3 12.3 - - + -
43B LEU* 3.5 36.3 - - + +
44B ALA 3.4 25.8 - - - -
45B GLY* 4.0 3.3 - - - +
80B PRO* 3.8 31.9 - - + +
81B LEU* 4.7 0.9 - - + -
107B ALA 3.0 15.4 + - - +
108B ALA* 3.2 5.8 + - - +
110B ASP* 1.3 76.1 - - - +
112B MET* 1.3 56.4 + - - +
114B LYS* 3.3 4.7 + - - +
115B HIS* 2.9 31.3 + - - +
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Residues in contact with MET 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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122A ASP 4.8 7.4 - - - +
123A LEU* 6.1 2.0 - - + -
80B PRO 3.7 2.7 - - - +
81B LEU* 3.6 46.4 - - + +
83B PRO* 3.5 35.9 - - + -
108B ALA 2.8 24.5 + - - +
109B TYR* 3.3 20.4 + - + +
111B LEU* 1.3 72.4 - - - +
113B GLY* 1.3 63.4 + - - +
115B HIS* 3.2 1.0 + - - +
116B TYR* 3.0 46.1 + - + -
123B LEU* 3.9 22.7 - - + -
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Residues in contact with GLY 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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109B TYR 2.9 12.6 + - - -
110B ASP 3.8 2.0 - - - -
112B MET* 1.3 76.8 - - - +
114B LYS* 1.3 57.6 + - - +
117B GLY* 2.8 26.3 + - - -
118B VAL* 2.9 37.8 + - - +
120B VAL* 5.0 0.4 - - - -
123B LEU* 3.7 4.7 - - - +
350B PRO* 3.8 1.2 - - - +
351B GLY* 3.6 10.8 - - - -
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Residues in contact with LYS 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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43B LEU* 4.0 24.8 - - + +
44B ALA* 2.9 33.1 + - - +
45B GLY* 4.7 0.2 - - - -
46B TRP* 4.8 9.7 - - - +
110B ASP* 3.0 42.4 + - - +
111B LEU 3.3 4.7 + - - +
113B GLY* 1.3 76.7 - - - +
115B HIS* 1.3 63.5 + - - +
117B GLY* 3.6 7.1 + - - -
350B PRO* 4.3 14.6 - - + +
351B GLY* 3.8 5.6 - - - +
354B ILE 4.8 11.0 + - - -
355B THR* 5.9 3.0 + - - +
356B PRO* 6.0 0.6 - - - +
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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* 3.2 31.6 - - + +
43B LEU* 3.8 15.0 - - + +
81B LEU* 4.0 16.3 - - + +
111B LEU 2.9 17.7 + - - +
112B MET 3.2 4.7 + - - +
114B LYS* 1.3 79.7 - - - +
116B TYR* 1.3 86.3 + + - +
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Residues in contact with TYR 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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116A TYR* 4.1 50.0 - + + +
117A GLY 5.4 1.8 - - - -
118A VAL* 3.7 31.2 - - + +
122A ASP* 4.9 3.2 + - - +
123A LEU* 5.2 5.6 - - + -
81B LEU* 3.8 25.4 + - + +
112B MET* 3.0 47.4 + - + +
115B HIS* 1.3 100.8 - + - +
117B GLY* 1.3 62.5 + - - +
118B VAL* 3.7 12.3 - - + -
123B LEU* 4.5 13.9 - - + -
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Residues in contact with GLY 117 (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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116A TYR* 5.4 1.9 - - - -
113B GLY 2.8 8.4 + - - -
114B LYS 3.6 5.9 + - - -
115B HIS 3.4 3.0 - - - -
116B TYR* 1.3 80.3 - - - +
118B VAL* 1.3 59.4 + - - +
350B PRO* 4.2 15.9 - - - +
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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
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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