Contacts of the helix formed by residues 94 - 117 (chain M) in PDB entry 2I2X
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 94 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M GLN* 3.1 34.2 + - - +
91M MET 3.3 6.2 - - - +
93M ASN* 1.3 84.1 - - - +
95M PRO* 1.3 67.1 - - - +
96M SER* 3.2 3.6 - - - +
97M TRP* 2.8 54.5 + - + +
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Residues in contact with PRO 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M MET 3.9 6.6 - - - +
92M SER 3.6 4.5 - - - +
93M ASN 3.2 14.1 - - - +
94M ASN* 1.3 82.8 - - - +
96M SER* 1.3 61.5 + - - +
97M TRP 3.3 0.3 + - - -
98M GLY* 3.4 3.1 + - - -
99M ALA* 3.2 20.6 + - - +
145M VAL* 3.8 18.6 - - + +
148M GLU* 3.8 32.5 - - + +
149M ALA* 3.9 18.5 - - - +
152M GLN* 3.9 17.5 - - + +
153M CYS* 5.0 1.9 - - - -
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Residues in contact with SER 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LYS* 5.3 1.4 + - - -
94M ASN* 2.9 2.8 + - - +
95M PRO* 1.3 73.6 - - - +
97M TRP* 1.3 77.3 + - - +
99M ALA* 3.4 8.2 + - - +
100M GLU* 3.0 39.5 + - - +
152M GLN* 4.7 8.4 - - - +
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Residues in contact with TRP 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLY 5.4 2.0 - - - -
53M ALA 4.9 4.7 - - - -
54M SER* 4.4 7.9 - - - -
55M LYS* 3.6 66.7 - - + +
58M LEU* 4.2 9.6 - - + -
90M GLN* 3.7 45.1 - - + +
91M MET* 4.0 5.4 - - + -
94M ASN* 2.8 46.5 + - + +
96M SER* 1.3 78.4 - - - +
98M GLY* 1.3 62.3 + - - +
100M GLU* 3.1 13.2 + - - +
101M VAL* 3.1 19.1 + - + +
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Residues in contact with GLY 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M HIS* 4.1 9.6 - - - -
91M MET* 3.4 36.0 + - - -
95M PRO 3.4 4.7 + - - -
96M SER 3.4 0.2 - - - -
97M TRP* 1.3 78.3 - - - +
99M ALA* 1.3 57.0 + - - +
101M VAL* 3.2 4.0 + - - +
102M ALA* 2.8 28.6 + - - +
124M HIS* 3.6 3.3 + - - -
153M CYS* 3.7 7.0 - - - -
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Residues in contact with ALA 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M PRO 3.2 13.9 + - - +
96M SER* 3.6 11.2 - - - +
97M TRP 3.3 0.2 - - - -
98M GLY* 1.3 74.8 - - - +
100M GLU* 1.3 57.1 + - + +
102M ALA* 3.3 3.1 + - - +
103M HIS* 2.9 24.1 + - - +
152M GLN* 3.5 34.1 - - + +
153M CYS* 3.7 9.8 - - - -
156M ASN* 3.4 26.0 - - - +
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LYS* 2.9 41.0 + - - +
59M ILE* 3.6 22.1 - - + +
96M SER* 3.0 29.1 + - - +
97M TRP* 3.1 4.7 + - - +
99M ALA* 1.3 75.4 - - + +
101M VAL* 1.3 66.2 + - - +
103M HIS* 3.2 8.0 + - + +
104M ALA* 2.9 24.3 + - - +
156M ASN* 5.6 2.9 - - - +
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Residues in contact with VAL 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M LYS* 6.2 0.7 - - + -
58M LEU* 4.7 4.5 - - + -
59M ILE* 4.0 25.1 - - + +
62M TYR* 3.5 42.8 - - + -
85M THR* 4.5 0.2 - - + -
91M MET* 3.9 23.3 - - + -
97M TRP 3.1 13.8 + - - +
98M GLY 3.5 6.7 - - - +
100M GLU* 1.3 75.6 - - - +
102M ALA* 1.3 63.8 + - - +
104M ALA* 3.0 5.6 + - - +
105M GLN* 2.9 48.7 + - - +
124M HIS* 4.2 1.1 - - - +
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Residues in contact with ALA 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M GLY 2.8 14.2 + - - +
99M ALA* 3.4 13.0 - - - +
100M GLU 3.2 0.2 - - - -
101M VAL* 1.3 77.0 - - - +
103M HIS* 1.3 56.1 + - - +
105M GLN* 4.4 0.2 - - - +
106M LYS* 2.9 31.2 + - - +
122M LEU* 3.7 7.4 - - + +
124M HIS* 3.6 30.3 + - + +
153M CYS* 4.4 5.4 - - - +
156M ASN 3.3 11.4 - - - +
158M ALA 4.3 13.0 - - - +
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Residues in contact with HIS 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M ALA 2.9 12.4 + - - +
100M GLU* 3.6 9.9 - - + +
102M ALA* 1.3 75.1 - - - +
104M ALA* 1.3 59.8 + - - +
106M LYS* 3.3 3.5 + - - +
107M THR* 2.8 49.3 + - - -
156M ASN* 3.0 38.7 + - - +
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Residues in contact with ALA 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ILE* 3.9 18.2 - - + +
62M TYR* 6.4 0.9 - - + -
63M GLU* 3.5 30.0 - - + +
100M GLU 2.9 16.4 + - - +
101M VAL* 3.6 3.6 - - - +
103M HIS* 1.3 77.7 + - - +
105M GLN* 1.3 64.0 + - + +
107M THR* 3.5 8.7 + - - -
108M ILE* 3.4 24.6 + - - +
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Residues in contact with GLN 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M TYR* 3.0 23.4 + - - -
62M TYR* 4.2 13.6 - - + +
63M GLU* 5.3 0.4 - - - +
66M THR* 3.2 29.6 + - - +
83M LEU* 4.4 2.9 - - - +
85M THR* 2.7 22.1 + - - -
101M VAL* 2.9 33.8 + - + +
102M ALA 3.7 3.6 - - - +
104M ALA* 1.3 77.0 - - + +
106M LYS* 1.3 62.4 + - - +
108M ILE* 3.1 7.4 + - - +
109M MET* 3.0 37.6 + - + +
122M LEU* 3.9 8.9 - - + +
124M HIS* 3.2 24.7 - - - -
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Residues in contact with LYS 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M GLY* 4.5 1.9 - - - -
30M LEU* 4.1 30.3 - - + +
102M ALA 2.9 18.6 + - - +
103M HIS* 3.9 3.6 - - - +
105M GLN* 1.3 76.2 - - - +
107M THR* 1.3 64.7 + - - +
109M MET* 3.2 22.7 + - + +
110M GLU* 2.9 39.1 + - - +
120M CYS 5.4 1.8 - - - -
122M LEU* 4.4 3.3 - - + +
157M GLY* 2.9 35.1 + - - +
159M ASP* 2.6 39.2 + - - +
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Residues in contact with THR 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M HIS* 2.8 39.3 + - - -
104M ALA* 3.5 10.6 - - - -
106M LYS* 1.3 77.3 - - - +
108M ILE* 1.3 65.3 + - + +
110M GLU* 3.3 15.1 + - - +
111M LYS* 3.2 19.6 + - + +
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Residues in contact with ILE 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M GLU* 3.7 36.6 - - + +
66M THR* 4.1 17.5 - - + +
67M THR* 3.6 30.1 - - - +
70M MET* 4.6 0.4 - - + -
104M ALA 3.4 11.6 + - - +
105M GLN 3.1 8.1 + - - +
107M THR* 1.3 75.9 - - + +
109M MET* 1.3 67.3 + - - +
111M LYS* 3.2 19.0 + - + +
112M TYR* 3.3 33.7 + - + -
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Residues in contact with MET 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LEU* 3.9 3.6 - - + +
66M THR* 3.8 17.7 - - + -
70M MET* 4.4 16.2 - - - -
83M LEU* 3.9 21.5 - - + -
105M GLN* 3.0 31.0 + - + +
106M LYS* 3.7 22.9 - - + +
108M ILE* 1.3 76.8 - - - +
110M GLU* 1.3 58.0 + - - +
112M TYR* 3.4 4.0 + - - +
113M HIS* 2.9 28.9 + - - +
120M CYS* 4.1 19.8 - - - -
121M ALA 4.5 8.3 - - - +
122M LEU* 3.5 41.3 - - + -
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Residues in contact with GLU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LEU* 3.9 28.5 - - + +
106M LYS* 2.9 30.6 + - + +
107M THR* 3.4 17.1 + - - +
109M MET* 1.3 74.0 - - - +
111M LYS* 1.3 59.8 + - - +
113M HIS* 3.7 0.4 - - - -
114M ASP* 2.8 45.7 + - - +
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Residues in contact with LYS 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M THR* 3.2 9.9 + - + +
108M ILE* 3.2 13.4 + - + +
110M GLU* 1.3 78.6 - - - +
112M TYR* 1.3 91.6 + - + +
114M ASP* 3.4 7.5 + - - +
115M GLU* 2.9 57.5 + - + +
116M TYR* 5.4 1.0 + - - -
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Residues in contact with TYR 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M THR* 3.8 19.4 - - + +
70M MET* 3.5 42.4 - - + -
71M GLU* 2.6 53.4 + - - +
74M VAL* 4.2 3.8 - - + -
108M ILE* 3.3 33.2 + - + +
109M MET 3.7 7.4 - - - +
110M GLU 3.3 0.2 - - - -
111M LYS* 1.3 103.7 + - + +
113M HIS* 1.3 58.3 + - - +
115M GLU* 4.4 1.3 - - - -
116M TYR* 2.8 65.2 + + - +
117M GLY 3.8 0.3 + - - -
118M ILE* 3.8 4.2 - - + +
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Residues in contact with HIS 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LEU* 3.6 53.5 + - + +
31M ASP* 3.9 13.5 - - + +
109M MET 2.9 17.9 + - - +
110M GLU* 3.3 2.6 + - - +
112M TYR* 1.3 74.1 - - - +
114M ASP* 1.3 71.0 + - - +
117M GLY* 2.7 38.7 + - - +
118M ILE* 3.0 35.8 - - - +
119M LYS* 5.6 0.2 - - - +
120M CYS* 4.6 0.9 - - - -
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Residues in contact with ASP 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M GLU* 2.8 32.0 + - - +
111M LYS* 3.7 6.0 - - - +
113M HIS* 1.3 87.7 + - - +
115M GLU* 1.3 62.2 + - - +
117M GLY 4.7 0.7 + - - -
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Residues in contact with GLU 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M LYS* 2.9 49.7 + - + +
114M ASP* 1.3 81.2 - - - +
116M TYR* 1.3 90.7 + - + +
20P LEU* 3.9 30.6 - - + +
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Residues in contact with TYR 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M GLU* 5.0 3.1 + - - -
74M VAL* 3.6 20.5 - - + +
111M LYS* 5.7 0.5 + - - -
112M TYR* 2.8 51.2 + + - +
115M GLU* 1.3 105.4 + - + +
117M GLY* 1.3 62.7 + - - +
118M ILE 4.2 1.8 - - - +
234O LEU* 3.2 36.0 - - + +
14P THR* 5.4 0.9 - - - +
16P TYR* 3.4 45.5 - + + -
20P LEU* 3.7 27.0 - - + +
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Residues in contact with GLY 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M PRO 4.9 0.3 - - - +
113M HIS* 2.7 34.2 + - - -
114M ASP 4.6 0.4 + - - -
115M GLU 3.8 0.2 - - - -
116M TYR* 1.3 73.4 - - - +
118M ILE* 1.3 65.1 + - - +
119M LYS* 3.3 10.4 + - - +
16P TYR* 4.7 1.6 - - - -
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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
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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