Contacts of the helix formed by residues 94 - 117 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O GLN* 3.1 27.5 + - - +
91O MET 3.2 11.9 - - - +
92O SER 3.1 0.2 - - - -
93O ASN* 1.3 87.5 - - - +
95O PRO* 1.3 57.4 - - - +
96O SER* 3.2 4.5 - - - +
97O TRP* 2.7 67.3 + - + +
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Residues in contact with PRO 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O MET 4.2 5.4 - - - +
92O SER 3.9 4.0 - - - +
93O ASN 3.5 11.4 - - - +
94O ASN* 1.3 81.3 - - - +
96O SER* 1.3 57.5 + - - +
97O TRP 3.2 0.3 + - - -
98O GLY* 3.2 3.8 + - - -
99O ALA* 2.9 26.2 + - - +
145O VAL* 3.9 13.9 - - + -
148O GLU* 3.6 36.6 - - + +
149O ALA* 4.0 11.2 - - - +
152O GLN* 3.7 27.6 - - + +
153O CYS* 4.9 2.1 - - - -
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Residues in contact with SER 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O LYS* 5.1 2.8 + - - +
94O ASN* 4.4 2.1 + - - +
95O PRO* 1.3 79.0 - - - +
97O TRP* 1.3 71.3 + - - +
99O ALA* 3.6 8.8 - - - +
100O GLU* 2.8 44.4 + - - +
152O GLN* 4.7 7.1 - - - +
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Residues in contact with TRP 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O GLY 4.8 1.6 - - - -
53O ALA 5.7 0.2 - - - -
54O SER* 4.0 9.4 - - - -
55O LYS* 3.5 67.6 - - + +
58O LEU* 4.0 12.6 - - + -
59O ILE* 5.2 0.2 - - - +
90O GLN* 3.7 35.7 - - + -
91O MET* 4.0 12.6 - - + -
94O ASN* 2.7 49.6 + - + +
96O SER* 1.3 77.2 - - - +
98O GLY* 1.3 64.6 + - - +
100O GLU* 3.4 2.1 + - - +
101O VAL* 3.1 29.5 + - + +
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Residues in contact with GLY 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O HIS* 3.7 19.5 - - - -
91O MET* 3.3 26.6 + - - +
95O PRO 3.2 4.9 + - - -
97O TRP* 1.3 76.7 - - - +
99O ALA* 1.3 63.0 + - - +
100O GLU 3.3 0.2 + - - -
101O VAL* 3.4 2.9 + - - +
102O ALA* 3.1 24.4 + - - +
124O HIS* 3.7 2.1 + - - -
153O CYS* 3.6 7.8 - - - -
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Residues in contact with ALA 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O PRO 2.9 17.3 + - - +
96O SER* 3.6 9.9 - - - +
97O TRP 3.2 0.2 - - - -
98O GLY* 1.3 78.4 - - - +
100O GLU* 1.3 58.2 + - + +
102O ALA* 3.5 0.9 + - - +
103O HIS* 3.1 22.2 + - - +
152O GLN* 3.7 35.2 - - + +
153O CYS* 3.8 9.7 - - - +
156O ASN* 3.4 22.4 - - - +
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Residues in contact with GLU 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O LYS* 3.4 36.9 + - - +
59O ILE* 3.7 22.6 - - + +
96O SER* 2.8 28.3 + - - +
97O TRP* 4.0 3.4 - - - +
98O GLY 3.2 0.2 - - - -
99O ALA* 1.3 75.1 - - + +
101O VAL* 1.3 60.7 + - - +
103O HIS* 3.4 7.8 + - + +
104O ALA* 2.9 29.2 + - - +
156O ASN* 6.1 0.2 - - - +
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Residues in contact with VAL 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O LYS* 6.4 0.2 - - + -
58O LEU* 4.9 3.6 - - + -
59O ILE* 4.1 20.8 - - + +
62O TYR* 3.6 39.0 - - + -
85O THR* 4.4 0.2 - - + -
91O MET* 4.0 20.0 - - + -
97O TRP 3.1 18.5 + - - +
98O GLY 3.7 4.0 - - - +
100O GLU* 1.3 75.0 - - - +
102O ALA* 1.3 56.8 + - - +
104O ALA* 2.9 7.7 + - - +
105O GLN* 2.8 56.7 + - + +
124O HIS* 4.1 5.6 - - - +
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Residues in contact with ALA 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O GLY 3.1 13.6 + - - +
99O ALA* 3.7 4.0 - - - +
101O VAL* 1.3 75.3 - - - +
103O HIS* 1.3 57.5 + - - +
105O GLN* 3.4 0.6 + - - +
106O LYS* 2.9 32.2 + - - +
122O LEU* 3.5 13.1 - - + +
124O HIS* 3.5 33.7 - - + +
153O CYS* 4.3 8.1 - - + +
156O ASN 3.3 11.4 - - - +
158O ALA 4.1 8.7 - - - +
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Residues in contact with HIS 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O ALA 3.1 8.7 + - - +
100O GLU* 3.6 12.6 - - + +
101O VAL 3.2 0.2 - - - -
102O ALA* 1.3 78.0 - - - +
104O ALA* 1.3 58.3 + - - +
106O LYS* 3.3 3.0 + - + +
107O THR* 2.8 47.4 + - - -
156O ASN* 2.9 43.5 + - + +
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Residues in contact with ALA 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O ILE* 3.8 27.8 - - + +
62O TYR* 6.3 0.9 - - + -
63O GLU* 3.8 19.6 - - + +
100O GLU 2.9 17.4 + - - +
101O VAL* 3.5 4.9 - - - +
103O HIS* 1.3 78.6 + - - +
105O GLN* 1.3 60.3 + - + +
107O THR* 3.8 6.9 - - - -
108O ILE* 3.6 26.5 + - - +
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Residues in contact with GLN 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O TYR* 3.0 24.6 + - - -
62O TYR* 4.4 13.7 - - + +
63O GLU* 5.8 0.2 - - - -
66O THR* 3.3 31.4 + - - +
83O LEU* 4.5 0.5 - - - +
85O THR* 2.6 22.9 + - - -
101O VAL* 2.8 32.9 + - + +
102O ALA 3.7 3.1 - - - +
104O ALA* 1.3 76.1 - - + +
106O LYS* 1.3 65.0 + - - +
107O THR 3.2 0.2 - - - -
108O ILE* 3.3 3.0 + - - -
109O MET* 3.0 40.0 + - + +
122O LEU* 3.6 8.0 - - + +
124O HIS* 3.0 25.1 - - - -
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Residues in contact with LYS 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O GLY* 4.9 1.1 - - - -
30O LEU* 3.9 30.1 - - + -
102O ALA 2.9 18.3 + - - +
103O HIS* 4.0 3.8 - - + +
105O GLN* 1.3 77.0 - - - +
107O THR* 1.3 52.2 + - - +
109O MET* 3.2 23.2 + - + +
110O GLU* 2.7 51.3 + - - +
120O CYS 6.0 0.2 - - - -
121O ALA* 5.2 1.3 - - - +
122O LEU* 4.4 2.6 - - + +
156O ASN 4.8 0.2 - - - +
157O GLY* 2.5 50.2 + - - +
159O ASP* 2.7 34.3 + - - -
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Residues in contact with THR 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O HIS* 2.8 39.8 + - - -
104O ALA* 3.8 8.8 - - - -
105O GLN 3.2 0.2 - - - -
106O LYS* 1.3 76.5 - - - +
108O ILE* 1.3 64.6 + - + +
110O GLU* 3.4 15.5 + - - +
111O LYS* 3.1 22.2 + - + +
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Residues in contact with ILE 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O GLU* 3.4 41.7 - - + +
66O THR* 4.0 18.2 - - + +
67O THR* 3.3 32.1 - - - +
70O MET* 4.6 0.7 - - + -
104O ALA 3.6 9.6 + - - +
105O GLN 3.3 7.5 + - - +
107O THR* 1.3 78.3 - - + +
109O MET* 1.3 62.7 + - - +
111O LYS* 3.1 9.4 + - + +
112O TYR* 3.1 43.6 + - + -
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Residues in contact with MET 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O LEU* 4.0 2.6 - - + +
66O THR* 3.8 17.9 - - + -
70O MET* 4.4 18.2 - - - -
83O LEU* 3.6 37.9 - - + -
105O GLN* 3.0 34.5 + - + +
106O LYS* 3.4 22.4 - - + +
108O ILE* 1.3 73.2 - - - +
110O GLU* 1.3 59.4 + - - +
112O TYR* 3.3 2.9 + - - +
113O HIS* 2.9 30.0 + - - +
120O CYS* 4.3 17.0 - - - -
121O ALA 4.5 7.9 - - - +
122O LEU* 4.0 26.0 - - + -
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Residues in contact with GLU 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O LEU* 3.8 28.2 - - + +
106O LYS* 2.7 37.6 + - + +
107O THR* 3.6 15.0 + - - +
109O MET* 1.3 73.3 - - - +
111O LYS* 1.3 57.2 + - - +
113O HIS* 3.7 1.5 - - - +
114O ASP* 2.8 43.2 + - - +
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Residues in contact with LYS 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O THR 3.1 14.7 + - - +
108O ILE* 3.1 12.5 + - + +
110O GLU* 1.3 77.6 - - - +
112O TYR* 1.3 86.1 + - + +
114O ASP* 3.4 6.9 + - - +
115O GLU* 3.1 39.5 + - + +
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Residues in contact with TYR 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O THR* 3.9 16.8 - - + +
70O MET* 3.6 46.7 - - + -
71O GLU* 2.7 51.3 + - - +
74O VAL* 4.2 4.5 - - + -
108O ILE* 3.1 36.9 + - + +
109O MET 3.8 2.2 - - - +
111O LYS* 1.3 98.1 + - + +
113O HIS* 1.3 56.7 + - - +
115O GLU* 3.3 0.4 + - - -
116O TYR* 2.9 65.0 + + - +
118O ILE* 3.9 4.0 - - + +
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Residues in contact with HIS 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LYS* 6.5 1.1 - - - -
30O LEU* 3.7 51.0 + - + +
31O ASP* 3.7 15.4 + - + +
109O MET 2.9 17.7 + - - +
110O GLU* 3.7 3.8 - - - +
112O TYR* 1.3 76.8 - - - +
114O ASP* 1.3 68.8 + - - +
117O GLY* 2.8 37.1 + - - -
118O ILE* 2.8 36.9 - - - +
119O LYS 4.5 0.4 - - - -
120O CYS* 4.7 1.3 - - - -
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Residues in contact with ASP 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O GLU* 2.8 35.1 + - - +
111O LYS* 3.7 6.6 - - - +
113O HIS* 1.3 85.5 + - - +
115O GLU* 1.3 59.6 + - - +
117O GLY 4.8 0.5 + - - -
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Residues in contact with GLU 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N LEU* 3.9 31.8 - - + +
111O LYS* 3.1 35.5 + - + +
112O TYR* 4.8 0.2 - - - -
114O ASP* 1.3 77.6 - - - +
116O TYR* 1.3 97.3 + - + +
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Residues in contact with TYR 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M LEU* 3.6 31.1 - - + +
14N THR* 5.4 1.2 - - - +
16N TYR* 3.4 43.0 - + + -
20N LEU* 3.3 32.5 - - + +
71O GLU* 5.1 3.8 + - - -
74O VAL* 3.8 16.7 - - + +
112O TYR* 2.9 48.4 + + - +
115O GLU* 1.3 107.0 + - + +
117O GLY* 1.3 62.1 + - - +
118O ILE 3.3 2.2 - - - +
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Residues in contact with GLY 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N TYR* 4.8 2.0 - - - -
31O ASP* 5.3 1.9 - - - +
79O PRO 5.0 0.3 - - - +
113O HIS* 2.8 27.3 + - - -
114O ASP 4.7 0.4 + - - -
115O GLU 3.8 0.4 - - - -
116O TYR* 1.3 78.5 - - - +
118O ILE* 1.3 63.1 + - - +
119O LYS* 3.5 9.9 + - - +
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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) + - + + + + + -
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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