Contacts of the helix formed by residues 97 - 119 (chain X) in PDB entry 2RAX
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 THR 97 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X LYS* 4.7 5.6 - - - +
95X GLU 3.8 1.3 + - - +
96X LEU* 1.3 76.8 - - - +
98X LEU* 1.3 57.1 + - - +
99X GLY* 3.7 1.4 + - - -
100X GLU* 2.7 47.5 + - - +
101X PHE* 2.8 26.7 + - - +
66Y ARG 3.1 17.3 + - - -
67Y GLU* 3.4 22.9 - - + +
68Y MET 3.3 6.1 - - - -
69Y ASN* 4.3 1.1 - - - +
70Y TRP 3.9 0.7 - - - -
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Residues in contact with LEU 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X THR* 1.3 72.1 - - - +
99X GLY* 1.3 62.7 + - - +
101X PHE* 3.4 13.6 + - + +
102X LEU* 3.1 35.5 + - + +
61Y LEU* 4.0 27.4 - - + -
65Y LEU 3.8 12.8 - - - +
66Y ARG 3.1 1.2 + - - -
68Y MET 2.7 17.0 + - - +
70Y TRP* 3.7 21.2 - - + +
73Y TYR* 3.7 58.6 - - + -
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Residues in contact with GLY 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97X THR* 4.0 1.6 - - - -
98X LEU* 1.3 79.0 - - - +
100X GLU* 1.3 61.6 + - - +
102X LEU* 3.3 10.7 + - - +
103X LYS* 3.3 20.7 + - - +
58Y ILE* 4.6 9.7 - - - +
61Y LEU* 4.6 7.2 - - - +
66Y ARG* 3.1 30.0 + - - +
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Residues in contact with GLU 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X LYS* 3.1 37.7 + - - -
96X LEU* 3.4 14.5 - - + +
97X THR* 2.7 50.7 + - - +
99X GLY* 1.3 74.9 - - - +
101X PHE* 1.3 61.1 + - - +
102X LEU 3.4 0.3 + - - -
103X LYS* 3.4 18.2 + - + +
104X LEU* 3.3 27.0 + - + +
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Residues in contact with PHE 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X TRP* 3.6 46.0 - + - -
13X PHE* 3.9 32.3 - + - -
96X LEU* 4.0 14.6 - - + +
97X THR 2.8 18.3 + - - +
98X LEU* 3.8 12.8 - - + +
99X GLY 3.3 0.2 - - - -
100X GLU* 1.3 73.7 - - - +
102X LEU* 1.3 80.5 + - + +
104X LEU* 3.2 3.1 + - - +
105X ASP* 2.9 31.0 + - + +
70Y TRP* 3.4 57.7 - + + -
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Residues in contact with LEU 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X TRP* 5.9 3.4 - - + -
98X LEU* 3.1 29.9 + - + +
99X GLY 3.3 1.8 + - - +
101X PHE* 1.3 92.3 - - + +
103X LYS* 1.3 65.9 + - - +
104X LEU 3.1 1.3 - - - -
105X ASP* 4.3 1.6 - - + +
106X ARG* 2.9 26.5 + - - +
54Y TYR* 3.3 21.0 - - + -
57Y GLU* 4.5 11.9 - - + +
58Y ILE* 3.6 36.3 - - + +
61Y LEU* 4.2 20.4 - - + -
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Residues in contact with LYS 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X GLY 3.3 14.2 + - - +
100X GLU* 3.5 18.4 - - + +
102X LEU* 1.3 78.1 - - - +
104X LEU* 1.3 64.2 + - + +
106X ARG* 3.2 50.3 + - - +
107X GLU* 3.3 6.1 + - - +
58Y ILE* 3.8 21.3 - - + +
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Residues in contact with LEU 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X PHE* 5.2 2.7 - - + -
59X PHE* 3.2 37.9 - - + -
85X ALA* 4.3 22.2 - - + +
89X VAL* 4.0 21.8 - - + -
93X PHE* 4.2 10.5 - - + -
96X LEU* 3.8 28.3 - - + -
100X GLU* 3.3 15.7 + - + +
101X PHE* 3.2 7.0 + - - +
102X LEU 3.1 0.4 - - - -
103X LYS* 1.3 79.9 - - + +
105X ASP* 1.3 60.2 + - - +
106X ARG 3.2 0.2 - - - -
107X GLU* 3.3 4.5 + - + -
108X ARG 2.8 22.7 + - - -
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Residues in contact with ASP 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X TRP* 3.3 39.7 + - - -
13X PHE* 4.1 10.3 - - + -
101X PHE* 2.9 31.9 + - + +
102X LEU* 3.9 1.5 - - - +
104X LEU* 1.3 73.8 - - - +
106X ARG* 1.3 57.6 + - - +
108X ARG* 3.0 13.3 + - - +
109X ALA* 2.7 35.3 + - - +
54Y TYR* 2.6 31.7 + - + -
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Residues in contact with ARG 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X LEU 2.9 18.6 + - - +
103X LYS* 3.2 49.0 + - - +
105X ASP* 1.3 76.0 - - - +
107X GLU* 1.3 87.9 + - - +
109X ALA* 3.2 4.0 + - - +
110X LYS* 3.2 28.6 + - - +
50Y VAL* 3.8 9.9 - - + +
51Y ASP* 3.6 24.1 + - - -
54Y TYR* 3.4 40.3 - - + +
55Y ASN* 3.3 29.5 + - - +
58Y ILE* 4.6 1.2 - - - +
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Residues in contact with GLU 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 4.0 10.8 - - + -
85X ALA* 4.8 15.7 - - + -
103X LYS 3.3 6.8 + - - +
104X LEU* 3.3 11.3 + - + +
105X ASP 3.2 0.4 - - - -
106X ARG* 1.3 109.6 + - - +
108X ARG* 1.3 60.8 + - - +
109X ALA 3.2 0.2 + - - -
110X LYS* 3.1 36.0 + - - +
111X ASN* 2.8 36.3 + - - +
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Residues in contact with ARG 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ALA* 2.6 34.7 + - - +
10X TRP* 4.7 2.4 - - - -
12X PRO* 4.1 12.5 - - - +
13X PHE* 4.0 19.4 - - + -
58X PHE* 2.7 44.5 + - - +
59X PHE* 3.6 32.5 - - + +
61X PHE* 3.5 21.6 - - + -
104X LEU 2.8 17.6 + - - +
105X ASP* 3.0 17.0 + - - +
107X GLU* 1.3 73.1 - - - +
109X ALA* 1.3 63.1 + - - +
111X ASN* 3.2 7.7 + - - +
112X LYS* 3.0 19.1 + - - +
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Residues in contact with ALA 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X ASP* 2.7 13.4 + - - +
106X ARG 3.4 9.9 - - - +
108X ARG* 1.3 73.3 - - - +
110X LYS* 1.3 62.6 + - - +
111X ASN 3.0 3.6 - - - -
112X LYS* 2.9 20.2 + - - +
113X ILE* 3.1 18.9 + - + +
50Y VAL* 4.0 17.0 - - + -
54Y TYR* 4.2 13.9 - - + +
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Residues in contact with LYS 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X ARG* 3.2 19.6 + - - +
107X GLU* 3.1 42.8 + - - +
109X ALA* 1.3 75.9 - - - +
111X ASN* 1.3 60.9 + - - +
113X ILE* 3.6 10.8 - - - +
114X ALA* 3.1 26.2 + - - +
47Y LEU* 4.0 27.9 - - + +
50Y VAL* 3.7 17.5 - - + +
51Y ASP* 3.1 32.9 + - - +
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Residues in contact with ASN 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 3.1 39.4 + - - +
60X CYS* 3.5 20.5 - - - +
61X PHE* 3.7 7.4 - - + -
84X CYS* 5.8 0.6 - - - +
85X ALA* 5.6 2.2 - - - +
107X GLU* 2.8 26.0 + - - +
108X ARG 3.3 8.5 - - - +
109X ALA 3.0 0.4 + - - -
110X LYS* 1.3 79.6 - - - +
112X LYS* 1.3 56.5 + - - +
114X ALA* 3.2 6.2 + - - +
115X LYS* 2.7 37.6 + - - +
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Residues in contact with LYS 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X PHE* 3.3 30.3 - - + -
108X ARG* 3.0 11.7 + - - +
109X ALA* 2.9 11.8 + - - +
111X ASN* 1.3 74.5 - - - +
113X ILE* 1.3 60.8 + - + +
115X LYS* 3.8 1.7 - - - -
116X GLU* 2.9 61.8 + - + +
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Residues in contact with ILE 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X ALA* 3.1 19.0 + - + +
110X LYS* 3.6 15.5 - - - +
112X LYS* 1.3 80.4 - - + +
114X ALA* 1.3 60.6 + - - +
116X GLU* 3.6 1.9 + - - -
117X THR* 2.7 34.4 + - - +
43Y ARG* 4.7 12.6 - - + +
46Y LEU* 3.8 39.5 - - + -
47Y LEU* 3.8 22.9 - - + -
50Y VAL* 4.7 11.2 - - + -
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Residues in contact with ALA 114 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110X LYS 3.1 16.2 + - - +
111X ASN* 3.5 8.1 - - - +
113X ILE* 1.3 75.9 - - - +
115X LYS* 1.3 65.4 + - - +
117X THR* 3.2 2.8 + - - -
118X ASN* 3.0 29.1 + - - +
43Y ARG* 4.1 18.7 + - - +
47Y LEU* 5.1 1.5 - - + +
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Residues in contact with LYS 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X GLN* 4.6 3.4 - - - +
60X CYS 4.5 4.3 - - - +
61X PHE* 3.1 52.2 + - + +
62X LYS* 3.6 12.9 - - + +
63X GLU* 3.4 35.9 + - - +
111X ASN 2.7 21.0 + - - +
112X LYS* 3.9 3.1 - - - +
114X ALA* 1.3 73.7 - - - +
116X GLU* 1.3 64.4 + - + +
117X THR 3.2 4.0 + - - -
118X ASN* 3.3 17.6 - - - +
119X ASN* 2.9 51.0 - - - +
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Residues in contact with GLU 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X LYS* 2.9 46.9 + - + +
113X ILE* 3.8 1.8 - - - +
115X LYS* 1.3 83.7 - - + +
117X THR* 1.3 62.7 + - - +
119X ASN* 4.3 8.3 - - - +
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Residues in contact with THR 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X ILE* 2.7 27.8 + - - +
114X ALA 3.2 2.0 + - - -
115X LYS 3.2 0.2 - - - -
116X GLU* 1.3 79.9 + - - +
118X ASN* 1.3 68.2 + - - +
119X ASN* 3.3 5.2 + - - -
39Y ILE* 5.8 7.2 - - + -
43Y ARG* 4.0 31.5 - - + +
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Residues in contact with ASN 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X LYS* 6.2 1.4 - - - +
114X ALA* 3.0 22.8 + - - +
115X LYS* 3.3 16.2 - - - +
117X THR* 1.3 73.4 - - - +
119X ASN* 1.3 71.4 + - - +
43Y ARG* 5.8 0.6 - - - +
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Residues in contact with ASN 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X GLU* 4.9 4.1 + - - +
115X LYS* 2.9 52.8 + - - +
116X GLU* 4.3 8.1 - - - +
117X THR 3.3 6.8 + - - -
118X ASN* 1.3 89.8 - - - +
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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