Contacts of the helix formed by residues 123 - 145 (chain I) in PDB entry 2EHO
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 SER 123 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I SER* 3.7 16.4 + - - -
48I PRO* 5.3 8.5 - - - -
122I LEU* 1.3 74.1 - - - +
124I PRO* 1.3 65.2 - - - +
125I GLU* 3.3 18.1 - - - +
126I GLU* 2.6 57.7 + - - +
127I LEU* 2.8 10.5 + - - +
124J TYR* 4.7 1.9 + - - -
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Residues in contact with PRO 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I LEU 3.8 2.7 - - - +
123I SER* 1.3 82.6 - - - +
125I GLU* 1.3 73.2 + - - +
127I LEU* 3.9 14.2 - - + +
128I ALA* 3.2 24.3 + - - +
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Residues in contact with GLU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I GLU* 5.0 6.9 - - - +
123I SER* 2.8 19.6 + - - +
124I PRO* 1.3 93.1 - - - +
126I GLU* 1.3 64.5 + - - +
128I ALA* 3.6 7.2 + - - +
129I PHE* 3.3 15.2 + - - +
124J TYR* 3.5 30.2 - - + +
127J SER* 3.8 42.7 - - - +
128J LEU* 5.4 3.4 - - + +
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Residues in contact with GLU 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I SER* 4.5 1.4 + - - -
93I LEU* 4.9 3.9 - - - +
96I ARG* 3.1 50.1 + - - +
97I LEU* 4.6 4.5 + - + +
100I ILE* 3.6 22.6 - - + +
122I LEU* 3.9 11.1 - - + +
123I SER* 2.6 43.6 + - - +
125I GLU* 1.3 70.7 - - - +
127I LEU* 1.3 59.4 + - - +
129I PHE* 3.1 9.3 + - - +
130I ALA* 2.9 26.5 + - - +
124J TYR* 3.8 27.9 + - + +
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Residues in contact with LEU 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I LEU* 3.4 27.4 - - + -
111I GLU* 4.1 23.6 - - + +
122I LEU* 3.8 25.5 - - + +
123I SER 2.8 12.3 + - - +
124I PRO* 3.9 12.1 - - + +
126I GLU* 1.3 75.2 - - - +
128I ALA* 1.3 65.4 + - - +
130I ALA* 3.2 1.1 + - - +
131I ARG* 3.0 59.6 + - - +
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Residues in contact with ALA 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I PRO 3.2 16.6 + - - +
125I GLU* 3.6 9.4 - - - +
127I LEU* 1.3 80.3 - - - +
129I PHE* 1.3 62.0 + - - +
131I ARG* 3.3 11.0 + - - +
132I GLU* 3.1 40.4 + - - +
123J THR* 6.2 2.9 - - + -
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Residues in contact with PHE 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I LEU* 3.8 28.3 - - + -
100I ILE* 4.9 7.2 - - + -
101I GLU* 3.3 39.5 - - + -
125I GLU 3.3 10.3 + - - +
126I GLU* 3.1 13.6 + - - +
128I ALA* 1.3 79.7 - - - +
130I ALA* 1.3 60.6 + - - +
132I GLU* 3.4 8.9 + - - +
133I PHE* 2.9 32.6 + + + +
117J TYR* 3.7 13.7 - + - -
120J SER* 3.8 27.2 + - - +
121J LEU* 3.7 31.4 - - + -
124J TYR* 4.1 14.1 - - + -
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Residues in contact with ALA 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I ILE* 3.8 25.1 - - + -
104I PHE* 4.7 5.0 - - + +
107I VAL* 5.1 1.1 - - + -
108I LEU* 3.7 26.7 - - + +
122I LEU* 4.8 4.9 - - + -
126I GLU 2.9 13.1 + - - +
127I LEU* 3.2 11.9 + - + +
129I PHE* 1.3 78.3 - - - +
131I ARG* 1.3 62.4 + - - +
133I PHE* 3.1 8.7 + - - +
134I MSE 3.0 22.9 + - - +
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Residues in contact with ARG 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I LEU* 3.7 22.1 - - + +
111I GLU* 6.0 0.2 - - - +
112I LYS* 5.9 4.8 - - - +
127I LEU* 3.0 54.1 + - - +
128I ALA* 3.7 9.1 - - - +
130I ALA* 1.3 75.4 - - - +
132I GLU* 1.3 63.8 + - + +
134I MSE 3.5 3.4 + - - +
135I ALA* 3.2 23.2 + - - +
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Residues in contact with GLU 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I ALA* 3.1 30.9 + - - +
129I PHE* 3.8 3.7 + - - +
131I ARG* 1.3 75.8 - - + +
133I PHE* 1.3 61.6 + - - +
135I ALA* 3.8 5.4 - - - +
136I ASN* 2.8 34.1 + - - +
119J ARG* 5.2 1.4 - - - +
120J SER* 2.7 41.8 + - - +
123J THR* 4.8 15.2 + - - +
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Residues in contact with PHE 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I ILE* 6.2 0.9 - - + -
101I GLU* 3.5 38.1 - - + -
104I PHE* 3.4 45.8 - + + -
129I PHE* 2.9 24.3 + + + +
130I ALA* 3.4 9.0 - - - +
132I GLU* 1.3 77.8 - - - +
134I MSE 1.3 58.6 - - - +
136I ASN* 3.7 4.1 - - + +
137I THR* 2.9 37.1 + - - -
81J TYR* 5.7 2.0 - + - -
88J ARG* 3.5 25.1 - - - -
113J TRP* 3.6 34.1 - + - -
117J TYR* 4.2 15.9 - + - -
120J SER* 5.0 1.1 + - - -
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Residues in contact with MSE 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I PHE* 3.3 33.2 - - + -
105I PRO* 4.6 9.2 - - + -
108I LEU* 4.0 21.5 - - + -
130I ALA 3.0 12.3 + - - +
131I ARG* 3.6 8.5 - - - +
133I PHE* 1.3 74.1 - - - +
135I ALA* 1.3 69.7 + - - +
137I THR* 3.1 4.2 + - - -
138I GLU* 2.8 57.7 + - + +
158I LEU* 3.3 39.3 - - + -
159I PHE 5.5 0.4 - - - +
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Residues in contact with ALA 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I ARG 3.2 14.1 + - - +
132I GLU* 3.8 5.6 - - - +
134I MSE 1.3 80.9 - - - +
136I ASN* 1.3 65.7 + - - +
138I GLU* 3.8 9.0 - - - +
139I SER* 2.9 28.2 + - - -
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Residues in contact with ASN 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I GLU 2.8 19.9 + - - +
133I PHE* 3.7 6.6 - - + +
135I ALA* 1.3 79.1 - - - +
137I THR* 1.3 58.7 + - - +
139I SER* 3.2 5.5 + - - -
140I TYR* 2.8 26.6 + - - +
112J GLU 5.2 0.2 - - - -
113J TRP* 2.9 49.3 + - + +
116J ASN* 3.2 37.0 - - + +
117J TYR* 3.5 8.1 + - - -
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Residues in contact with THR 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I PHE* 4.8 5.2 - - + -
133I PHE* 2.9 25.2 + - - -
134I MSE 3.1 4.1 + - - -
136I ASN* 1.3 73.8 - - - +
138I GLU* 1.3 65.4 + - - +
140I TYR* 3.2 0.7 + - - +
141I LEU* 2.9 39.3 + - + +
158I LEU* 4.4 11.7 - - + -
81J TYR* 4.6 15.7 - - + -
84J LEU* 3.7 21.3 - - + -
113J TRP* 3.3 24.9 + - - +
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Residues in contact with GLU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I MSE 2.8 50.7 + - - +
135I ALA* 3.8 7.8 - - - +
137I THR* 1.3 73.5 - - - +
139I SER* 1.3 64.8 + - - +
141I LEU* 3.2 6.3 + - - +
142I LYS* 2.9 24.6 + - - +
146I LEU* 5.6 0.2 - - - +
156I VAL 5.2 5.6 - - - +
158I LEU* 3.8 22.5 + - + +
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Residues in contact with SER 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I ALA 2.9 18.7 + - - -
136I ASN* 3.4 6.3 - - - -
138I GLU* 1.3 76.6 - - - +
140I TYR* 1.3 64.4 + - - +
142I LYS* 3.2 2.5 + - - +
143I ASN* 2.6 39.2 + - - -
1002I SO4 3.6 25.5 + - - -
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Residues in contact with TYR 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ASN* 2.8 11.0 + - - +
137I THR 3.2 4.0 + - - +
139I SER* 1.3 76.4 + - - +
141I LEU* 1.3 87.4 + - + +
143I ASN* 3.3 2.2 + - - +
144I VAL* 3.1 56.7 + - + +
24J PHE* 3.9 0.5 - - - -
80J LEU* 3.5 29.6 + - + +
84J LEU* 3.9 25.6 - - + -
109J GLU* 3.4 17.5 - - + -
110J GLU* 3.3 43.7 + - + +
113J TRP* 3.4 34.3 - + + -
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Residues in contact with LEU 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I THR* 2.9 33.2 + - + +
138I GLU* 3.5 5.4 - - - +
140I TYR* 1.3 96.3 - - + +
142I LYS* 1.3 63.5 + - - +
144I VAL* 4.5 0.8 - - - +
145I ALA* 3.4 7.8 + - - +
146I LEU* 3.3 41.5 + - + +
156I VAL* 5.4 1.1 - - + -
158I LEU* 4.1 28.3 - - + -
77J VAL* 4.6 20.2 - - + +
80J LEU* 4.0 27.1 - - + +
81J TYR* 5.1 7.9 - - + +
84J LEU* 5.5 1.1 - - + -
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Residues in contact with LYS 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I GLU 2.9 13.2 + - - +
139I SER* 3.2 9.2 + - - +
141I LEU* 1.3 79.3 - - - +
143I ASN* 1.3 68.5 + - - +
144I VAL 3.4 0.5 + - - -
145I ALA 3.7 0.3 + - - -
146I LEU* 3.6 13.3 + - + +
147I LYS* 2.8 43.8 + - + +
155I LYS* 4.3 21.1 - - - +
1002I SO4 3.3 35.5 + - - +
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Residues in contact with ASN 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I SER* 2.6 40.5 + - - +
140I TYR* 4.3 2.2 - - - +
142I LYS* 1.3 83.0 - - - +
144I VAL* 1.3 61.4 + - + +
147I LYS* 3.2 38.8 + - - +
148I HIS* 4.1 10.3 + - - -
1002I SO4 3.5 23.8 + - - -
109J GLU* 4.0 16.2 - - + +
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Residues in contact with VAL 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I TYR* 3.1 54.7 + - + +
141I LEU 4.5 0.9 - - - +
142I LYS 3.3 0.2 - - - -
143I ASN* 1.3 78.4 - - - +
145I ALA* 1.3 61.2 + - - +
148I HIS* 4.4 11.9 + - - -
24J PHE* 4.0 22.9 - - + -
29J LEU* 3.8 16.0 - - + +
33J LEU* 4.7 1.7 - - - +
80J LEU* 4.1 8.1 - - + -
109J GLU* 3.1 37.9 - - + -
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Residues in contact with ALA 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I LEU 3.4 2.4 + - - -
142I LYS 3.9 0.2 - - - -
143I ASN 3.6 1.0 - - - -
144I VAL* 1.3 81.6 - - - +
146I LEU* 1.3 64.3 + - + +
147I LYS 3.1 1.8 - - - -
148I HIS* 2.7 34.6 + - - +
149I MSE 3.4 10.9 + - - +
29J LEU* 4.5 12.1 - - + -
33J LEU* 4.1 12.3 - - + +
76J THR* 4.5 9.9 - - - +
80J LEU* 3.7 25.8 - - + -
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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