Contacts of the helix formed by residues 123 - 145 (chain B) in PDB entry 2Q9Q
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B SER* 3.6 14.7 + - - -
48B PRO* 5.2 8.5 - - - -
122B LEU* 1.3 76.1 - - - +
124B PRO* 1.3 76.5 - - - +
125B GLU* 3.3 12.8 + - - +
126B GLU* 2.9 39.1 + - - +
127B LEU* 3.0 19.6 + - - +
124C TYR* 4.8 1.0 + - - -
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Residues in contact with PRO 124 (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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48B PRO* 5.8 4.9 - - + -
122B LEU 4.6 0.9 - - - +
123B SER* 1.3 86.9 - - - +
125B GLU* 1.3 76.6 + - - +
127B LEU* 3.5 13.5 + - + +
128B ALA* 3.2 20.6 + - - +
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Residues in contact with GLU 125 (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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123B SER* 3.3 13.1 + - - +
124B PRO* 1.3 91.3 - - - +
126B GLU* 1.3 64.4 + - - +
128B ALA* 3.2 9.0 + - - +
129B PHE* 3.0 21.0 + - - +
124C TYR* 3.8 21.1 - - + +
127C SER* 3.1 38.9 - - - +
128C LEU* 5.6 2.9 - - + -
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Residues in contact with GLU 126 (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 SER* 4.2 1.2 + - - -
93B LEU* 4.9 2.4 - - - +
96B ARG* 2.7 54.3 + - - +
97B LEU* 4.8 1.6 - - + +
100B ILE* 3.7 16.4 - - + +
122B LEU* 3.6 16.0 - - + +
123B SER* 2.9 39.1 + - - +
125B GLU* 1.3 73.0 - - - +
127B LEU* 1.3 61.3 + - - +
129B PHE* 3.3 6.5 + - - +
130B ALA* 2.9 29.8 + - - +
124C TYR* 3.7 29.5 + - + +
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Residues in contact with LEU 127 (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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108B LEU* 4.0 18.4 - - + -
111B GLU* 4.1 23.8 - - + +
122B LEU* 4.0 25.5 - - + +
123B SER 3.0 12.9 + - - +
124B PRO* 3.5 15.3 - - + +
126B GLU* 1.3 76.7 - - - +
128B ALA* 1.3 63.6 + - - +
130B ALA* 3.1 3.9 + - - +
131B ARG* 2.9 66.5 + - - +
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Residues in contact with ALA 128 (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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124B PRO 3.2 9.6 + - - +
125B GLU* 3.2 11.1 + - - +
127B LEU* 1.3 79.3 - - - +
129B PHE* 1.3 63.0 + - - +
131B ARG* 3.1 16.5 + - - +
132B GLU* 3.0 42.1 + - - +
123C THR* 6.5 1.1 - - + -
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Residues in contact with PHE 129 (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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97B LEU* 3.7 30.1 - - + -
100B ILE* 4.4 10.1 - - + -
101B GLU* 3.7 37.5 - - + -
125B GLU 3.0 12.9 + - - +
126B GLU* 3.4 11.9 - - - +
128B ALA* 1.3 76.4 - - - +
130B ALA* 1.3 57.9 + - - +
132B GLU* 3.4 9.6 + - - +
133B PHE* 3.0 32.4 + + + +
117C TYR* 3.9 19.7 - + - -
120C SER* 3.9 23.7 - - - -
121C LEU* 3.8 32.3 - - + -
124C TYR* 4.1 16.2 - + + -
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Residues in contact with ALA 130 (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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100B ILE* 3.5 25.6 - - + +
104B PHE* 4.8 4.7 - - + +
107B VAL* 4.4 11.2 - - + -
108B LEU* 3.8 21.8 - - + +
122B LEU* 4.9 0.2 - - + -
126B GLU 2.9 13.8 + - - +
127B LEU* 3.5 9.6 - - - +
129B PHE* 1.3 72.9 - - - +
131B ARG* 1.3 67.2 + - - +
133B PHE* 3.3 7.6 + - - +
134B MET* 3.1 22.5 + - - +
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Residues in contact with ARG 131 (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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108B LEU* 4.0 20.6 - - + +
127B LEU* 2.9 52.5 + - - +
128B ALA* 3.5 14.7 - - - +
130B ALA* 1.3 75.5 - - - +
132B GLU* 1.3 66.3 + - + +
134B MET* 3.2 6.4 + - - +
135B ALA* 3.0 22.6 + - - +
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Residues in contact with GLU 132 (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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128B ALA* 3.0 39.2 + - - +
129B PHE* 3.7 5.7 - - - +
131B ARG* 1.3 76.1 - - + +
133B PHE* 1.3 66.0 + - - +
135B ALA* 3.9 5.6 - - - +
136B ASN* 2.9 28.3 + - - +
120C SER* 2.7 45.8 + - - +
123C THR* 5.2 7.4 - - - +
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Residues in contact with PHE 133 (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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100B ILE* 6.0 0.9 - - + -
101B GLU* 3.4 46.4 - - + -
104B PHE* 3.6 43.1 - + + -
129B PHE* 3.0 19.8 + + + +
130B ALA* 3.5 12.1 - - - +
132B GLU* 1.3 76.1 - - - +
134B MET* 1.3 60.6 + - - +
136B ASN* 3.8 5.1 - - - +
137B THR* 2.8 42.0 + - + -
81C TYR* 5.0 6.1 - + - -
85C LEU* 5.6 8.7 - - + -
88C ARG* 5.4 0.9 - - + -
113C TRP* 3.6 30.7 - + - -
117C TYR* 3.9 19.5 - + - -
120C SER* 5.9 0.2 - - - -
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Residues in contact with MET 134 (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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104B PHE* 3.9 16.6 - - + -
105B PRO* 4.0 23.6 - - + +
108B LEU* 3.4 40.8 - - + -
130B ALA 3.1 3.0 + - - +
131B ARG 3.3 9.0 - - - +
133B PHE* 1.3 77.0 - - - +
135B ALA* 1.3 61.5 + - + +
137B THR* 3.3 1.4 + - - -
138B GLU* 2.8 49.8 + - - +
158B LEU* 3.9 28.7 - - + -
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Residues in contact with ALA 135 (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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131B ARG 3.0 15.2 + - - +
132B GLU* 3.9 6.3 - - - +
134B MET* 1.3 77.9 - - - +
136B ASN* 1.3 57.6 + - - +
138B GLU* 4.0 5.7 - - - +
139B SER* 2.9 34.5 + - - -
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Residues in contact with ASN 136 (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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132B GLU 2.9 18.6 + - - +
133B PHE* 3.8 5.1 + - - +
135B ALA* 1.3 77.8 - - - +
137B THR* 1.3 56.7 + - - +
139B SER* 3.8 4.3 - - - -
140B TYR* 2.9 28.8 + - - +
113C TRP* 3.0 53.8 + - - +
116C ASN* 2.8 41.2 + - + +
117C TYR* 3.9 7.7 - - - +
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Residues in contact with THR 137 (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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104B PHE* 4.5 15.7 - - + -
133B PHE* 2.8 33.2 + - - -
134B MET 3.9 2.0 - - - -
136B ASN* 1.3 72.8 - - - +
138B GLU* 1.3 62.0 + - - +
140B TYR* 3.7 1.3 - - - +
141B LEU* 2.9 43.3 + - + +
158B LEU* 5.9 1.8 - - + -
81C TYR* 4.4 17.7 - - + -
84C LEU* 3.9 19.5 - - + -
113C TRP* 3.1 20.5 + - + +
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Residues in contact with GLU 138 (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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134B MET* 2.8 37.0 + - - +
135B ALA* 4.0 5.2 - - - +
137B THR* 1.3 73.5 - - - +
139B SER* 1.3 58.7 + - - +
141B LEU* 3.4 6.9 + - - +
142B LYS* 2.9 30.4 + - + +
146B LEU* 5.6 0.9 - - - +
156B VAL 5.3 1.6 - - - +
158B LEU* 3.2 33.7 - - + +
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Residues in contact with SER 139 (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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135B ALA 2.9 20.0 + - - -
136B ASN* 3.8 4.9 - - - -
138B GLU* 1.3 74.2 - - - +
140B TYR* 1.3 66.4 + - - +
142B LYS* 3.1 8.0 + - - +
143B ASN* 3.0 43.9 + - - +
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Residues in contact with TYR 140 (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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136B ASN* 2.9 18.7 + - - +
137B THR 3.7 3.1 - - - +
139B SER* 1.3 77.5 - - - +
141B LEU* 1.3 78.3 + - + +
143B ASN* 4.1 2.0 - - - -
144B VAL* 3.0 55.9 + - + +
24C PHE* 3.9 12.8 - - - -
80C LEU* 4.0 18.1 + - + +
84C LEU* 3.7 32.5 - - + -
107C ALA* 5.1 0.3 - - - +
109C GLU* 3.5 37.8 - - + +
110C GLU* 3.2 31.1 + - + +
113C TRP* 3.8 16.4 - - + -
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Residues in contact with LEU 141 (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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137B THR* 2.9 29.5 + - + +
138B GLU* 3.7 6.7 - - - +
140B TYR* 1.3 99.1 - - + +
142B LYS* 1.3 61.0 + - - +
144B VAL* 5.0 1.1 - - - -
145B ALA* 3.3 9.9 + - - +
146B LEU* 3.2 37.4 + - + +
156B VAL* 6.3 1.8 - - + -
158B LEU* 4.4 21.8 - - + -
77C VAL* 4.5 23.1 - - + -
80C LEU* 4.2 22.0 - - + -
81C TYR* 4.9 11.7 - - + +
84C LEU* 4.8 7.6 - - + -
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Residues in contact with LYS 142 (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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138B GLU* 2.9 18.0 + - + +
139B SER* 3.1 8.5 + - - +
141B LEU* 1.3 78.8 - - - +
143B ASN* 1.3 73.5 + - - +
146B LEU* 3.6 15.6 + - + +
147B LYS* 3.0 47.5 + - + +
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Residues in contact with ASN 143 (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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139B SER* 3.0 30.4 + - - +
140B TYR* 4.3 2.8 - - - +
142B LYS* 1.3 96.4 - - - +
144B VAL* 1.3 61.5 + - + +
147B LYS* 3.0 37.7 + - - +
148B HIS* 3.3 9.5 + - - -
109C GLU* 5.7 5.3 - - + +
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Residues in contact with VAL 144 (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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140B TYR* 3.0 58.3 + - + +
141B LEU 4.6 0.7 - - - +
143B ASN* 1.3 80.4 - - + +
145B ALA* 1.3 58.9 + - - +
148B HIS* 3.5 12.5 - - - -
24C PHE* 4.3 6.1 - - + -
29C LEU* 4.1 27.6 - - + +
33C LEU* 4.7 2.3 - - - +
80C LEU* 4.2 15.3 - - + -
109C GLU* 3.7 27.8 - - + -
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Residues in contact with ALA 145 (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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141B LEU 3.3 5.0 + - - +
143B ASN 3.6 1.2 - - - -
144B VAL* 1.3 81.9 - - - +
146B LEU* 1.3 63.6 + - + +
147B LYS 3.3 2.5 - - - -
148B HIS* 2.9 27.2 + - - +
149B MET* 3.4 20.4 + - + +
29C LEU* 4.7 5.4 - - + -
33C LEU* 4.1 9.3 - - + +
76C THR* 4.2 13.2 - - - +
77C VAL* 6.0 0.9 - - + -
80C LEU* 3.7 25.4 - - + -
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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