Contacts of the helix formed by residues 121 - 145 (chain B) in PDB entry 3GTU
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 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B TYR 3.5 1.6 + - - -
120B SER* 1.3 69.0 + - - +
122B ASP* 1.3 70.3 + - - +
123B HIS* 3.0 11.7 + - - +
124B GLU* 4.5 1.7 + - - +
125B LYS* 4.2 5.4 + - - -
217B GLN* 3.9 22.0 - - - +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.2 13.7 + - - +
121B SER* 1.3 82.9 + - - +
123B HIS* 1.3 64.4 + - - +
124B GLU 2.9 5.4 + - - -
125B LYS* 3.0 39.0 + - + +
126B LEU* 2.9 33.7 + - + +
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Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 2.8 52.2 + - + +
118B CYS* 3.8 1.3 - - - -
120B SER* 3.2 20.2 + - - +
121B SER 3.0 3.0 - - - +
122B ASP* 1.3 76.2 - - - +
124B GLU* 1.3 61.4 + - + +
126B LEU* 4.6 0.4 - - - -
127B LYS* 2.8 43.2 + - + +
173B PHE* 3.7 21.2 - + - -
217B GLN* 3.4 35.2 + - + -
218B TRP* 3.8 20.8 - - + +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER 4.5 1.9 + - - +
122B ASP 2.9 2.2 + - - -
123B HIS* 1.3 83.1 - - + +
125B LYS* 1.3 69.9 + - - +
127B LYS* 3.1 27.7 + - - +
128B PRO* 3.0 28.8 - - - +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER 4.2 4.6 + - - -
122B ASP* 3.0 55.6 + - + +
124B GLU* 1.3 85.9 - - - +
126B LEU* 1.3 68.0 + - + +
128B PRO* 3.3 12.8 - - - +
129B GLN* 4.1 13.2 + - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 5.6 4.9 - - + +
117B LEU* 3.7 22.7 - - + +
120B SER* 4.0 25.8 - - - +
122B ASP* 2.9 20.3 + - + +
125B LYS* 1.3 94.3 - - + +
127B LYS* 1.3 66.9 + - - +
128B PRO 3.4 0.2 - - - -
129B GLN* 3.0 25.5 + - + +
130B TYR* 3.1 9.7 + - - +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.5 9.6 - - + +
123B HIS* 2.8 23.5 + - - +
124B GLU* 3.2 33.4 - - - +
126B LEU* 1.3 75.1 - - - +
128B PRO* 1.4 65.9 - - + +
130B TYR* 3.2 4.9 + - - +
131B LEU* 3.1 48.8 + - + +
173B PHE* 3.7 41.5 + - + -
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Residues in contact with PRO 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 GLU* 3.0 29.2 - - - +
125B LYS* 3.3 13.7 - - - +
126B LEU 3.5 0.2 - - - -
127B LYS* 1.4 81.9 - - + +
129B GLN* 1.3 65.6 + - - +
131B LEU* 3.2 12.3 + - + +
132B GLU* 2.9 35.3 + - - +
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Residues in contact with GLN 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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125B LYS 4.1 13.9 + - - +
126B LEU* 3.0 18.1 + - + +
128B PRO* 1.3 84.3 - - - +
130B TYR* 1.3 65.1 + - - +
132B GLU* 3.0 41.9 + - - +
133B GLU* 2.9 27.2 + - - +
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Residues in contact with TYR 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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110B PHE* 3.5 16.7 - + - -
113B GLN* 4.1 18.8 - - + -
114B LEU* 3.5 44.4 - - + +
117B LEU* 3.9 28.0 - - + -
126B LEU 3.1 4.8 + - - +
127B LYS 3.5 7.9 - - - +
129B GLN* 1.3 78.9 - - - +
131B LEU* 1.3 61.0 + - + +
133B GLU* 3.3 7.7 + - + +
134B LEU* 2.8 41.4 + - + +
170B ASN* 2.8 39.7 + - - -
173B PHE* 4.1 22.9 - + - -
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Residues in contact with LEU 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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127B LYS* 3.1 44.9 + - + +
128B PRO* 3.6 9.4 - - + +
130B TYR* 1.3 78.1 - - + +
132B GLU* 1.3 56.7 + - - +
134B LEU* 3.1 20.0 + - + +
135B PRO* 2.9 28.9 - - - +
173B PHE* 3.7 29.6 - - + -
174B ASP* 4.5 16.6 - - + +
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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 PRO* 2.9 14.0 + - - +
129B GLN* 3.0 56.2 + - - +
131B LEU* 1.3 77.1 - - - +
133B GLU* 1.3 67.0 + - + +
135B PRO* 4.0 8.0 - - - +
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Residues in contact with GLU 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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113B GLN* 5.6 2.3 - - - +
129B GLN* 2.9 34.6 + - - +
130B TYR* 3.9 6.0 + - + +
131B LEU 3.1 0.4 - - - -
132B GLU* 1.3 89.1 - - + +
134B LEU* 1.3 63.4 + - - +
135B PRO* 3.5 1.3 - - - -
136B GLY* 3.4 11.6 + - - -
137B GLN* 3.6 9.7 + - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.6 14.6 - - + -
130B TYR* 2.8 28.2 + - + +
131B LEU* 3.4 23.6 - - + +
133B GLU* 1.3 77.0 - - - +
135B PRO* 1.4 71.6 - - + +
137B GLN* 3.0 15.6 + - - +
138B LEU* 3.1 37.0 - - + +
170B ASN* 3.3 33.4 - - + +
173B PHE* 5.6 0.7 - - + -
174B ASP* 4.8 7.2 - - + +
177B CYS* 4.0 26.5 - - + -
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Residues in contact with PRO 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 LEU 2.9 26.2 - - - +
132B GLU* 4.0 7.9 - - - +
133B GLU 3.6 2.9 - - - -
134B LEU* 1.4 81.3 - - + +
136B GLY* 1.3 55.4 + - - +
138B LEU* 3.4 7.1 + - + -
139B LYS* 2.8 32.0 + - - +
177B CYS* 6.0 2.7 - - + +
180B GLU* 4.4 21.5 - - - +
181B PHE* 3.6 8.1 - - + -
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Residues in contact with GLY 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 5.5 0.8 + - - -
133B GLU 3.4 8.0 + - - -
134B LEU 3.1 1.6 - - - -
135B PRO* 1.3 78.7 - - - +
137B GLN* 1.3 60.5 + - - +
139B LYS* 3.2 13.6 - - - +
140B GLN* 3.2 28.2 + - - +
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Residues in contact with GLN 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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56A PHE* 4.3 1.7 - - - -
106B GLN* 3.6 21.7 + - - +
109B ASP* 6.1 0.6 - - - +
110B PHE* 3.6 40.0 - - + +
113B GLN* 4.6 14.5 - - - +
133B GLU 3.6 8.3 + - - +
134B LEU* 3.0 9.2 + - - +
136B GLY* 1.3 72.7 - - - +
138B LEU* 1.3 66.6 + - - +
140B GLN* 3.1 39.9 + - - +
141B PHE* 3.1 37.0 + - + -
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Residues in contact with LEU 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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110B PHE* 3.9 12.3 - - + -
134B LEU* 3.1 56.7 + - + +
135B PRO* 3.8 4.0 - - + +
137B GLN* 1.3 71.9 - - - +
139B LYS* 1.3 65.4 + - - +
141B PHE* 3.1 7.3 + - + +
142B SER* 3.0 22.5 + - - -
167B LEU* 3.4 33.0 - - + -
170B ASN* 5.2 4.5 - - + -
177B CYS* 4.9 7.0 - - + +
178B LEU* 4.2 16.4 - - + -
181B PHE* 3.6 25.6 - - + -
184B LEU* 3.8 14.7 - - + +
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Residues in contact with LYS 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 PRO 2.8 20.0 + - - +
136B GLY* 3.2 13.2 - - - +
138B LEU* 1.3 76.8 - - - +
140B GLN* 1.3 58.8 + - + +
142B SER* 3.2 5.0 + - - -
143B MET* 2.9 32.0 + - + +
181B PHE* 3.6 23.1 - - + -
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Residues in contact with GLN 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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50A PHE* 5.2 5.9 - - - -
55A ASP 4.3 5.8 - - - +
56A PHE* 3.7 28.6 - - + +
57A PRO* 3.3 30.3 + - - +
106B GLN* 5.0 1.6 - - - +
136B GLY 3.4 11.9 - - - +
137B GLN* 3.1 36.2 + - - +
139B LYS* 1.3 79.3 - - + +
141B PHE* 1.3 56.8 + - - +
143B MET* 3.4 10.6 + - - +
144B PHE* 2.9 29.8 + - - +
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Residues in contact with PHE 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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56A PHE* 4.5 10.1 - + - -
103B ILE* 4.5 11.9 - - + -
106B GLN* 4.1 17.0 - - + -
107B VAL* 4.2 21.5 - - + -
110B PHE* 3.7 32.5 - + + -
137B GLN* 3.1 43.0 + - + -
138B LEU* 3.1 9.7 + - - +
140B GLN* 1.3 75.1 - - - +
142B SER* 1.3 60.2 + - - +
144B PHE* 3.5 3.5 + - - +
145B LEU* 2.9 31.0 + - - +
151B PHE* 3.6 27.3 - + + -
163B THR* 4.1 16.8 - - + -
166B ILE* 5.3 1.3 - - + -
167B LEU* 5.0 7.0 - - + -
184B LEU* 4.1 16.2 - - + -
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Residues in contact with SER 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 LEU 3.0 12.0 + - - -
139B LYS 3.2 8.0 + - - -
141B PHE* 1.3 75.2 - - - +
143B MET* 1.3 63.7 + - - +
145B LEU 3.4 0.2 + - - -
146B GLY* 3.0 10.4 + - - -
181B PHE* 3.9 22.4 - - - +
183B ASN* 2.9 47.4 + - - +
184B LEU* 4.0 13.8 - - - +
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Residues in contact with MET 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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54A LEU 5.3 0.7 - - - +
55A ASP* 3.3 50.7 - - - +
139B LYS* 2.9 18.9 + - + +
140B GLN* 3.6 7.9 - - - +
142B SER* 1.3 78.8 - - - +
144B PHE* 1.3 65.9 + - - +
146B GLY* 3.8 8.5 + - - -
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Residues in contact with PHE 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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55A ASP* 3.6 27.1 - - + -
56A PHE* 3.4 29.6 - + + -
99B ARG* 3.0 83.3 + - + +
102B ILE* 5.1 9.6 - - + -
103B ILE* 3.6 24.2 - - + -
140B GLN 2.9 17.3 + - - +
141B PHE* 3.7 4.0 - - - +
142B SER 3.3 0.2 - - - -
143B MET* 1.3 84.6 - - - +
145B LEU* 1.3 62.4 + - - +
146B GLY* 4.5 0.3 - - - -
151B PHE* 3.4 27.6 - + - -
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Residues in contact with LEU 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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99B ARG* 4.8 1.3 - - - +
141B PHE 2.9 19.3 + - - +
144B PHE* 1.3 80.0 - - - +
146B GLY* 1.3 68.5 + - - +
148B PHE* 3.2 50.6 + - - +
149B SER 4.5 1.3 - - - +
150B TRP* 3.6 30.5 - - - +
151B PHE* 3.9 22.2 - - + +
183B ASN* 3.8 35.9 - - - +
184B LEU* 4.2 8.5 - - + -
187B PHE* 4.0 19.3 - - + -
190B ARG* 4.9 2.0 - - - +
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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