Contacts of the helix formed by residues 109 - 132 (chain A) in PDB entry 1VGO
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 ASP 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 1.3 76.0 - - - +
110A ARG* 1.3 71.6 + - - +
111A VAL* 2.8 40.7 + - - +
112A THR* 2.8 22.3 + - - -
113A ILE* 3.2 25.4 + - - +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 1.3 79.3 - - - +
111A VAL* 1.3 62.1 + - + +
113A ILE* 3.6 14.5 - - + +
114A GLY* 3.0 24.4 + - - -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 2.8 21.7 + - - +
110A ARG* 1.3 71.8 - - + +
112A THR* 1.3 58.7 + - - +
114A GLY* 3.0 3.6 + - - -
115A THR* 2.8 38.6 + - + +
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 4.2 12.1 - - + +
109A ASP* 2.8 29.3 + - - -
111A VAL* 1.3 75.2 - - - +
113A ILE* 1.3 67.7 + - - +
115A THR* 3.1 10.8 + - - +
116A LEU* 2.8 24.7 + - - +
156A TYR* 3.7 27.5 - - + -
160A SER* 4.5 8.7 - - - +
161A LEU* 4.0 20.6 - - + -
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.5 20.4 - - + -
103A ALA* 3.6 28.7 - - + -
104A LEU* 5.5 4.5 - - + -
108A VAL* 4.0 13.7 - - + +
109A ASP 3.2 21.3 + - - +
110A ARG* 3.6 14.4 - - + +
112A THR* 1.3 75.4 - - - +
114A GLY* 1.3 56.2 + - - +
116A LEU* 3.0 9.0 + - - +
117A ILE* 2.8 57.9 + - + +
161A LEU* 6.5 0.2 - - - -
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG 3.0 15.6 + - - -
111A VAL 3.0 4.2 + - - -
113A ILE* 1.3 78.5 - - - +
115A THR* 1.3 56.7 + - - +
117A ILE* 4.1 4.0 - - - +
118A GLY* 3.0 25.5 + - - -
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 2.8 27.0 + - + +
112A THR* 3.3 17.0 - - - +
114A GLY* 1.3 72.6 - - - +
116A LEU* 1.3 57.3 + - - +
118A GLY* 3.9 1.0 - - - +
119A VAL* 3.0 38.7 + - - +
156A TYR* 3.1 29.3 + - + +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.8 47.6 - - + +
103A ALA* 5.2 2.0 - - + -
112A THR* 2.8 13.5 + - + +
113A ILE* 3.2 12.1 - - - +
115A THR* 1.3 74.4 + - - +
117A ILE* 1.3 69.9 + - + +
119A VAL* 3.4 5.0 + - + +
120A ASP* 3.0 18.9 + - - +
153A VAL* 4.2 26.2 - - + +
156A TYR* 4.2 27.1 - - + -
157A LEU* 4.4 12.8 - - + -
161A LEU* 4.6 15.3 - - + -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 4.3 39.7 - - + +
99A LEU* 4.5 10.5 - - + -
100A LEU* 5.1 7.4 - - + +
103A ALA* 5.9 0.2 - - + -
113A ILE* 2.8 53.1 + - + +
114A GLY* 4.2 4.5 - - - +
116A LEU* 1.3 78.7 - - + +
118A GLY* 1.3 68.3 + - - +
120A ASP* 3.1 7.9 + - - +
121A ALA* 2.9 25.0 + - + +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLY 3.0 18.1 + - - -
115A THR* 3.9 2.0 - - - -
117A ILE* 1.3 81.2 - - - +
119A VAL* 1.3 61.4 + - - +
121A ALA* 3.3 7.3 + - - +
122A LEU* 3.2 21.3 + - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 3.0 29.5 + - - +
116A LEU* 3.9 5.2 - - + +
118A GLY* 1.3 74.7 - - - +
120A ASP* 1.3 66.1 + - - +
122A LEU* 3.4 15.5 - - + +
123A MET* 3.2 19.9 + - - +
149A ALA* 3.5 30.8 - - + +
152A PHE* 3.7 28.9 - - + -
153A VAL* 4.2 6.7 - - + +
156A TYR* 6.0 3.8 - - + -
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 4.8 0.3 - - - +
95A THR* 2.4 34.9 + - - -
96A PRO* 3.3 15.6 - - - +
99A LEU* 3.4 32.4 - - + +
116A LEU 3.0 8.5 + - - +
117A ILE* 3.1 8.5 + - - +
119A VAL* 1.3 74.9 - - - +
121A ALA* 1.3 65.1 + - - +
123A MET* 3.1 34.2 + - - +
124A ILE* 3.2 13.0 + - - +
153A VAL* 4.1 10.2 - - + +
187A TRP* 3.7 4.3 - - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.2 24.7 - - + +
96A PRO* 5.6 2.5 - - + -
117A ILE* 2.9 16.3 + - + +
118A GLY* 3.6 10.8 - - - +
120A ASP* 1.3 79.4 + - - +
122A LEU* 1.3 62.2 + - - +
124A ILE* 3.2 3.8 + - - +
125A VAL* 2.9 26.9 + - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLY 3.2 10.2 + - - +
119A VAL* 3.4 19.7 - - + +
121A ALA* 1.3 77.0 - - - +
123A MET* 1.3 53.0 + - - +
125A VAL* 2.8 28.6 - - + +
126A THR* 2.6 39.6 + - + +
145A PHE* 4.9 16.4 - - + -
149A ALA* 4.9 10.3 - - + -
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Residues in contact with MET 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 4.7 1.6 - - + -
119A VAL 3.2 9.6 + - - +
120A ASP* 3.1 36.2 + - - +
122A LEU* 1.3 79.2 - - - +
124A ILE* 1.3 79.7 + - + +
126A THR* 3.2 4.6 + - - -
127A GLY* 3.1 10.2 + - - -
146A SER* 2.7 36.8 + - - +
149A ALA* 3.8 15.6 - - + +
150A PHE* 3.7 36.8 - - - -
153A VAL* 4.9 4.0 - - - -
187A TRP* 4.3 6.7 - - + -
260A RET 3.6 35.3 - - + +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.3 41.0 - - + +
91A TRP* 3.5 46.9 - - + +
92A LEU* 3.8 17.3 - - + +
95A THR* 4.0 7.4 - - + +
120A ASP* 3.2 12.1 + - - +
121A ALA 3.2 5.4 + - - +
123A MET* 1.3 95.2 - - + +
125A VAL* 1.3 60.3 + - - +
127A GLY* 3.1 3.3 + - - -
128A LEU* 2.9 25.8 + - - +
260A RET 4.2 14.4 - - + -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 5.0 6.0 - - + +
121A ALA 2.9 18.0 + - - +
122A LEU* 2.8 41.5 - - + +
124A ILE* 1.3 78.9 - - - +
126A THR* 1.3 67.6 + - + +
128A LEU* 3.2 12.8 + - + +
129A ILE* 3.0 38.0 + - + +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 2.6 40.0 + - + +
123A MET 3.2 5.5 + - - -
125A VAL* 1.3 79.5 - - + +
127A GLY* 1.3 62.8 + - - +
129A ILE* 3.2 11.2 + - + +
130A GLY 3.0 17.8 + - - -
142A TRP* 3.4 43.1 - - + +
145A PHE* 4.3 15.3 - - + -
146A SER* 3.3 22.1 - - - -
149A ALA* 5.5 0.3 - - - +
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.9 8.8 - - - -
123A MET 3.1 13.2 + - - -
124A ILE 3.1 8.4 + - - -
126A THR* 1.3 79.1 + - - +
128A LEU* 1.3 59.4 + - - +
130A GLY* 3.2 3.1 + - - -
131A ALA* 3.1 21.1 + - - +
142A TRP 5.0 1.6 - - - -
143A TRP* 5.6 0.7 - - - -
146A SER* 4.0 11.2 - - - -
194A TRP* 4.1 7.6 - - - -
260A RET 4.1 16.8 - - - -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 4.2 7.2 - - + -
85A TYR* 4.2 27.1 - - + +
88A TYR* 3.7 49.3 - - + -
124A ILE 2.9 9.6 + - - +
125A VAL* 3.5 15.0 - - + +
127A GLY* 1.3 74.0 - - - +
129A ILE* 1.3 66.6 + - + +
131A ALA* 3.3 1.8 + - + -
132A LEU* 3.1 38.4 + - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 3.0 29.7 + - + +
126A THR* 3.2 18.3 + - + +
128A LEU* 1.3 78.5 - - + +
130A GLY* 1.3 59.7 + - - +
132A LEU* 3.5 11.0 + - + +
133A SER* 2.8 27.8 + - - +
142A TRP* 3.8 33.2 - - + +
301A BNG 3.7 43.5 - - + -
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR 3.0 9.9 + - - -
127A GLY* 3.2 4.5 + - - -
128A LEU 3.1 0.2 - - - -
129A ILE* 1.3 78.5 - - - +
131A ALA* 1.3 57.7 + - - +
133A SER* 3.0 25.6 + - - -
139A ARG* 3.3 23.5 + - - +
142A TRP* 3.6 20.8 - - - +
143A TRP 5.0 0.9 - - - -
194A TRP* 4.1 8.7 - - - -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.2 3.1 - - - +
83A ILE* 3.3 40.5 - - + +
88A TYR* 3.7 25.8 - - + +
127A GLY 3.1 8.8 + - - +
128A LEU 3.3 8.7 + - - +
130A GLY* 1.3 76.5 - - - +
132A LEU* 1.3 57.4 + - - +
133A SER 3.3 0.4 - - - -
139A ARG* 3.1 21.2 + - - +
194A TRP* 3.8 11.3 - - + +
199A GLU* 5.2 2.9 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 4.1 7.6 - - + -
73A VAL* 3.7 20.1 - - + +
83A ILE* 3.9 31.4 - - + -
85A TYR* 4.0 32.5 - - + +
128A LEU* 3.1 28.6 + - + +
129A ILE* 3.9 10.3 - - + +
130A GLY 3.2 0.4 - - - -
131A ALA* 1.3 76.3 - - - +
133A SER* 1.3 62.4 + - - +
134A LYS 3.8 0.9 + - - -
301A BNG 3.6 20.9 + - - +
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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
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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