Contacts of the helix formed by residues 123 - 140 (chain D) in PDB entry 2VGB
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D GLY* 1.3 72.1 - - - -
124D HIS* 1.3 66.5 + - - +
125D GLU* 3.1 21.7 + - - +
126D TYR* 3.1 19.7 + - - +
127D HIS* 3.0 27.0 + - - -
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Residues in contact with HIS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PHE* 3.9 14.6 - + - -
123D SER* 1.3 74.6 - - - +
125D GLU* 1.3 75.4 + - - +
127D HIS* 3.1 3.9 + - - -
128D ALA* 2.9 19.9 + - - +
267D GLN* 3.6 13.7 + - - -
270D ARG* 4.0 22.8 + - - +
271D ASP* 2.9 35.6 + - - -
274D PHE* 3.4 38.7 - + + +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER* 3.1 22.7 + - - +
124D HIS* 1.3 84.2 + - - +
126D TYR* 1.3 62.5 + - - +
128D ALA* 3.3 8.2 + - - +
129D GLU* 3.1 32.4 + - - +
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 4.7 4.2 + - + -
95D GLY* 4.0 17.0 - - - -
96D PRO* 4.2 6.9 - - - +
99D ARG* 2.9 72.2 + - - +
121D HIS 5.0 1.3 - - - -
122D GLY* 4.1 13.7 - - - -
123D SER* 3.1 24.4 + - - +
124D HIS 3.1 0.4 - - - -
125D GLU* 1.3 82.2 - - - +
127D HIS* 1.3 84.6 + + - +
129D GLU* 3.5 4.9 + - - -
130D SER* 3.3 13.9 + - - -
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Residues in contact with HIS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.9 15.6 - - + +
118D ASN 3.5 22.9 - - - -
119D PHE* 3.4 53.1 - + + -
121D HIS 2.9 28.3 + - - -
122D GLY 3.5 8.1 + - - -
123D SER 3.0 23.9 + - - -
124D HIS 3.1 4.2 + - - +
126D TYR* 1.3 89.1 - + - +
128D ALA* 1.3 61.0 + - - +
130D SER* 3.2 7.2 + - - -
131D ILE* 2.9 31.9 + - - +
274D PHE* 4.2 6.7 - - + -
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D HIS 2.9 13.2 + - - +
125D GLU* 3.3 12.8 + - - +
127D HIS* 1.3 76.5 - - - +
129D GLU* 1.3 56.4 + - + +
131D ILE* 3.3 8.1 + - - +
132D ALA* 2.8 30.4 + - - +
274D PHE* 3.8 15.6 - - + -
278D HIS* 4.1 16.2 - - + +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG* 2.7 40.1 + - - +
125D GLU* 3.1 18.3 + - - +
126D TYR* 3.6 6.4 - - - +
128D ALA* 1.3 75.4 - - + +
130D SER* 1.3 58.7 + - - +
132D ALA* 3.4 6.8 + - - +
133D ASN* 2.9 40.6 + - - +
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 3.9 13.0 - - - +
99D ARG* 3.1 32.7 + - - +
104D LEU* 5.6 0.2 - - - +
117D LEU* 4.1 19.1 - - - -
126D TYR* 3.3 12.5 + - - -
127D HIS* 3.2 13.5 + - - -
129D GLU* 1.3 76.2 - - - +
131D ILE* 1.3 67.0 + - - +
133D ASN* 3.1 5.7 + - - +
134D VAL* 2.9 28.9 + - - +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.8 23.3 - - + -
127D HIS 2.9 17.7 + - - +
128D ALA* 3.5 6.5 - - - +
130D SER* 1.3 76.5 - - - +
132D ALA* 1.3 66.4 + - - +
134D VAL* 3.6 2.5 - - - +
135D ARG* 2.9 65.4 + - - +
153D ILE* 4.2 17.7 - - + -
274D PHE* 3.9 16.8 - - + -
278D HIS* 3.7 30.3 - - + +
280D VAL* 4.3 10.8 - - + -
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ALA 2.8 17.6 + - - +
129D GLU* 3.6 9.0 - - - +
130D SER 3.2 0.2 - - - -
131D ILE* 1.3 79.0 - - - +
133D ASN* 1.3 62.8 + - - +
135D ARG* 3.7 5.6 + - - +
136D GLU* 3.1 27.6 + - - +
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Residues in contact with ASN 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG* 2.8 33.3 + - - +
100D SER* 4.4 1.4 - - - -
101D VAL* 3.8 27.4 + - + +
104D LEU* 4.1 6.3 - - + -
129D GLU* 2.9 26.1 + - - +
130D SER* 3.1 4.0 + - - +
132D ALA* 1.3 81.5 + - - +
134D VAL* 1.3 54.9 + - - +
136D GLU* 3.1 7.5 + - - +
137D ALA* 2.8 35.3 + - - +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 4.4 11.9 - - + -
104D LEU* 4.3 22.4 - - + +
112D MET* 5.3 3.6 - - + -
115D ALA* 4.0 19.7 - - + -
117D LEU* 5.5 2.0 - - + -
130D SER* 2.9 22.1 + - - +
131D ILE* 3.6 4.5 - - - +
133D ASN* 1.3 74.5 - - - +
135D ARG* 1.3 55.1 + - + +
137D ALA* 2.9 4.1 + - - +
138D VAL* 2.7 53.1 + - + +
151D VAL* 4.1 17.3 - - + +
153D ILE* 4.0 22.2 - - + -
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Residues in contact with ARG 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 2.9 41.9 + - + +
132D ALA* 4.1 5.8 - - - +
134D VAL* 1.3 75.3 - - + +
136D GLU* 1.3 58.5 + - - +
138D VAL* 3.4 6.6 + - + +
139D GLU* 2.9 42.9 + - + +
153D ILE* 4.2 17.9 - - + +
278D HIS* 2.4 35.1 + - - +
279D GLY* 3.3 19.0 + - - -
280D VAL* 4.3 0.4 - - - +
281D ASP* 5.1 1.4 + - - -
504D ARG* 5.7 6.1 - - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 3.7 29.3 - - + +
105D LYS* 6.1 0.2 - - - -
132D ALA 3.1 19.3 + - - +
133D ASN* 3.4 9.4 + - - +
134D VAL 3.1 0.6 - - - -
135D ARG* 1.3 74.4 - - - +
137D ALA* 1.3 66.6 + - - +
139D GLU* 3.2 4.7 + - - +
140D SER* 3.1 22.9 + - - -
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 3.8 17.2 - - + +
104D LEU* 3.5 33.7 - - + -
105D LYS* 3.9 12.8 - - + +
108D ILE* 4.1 7.0 - - + -
133D ASN 2.8 12.5 + - - +
134D VAL* 3.5 6.7 - - - +
136D GLU* 1.3 73.0 - - - +
138D VAL* 1.3 60.7 + - - +
140D SER* 2.6 26.5 + - - -
141D PHE* 3.2 9.5 - - - -
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ILE* 3.7 16.6 - - + -
134D VAL* 2.7 38.7 + - + +
135D ARG* 3.8 5.4 - - - +
137D ALA* 1.3 73.4 - - - +
139D GLU* 1.3 74.2 + - - +
140D SER 3.1 1.4 + - - -
141D PHE* 3.4 16.1 + - - +
148D TYR* 3.7 19.0 - - + +
149D ARG 3.6 23.9 - - - +
151D VAL* 3.6 32.5 - - + +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ARG* 2.9 29.7 + - + +
136D GLU* 3.8 4.0 - - - +
138D VAL* 1.3 80.7 - - - +
140D SER* 1.3 59.9 + - - +
141D PHE 3.0 6.5 + - - -
142D ALA* 3.2 27.0 + - + +
148D TYR* 3.0 31.8 + - - -
518D ARG* 4.6 7.6 + - - -
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Residues in contact with SER 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LYS* 3.5 29.1 - - - +
136D GLU* 3.1 10.7 + - - -
137D ALA 2.6 21.2 + - - -
138D VAL 3.1 0.2 - - - -
139D GLU* 1.3 77.4 - - - +
141D PHE* 1.3 70.1 + - - +
142D ALA 3.4 1.5 + - - -
143D GLY* 4.6 3.5 + - - -
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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