Contacts of the helix formed by residues 134 - 147 (chain A) in PDB entry 2VGO
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 VAL 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.6 33.0 - - + -
129A LEU* 3.1 28.9 + - + +
132A GLU* 3.7 15.0 - - + +
133A GLY* 1.3 80.3 - - - +
135A GLU* 1.3 57.8 + - - +
136A HIS 3.4 2.0 - - - -
137A GLN* 3.3 34.6 + - + +
138A LEU* 2.9 28.7 + - + +
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Residues in contact with GLU 135 (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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129A LEU 4.1 0.4 - - - +
130A GLU* 3.4 39.1 - - - +
133A GLY* 3.3 22.8 - - - +
134A VAL* 1.3 77.2 - - - +
136A HIS* 1.3 65.1 + - + +
138A LEU* 3.5 2.8 + - - +
139A ARG* 3.0 31.1 + - - +
837D PHE* 3.7 54.4 - - + -
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Residues in contact with HIS 136 (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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133A GLY 5.3 0.8 + - - -
135A GLU* 1.3 84.4 + - + +
137A GLN* 1.3 59.9 + - - +
139A ARG* 3.5 40.4 + - - +
140A ARG* 3.1 36.7 + - - +
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Residues in contact with GLN 137 (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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133A GLY 5.4 0.3 - - - +
134A VAL* 3.3 37.1 - - + +
135A GLU 3.2 0.2 - - - -
136A HIS* 1.3 76.0 - - - +
138A LEU* 1.3 64.6 + - - +
140A ARG* 3.3 21.7 + - - +
141A GLU* 3.2 40.3 + - + +
236A GLY 5.1 8.9 + - - +
237A TRP* 6.3 0.6 - - - -
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Residues in contact with LEU 138 (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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124A LEU* 3.5 36.6 - - + -
129A LEU* 3.8 28.0 - - + -
134A VAL* 2.9 16.3 + - + +
135A GLU* 3.9 3.6 - - - +
137A GLN* 1.3 74.0 - - - +
139A ARG* 1.3 66.0 + - - +
141A GLU* 3.3 15.3 + - + +
142A ILE* 3.0 47.1 + - + +
166A ILE* 4.0 15.5 - - + -
168A LEU* 4.7 5.4 - - + -
836D LEU* 5.5 0.9 - - + -
837D PHE* 4.1 8.1 - - + -
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Residues in contact with ARG 139 (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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135A GLU* 3.0 20.8 + - - +
136A HIS* 3.6 38.4 + - - +
137A GLN 3.3 0.2 - - - -
138A LEU* 1.3 79.1 - - - +
140A ARG* 1.3 56.8 + - - +
142A ILE* 3.5 5.1 + - - +
143A GLU* 3.0 30.4 + - - +
833D LEU* 3.5 54.3 + - + +
834D GLU* 3.9 29.9 + - - +
836D LEU* 5.5 2.7 - - + -
837D PHE* 5.7 7.6 - - + -
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Residues in contact with ARG 140 (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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136A HIS* 3.1 16.6 + - - +
137A GLN* 3.6 26.8 + - - +
138A LEU 3.2 0.4 - - - -
139A ARG* 1.3 74.3 - - - +
141A GLU* 1.3 61.0 + - + +
143A GLU* 3.3 6.0 + - + +
144A ILE* 3.0 44.6 + - + +
238A SER 3.6 21.5 - - - -
239A VAL* 4.8 10.9 - - - +
240A HIS 5.6 0.4 - - - +
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Residues in contact with GLU 141 (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 LYS* 5.9 0.9 + - - -
137A GLN* 3.2 28.2 + - + +
138A LEU* 3.6 19.1 - - + +
140A ARG* 1.3 78.8 - - + +
142A ILE* 1.3 59.3 + - + +
144A ILE* 3.6 4.6 + - - +
145A GLN* 3.0 34.2 + - - +
156A MET* 5.4 1.1 - - - -
234A ASP* 4.6 7.1 - - - +
235A PHE* 3.7 25.9 + - + +
236A GLY* 3.5 32.4 + - - +
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Residues in contact with ILE 142 (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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138A LEU* 3.0 45.7 + - + +
139A ARG* 3.8 4.0 - - - +
141A GLU* 1.3 74.3 - - + +
143A GLU* 1.3 60.6 + - - +
146A SER* 2.8 36.6 + - - +
156A MET* 4.0 14.8 - - + -
159A TYR* 3.6 34.3 - - + -
166A ILE* 4.8 0.4 - - + -
168A LEU* 3.7 28.0 - - + -
833D LEU* 3.8 14.1 - - + -
836D LEU* 3.8 24.2 - - + -
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Residues in contact with GLU 143 (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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139A ARG* 3.0 15.1 + - + +
140A ARG* 3.3 6.9 + - - +
142A ILE* 1.3 77.7 - - - +
144A ILE* 1.3 63.7 + - + +
146A SER* 3.4 6.8 + - - -
147A HIS* 2.7 54.0 + - + -
159A TYR* 4.3 6.1 + - - -
833D LEU* 3.0 36.0 - - + +
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Residues in contact with ILE 144 (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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140A ARG* 3.0 34.0 + - + +
141A GLU* 4.0 5.4 - - - +
143A GLU* 1.3 80.0 - - + +
145A GLN* 1.3 64.6 + - - +
147A HIS* 3.3 10.5 + - - +
148A LEU* 3.3 21.2 + - + +
212A VAL* 3.9 28.5 - - + -
235A PHE* 3.9 21.1 - - + +
238A SER* 3.8 33.9 - - - +
239A VAL* 3.9 10.1 - - - +
240A HIS* 4.1 15.3 - - + +
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Residues in contact with GLN 145 (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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141A GLU* 3.0 18.8 + - - +
144A ILE* 1.3 77.0 - - - +
146A SER* 1.3 62.2 + - - +
147A HIS 3.1 1.7 + - - -
148A LEU* 3.3 25.2 + - - +
153A ILE* 5.1 1.6 - - + -
154A LEU* 2.9 41.2 + - - +
155A ARG* 5.8 0.2 - - - -
156A MET* 4.0 31.3 + - + +
170A LEU* 4.4 9.6 - - - +
233A ALA 3.8 19.0 + - - +
234A ASP* 5.2 0.2 - - - -
235A PHE* 4.0 33.3 + - + +
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Residues in contact with SER 146 (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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142A ILE 2.8 26.2 + - - -
143A GLU* 3.4 19.4 + - - -
144A ILE 3.3 0.2 + - - -
145A GLN* 1.3 72.7 - - - +
147A HIS* 1.3 65.0 + - - +
148A LEU 3.5 1.6 + - - +
149A ARG* 5.3 7.8 + - - +
155A ARG* 5.9 1.4 - - - -
156A MET* 4.0 34.3 - - - +
158A ASN* 6.5 0.2 - - - -
159A TYR* 4.1 18.4 + - - -
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Residues in contact with HIS 147 (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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143A GLU* 2.7 53.4 + - + +
144A ILE* 3.3 4.4 + - - +
145A GLN 3.1 1.0 - - - -
146A SER* 1.3 88.2 + - - +
148A LEU* 1.3 67.1 + - + +
149A ARG* 4.1 7.0 + - - +
206A TYR* 4.2 5.2 + - - -
210A ARG* 5.2 4.0 + - - -
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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
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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