Contacts of the helix formed by residues 138 - 150 (chain A) in PDB entry 2VAA
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 MET 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASP* 1.3 74.8 - - - +
139A ALA* 1.3 66.2 + - - +
141A LEU* 3.1 33.7 - - + +
142A ILE* 3.5 10.7 + - - +
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Residues in contact with ALA 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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84A TYR* 3.8 20.4 - - + +
85A TYR* 3.4 37.0 - - + +
123A TYR* 3.5 10.8 + - + -
137A ASP* 3.1 9.0 + - - +
138A MET* 1.3 75.9 - - - +
140A ALA* 1.3 55.1 + - - +
142A ILE* 2.8 43.6 + - - +
143A THR 3.6 0.2 + - - -
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Residues in contact with ALA 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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123A TYR* 3.0 53.8 + - + +
124A ILE* 3.9 4.0 - - + +
135A ALA* 3.5 15.4 - - + +
136A ALA 4.0 0.9 - - - +
137A ASP* 2.8 17.1 + - - +
139A ALA* 1.3 75.9 - - - +
141A LEU* 1.3 57.5 + - - +
142A ILE 3.1 0.2 - - - -
143A THR* 3.2 3.5 + - - -
144A LYS* 2.9 28.8 + - - +
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Residues in contact with LEU 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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135A ALA* 4.3 7.6 - - + -
137A ASP 3.1 10.0 + - - +
138A MET* 3.1 33.9 - - + +
139A ALA 3.0 0.6 - - - -
140A ALA* 1.3 77.9 - - - +
142A ILE* 1.3 59.9 + - + +
144A LYS* 3.5 28.3 - - + +
145A HIS* 3.1 51.2 + - + +
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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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84A TYR* 3.6 50.9 - - + +
138A MET 3.6 8.3 - - - +
139A ALA* 2.8 22.4 + - - +
141A LEU* 1.3 76.3 - - + +
143A THR* 1.3 62.3 + - - +
145A HIS* 3.4 10.2 + - - +
146A LYS* 3.2 29.4 + - + +
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Residues in contact with THR 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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84A TYR* 3.5 1.6 - - - -
123A TYR* 2.7 32.9 + - + -
124A ILE* 4.3 3.6 - - + -
139A ALA 3.6 0.4 + - - -
140A ALA 3.2 8.0 + - - -
142A ILE* 1.3 74.5 - - - +
144A LYS* 1.3 66.2 - - - +
146A LYS* 3.1 5.4 + - - +
147A TRP* 2.9 62.3 + - + +
8P LEU* 2.8 37.5 + - + +
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Residues in contact with LYS 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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124A ILE* 3.8 12.7 - - + +
132A THR* 6.2 0.8 - - - -
133A TRP* 3.4 38.4 + - + +
134A THR* 4.8 0.4 - - - +
135A ALA* 4.3 13.5 - - + +
140A ALA 2.9 16.2 + - - +
141A LEU* 3.5 28.0 - - + +
143A THR* 1.3 75.3 - - - +
145A HIS* 1.3 64.3 + - + +
147A TRP* 3.3 4.8 + - - +
148A GLU* 2.8 66.6 + - - +
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Residues in contact with HIS 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 LEU* 3.1 44.0 + - + +
142A ILE* 3.7 9.2 - - - +
144A LYS* 1.3 83.6 - - + +
146A LYS* 1.3 61.8 + - - +
148A GLU* 3.2 20.2 + - - +
149A GLN* 3.0 31.0 + - + +
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Residues in contact with LYS 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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80A THR* 4.5 5.5 - - - +
84A TYR* 3.0 26.0 + - - +
142A ILE* 3.2 21.6 + - + +
143A THR* 3.1 7.9 + - - +
145A HIS* 1.3 77.0 - - - +
147A TRP* 1.3 65.0 + - + +
149A GLN* 3.4 6.1 + - - +
150A ALA* 3.0 28.8 + - - +
7P GLY 5.0 2.2 - - - +
8P LEU* 3.1 29.2 + - - +
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Residues in contact with TRP 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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114A GLN* 4.8 1.6 - - - -
116A TYR* 3.4 34.5 - + - -
124A ILE* 3.7 26.0 - - + -
133A TRP* 3.5 56.1 - + + +
143A THR* 2.9 25.8 + - + +
144A LYS 3.7 3.4 - - - +
146A LYS* 1.3 79.8 - - + +
148A GLU* 1.3 65.9 + - - +
150A ALA* 3.4 2.0 + - + +
151A GLY 3.0 3.3 + - - -
152A GLU* 3.0 42.6 + - + +
153A ALA 4.5 0.7 + - - -
6P GLN* 3.4 32.0 - - + +
7P GLY 3.0 22.1 + - - -
8P LEU* 3.4 26.5 - - + -
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Residues in contact with GLU 148 (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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132A THR* 5.9 2.3 - - - +
133A TRP* 4.2 18.9 + - + +
144A LYS* 2.8 50.4 + - - +
145A HIS* 3.7 24.0 + - - +
147A TRP* 1.3 75.2 - - - +
149A GLN* 1.3 62.9 + - + +
151A GLY* 3.2 13.0 + - - -
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Residues in contact with GLN 149 (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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145A HIS* 3.0 19.7 + - + +
146A LYS* 3.8 5.6 - - - +
148A GLU* 1.3 79.8 - - + +
150A ALA* 1.3 58.9 + - - +
151A GLY 3.6 0.3 + - - -
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Residues in contact with ALA 150 (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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146A LYS 3.0 18.1 + - - +
147A TRP* 3.4 6.7 + - + +
148A GLU 3.3 0.4 - - - -
149A GLN* 1.3 75.9 - - - +
151A GLY* 1.3 63.1 + - - +
152A GLU* 4.4 3.1 - - + +
6P GLN* 4.6 19.5 - - + +
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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