Contacts of the helix formed by residues 138 - 149 (chain A) in PDB entry 2ERY
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 THR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ARG* 3.5 6.1 + - + +
136A GLN 6.0 0.7 - - - -
137A VAL* 1.3 79.6 - - - +
139A GLN* 1.3 65.3 + - - +
140A GLU* 3.4 10.1 + - - +
141A GLU* 2.9 42.4 + - - +
142A GLY* 3.0 17.7 + - - -
153A TYR* 4.8 0.3 + - - -
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Residues in contact with GLN 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 ARG* 3.3 8.2 + - - +
138A THR* 1.3 73.2 - - - +
140A GLU* 1.3 57.7 + - - +
142A GLY* 3.1 3.0 + - - +
143A GLN* 2.9 49.9 + - - +
153A TYR* 3.8 5.6 - - + -
155A GLU* 3.5 43.3 + - - +
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Residues in contact with GLU 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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138A THR* 3.2 9.9 + - - +
139A GLN* 1.3 79.3 - - - +
141A GLU* 1.3 56.5 + - + +
143A GLN* 3.3 17.3 + - - +
144A GLN* 2.9 29.2 + - + +
147A ARG* 4.8 7.0 + - - +
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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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98A ARG* 2.9 40.1 + - - +
101A PHE* 3.4 16.8 - - + -
136A GLN 4.2 0.5 - - - +
137A VAL* 3.5 8.2 - - + -
138A THR* 2.9 45.0 + - - +
140A GLU* 1.3 78.0 - - + +
142A GLY* 1.3 56.7 + - - +
144A GLN* 3.4 7.2 + - - +
145A LEU 3.0 23.4 + - - -
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Residues in contact with GLY 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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93A PHE* 4.5 1.8 - - - -
101A PHE* 4.0 14.4 - - - -
124A LEU* 3.6 7.3 - - - +
137A VAL* 4.3 1.2 - - - +
138A THR 3.0 10.5 + - - -
139A GLN 3.1 3.8 + - - -
141A GLU* 1.3 76.4 - - - +
143A GLN* 1.3 55.4 + - - +
145A LEU* 3.3 1.0 + - - +
146A ALA* 3.0 28.2 + - - +
153A TYR* 3.7 28.4 - - - -
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Residues in contact with GLN 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 GLN* 2.9 40.2 + - - +
140A GLU* 3.3 20.2 + - - +
142A GLY* 1.3 75.8 - - - +
144A GLN* 1.3 56.3 + - - +
146A ALA* 3.3 6.4 + - - +
147A ARG* 2.9 48.2 + - - +
153A TYR* 3.7 20.1 - - + -
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Residues in contact with GLN 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 GLU* 2.9 17.6 + - + +
141A GLU* 3.6 8.3 - - - +
142A GLY 3.3 0.2 - - - -
143A GLN* 1.3 72.7 - - - +
145A LEU* 1.3 67.4 + - - +
147A ARG* 3.1 34.6 + - - +
148A GLN* 3.0 52.8 + - - +
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Residues in contact with LEU 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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101A PHE* 3.4 38.4 - - + +
104A ILE* 4.0 27.6 - - + -
105A TYR* 3.4 44.4 - - + +
124A LEU* 4.0 9.4 - - + -
141A GLU 3.0 18.3 + - - +
142A GLY 3.7 4.3 - - - +
144A GLN* 1.3 75.9 - - - +
146A ALA* 1.3 57.9 + - - +
148A GLN* 3.1 10.1 + - - +
149A LEU* 2.9 44.7 + - + +
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Residues in contact with ALA 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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124A LEU* 3.8 8.6 - - + +
142A GLY 3.0 8.5 + - - +
143A GLN* 3.6 8.5 - - - +
144A GLN 3.3 0.2 - - - -
145A LEU* 1.3 76.8 - - - +
147A ARG* 1.3 57.2 + - + +
149A LEU 3.4 0.3 + - - -
150A LYS* 2.8 23.7 + - - -
151A VAL* 2.9 43.3 + - + +
153A TYR* 3.6 28.5 - - + +
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Residues in contact with ARG 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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140A GLU* 4.8 7.9 + - - +
143A GLN* 2.9 34.5 + - - +
144A GLN* 3.1 46.9 + - - +
145A LEU 3.2 0.2 - - - -
146A ALA* 1.3 78.1 - - + +
148A GLN* 1.3 61.8 + - - +
150A LYS* 3.1 20.9 + - - +
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Residues in contact with GLN 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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105A TYR* 3.1 37.0 + - + -
144A GLN* 3.0 43.2 + - - +
145A LEU* 3.5 13.1 - - + +
147A ARG* 1.3 77.5 - - - +
149A LEU* 1.3 63.8 + - + +
150A LYS* 3.3 8.4 + - - +
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Residues in contact with LEU 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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91A LEU* 4.7 6.3 - - + -
104A ILE* 3.6 31.9 - - + +
105A TYR* 4.3 23.3 - - + -
108A GLN* 3.8 50.0 + - + +
124A LEU* 5.1 1.8 - - + -
145A LEU* 2.9 32.1 + - + +
146A ALA 4.1 2.7 - - - +
148A GLN* 1.3 79.0 - - + +
150A LYS* 1.3 71.0 + - - +
151A VAL* 3.4 22.0 + - + +
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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