Contacts of the helix formed by residues 146 - 158 (chain A) in PDB entry 2E7G
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 ALA 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A SER* 1.3 71.8 - - - +
147A GLU* 1.3 57.5 + - + +
149A ASN* 3.7 8.3 - - - +
150A ALA* 2.8 37.8 + - - +
183A GLN* 5.5 2.8 + - - +
187A ASN* 6.1 0.9 - - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A SER* 3.2 4.7 - - - -
146A ALA* 1.3 80.2 - - + +
148A GLN* 1.3 60.9 + - - +
150A ALA* 3.6 5.5 - - - +
151A HIS* 3.2 23.7 + - - +
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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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120A LEU* 4.8 2.3 - - - +
143A THR* 3.3 42.9 - - + +
145A SER* 3.1 12.4 + - - +
147A GLU* 1.3 76.1 - - - +
149A ASN* 1.3 67.3 + - - +
151A HIS* 3.4 13.3 + - - +
152A MET* 3.0 47.7 + - - +
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Residues in contact with ASN 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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140A TRP* 4.0 5.4 - - - -
142A THR* 3.2 20.2 + - + +
143A THR* 2.7 50.6 + - - +
144A LEU 4.8 0.2 - - - -
145A SER 2.8 24.6 + - - +
146A ALA* 3.8 5.7 - - - +
148A GLN* 1.3 78.6 + - - +
150A ALA* 1.3 52.9 + - - +
152A MET* 3.9 0.3 - - - +
153A GLU* 2.7 39.4 + - - +
183A GLN* 3.8 23.9 - - - +
187A ASN* 5.9 1.4 + - - -
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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 ALA 2.8 22.6 + - - +
147A GLU* 3.6 7.2 - - - +
149A ASN* 1.3 73.3 - - - +
151A HIS* 1.3 56.5 + - - +
153A GLU* 3.7 4.0 - - - +
154A ALA* 2.8 32.5 + - - +
183A GLN* 5.1 2.2 - - - +
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Residues in contact with HIS 151 (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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116A GLU* 5.5 9.1 - - + +
120A LEU* 3.7 24.9 - - + +
147A GLU 3.2 14.4 + - - +
148A GLN* 3.8 13.2 - - - +
150A ALA* 1.3 78.6 - - - +
152A MET* 1.3 70.9 + - - +
154A ALA* 3.3 7.2 + - - +
155A VAL* 3.0 31.0 + - + +
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Residues in contact with MET 152 (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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117A LEU* 5.2 2.0 - - + -
120A LEU* 3.8 41.6 - - + +
122A VAL* 3.6 31.4 - - + -
140A TRP* 3.4 34.1 - - + -
141A LYS 5.2 2.2 - - - +
143A THR* 4.9 4.9 - - - -
148A GLN* 3.0 47.1 + - - +
151A HIS* 1.3 76.4 - - - +
153A GLU* 1.3 54.1 + - - +
155A VAL* 2.7 25.1 - - - +
156A LEU* 2.8 22.2 + - + +
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Residues in contact with GLU 153 (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 TRP* 3.3 31.8 + - + -
149A ASN 2.7 24.6 + - - +
150A ALA* 3.7 5.4 - - - +
152A MET* 1.3 72.6 - - - +
154A ALA* 1.3 54.9 + - - +
156A LEU* 4.1 2.8 - - - +
157A GLN* 2.7 65.0 + - - +
181A PHE* 3.2 32.2 - - - +
182A VAL* 4.5 0.9 + - - -
183A GLN* 4.3 20.2 - - + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA 2.8 19.1 + - - +
151A HIS* 3.5 7.0 - - - +
153A GLU* 1.3 77.8 - - - +
155A VAL* 1.3 60.9 + - - +
157A GLN* 3.9 5.1 - - - +
158A ARG* 3.2 36.2 + - - +
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Residues in contact with VAL 155 (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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116A GLU* 3.3 39.3 - - + -
117A LEU* 4.4 3.6 - - - +
120A LEU* 3.4 18.6 - - + -
151A HIS* 3.0 22.9 + - + +
152A MET* 2.7 32.5 - - - +
154A ALA* 1.3 73.5 - - - +
156A LEU* 1.3 62.1 + - - +
158A ARG* 3.1 31.0 - - - +
159A SER* 3.1 35.3 + - - +
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Residues in contact with LEU 156 (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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108A LEU* 5.0 6.3 - - + -
117A LEU* 3.4 43.3 - - + -
122A VAL* 5.1 2.7 - - + -
140A TRP* 3.7 34.8 - - + +
152A MET* 2.8 23.3 + - + +
153A GLU* 4.0 2.9 - - - +
155A VAL* 1.3 71.0 - - - +
157A GLN* 1.3 65.2 + - - +
159A SER* 3.1 12.5 + - - -
160A ALA 3.2 9.2 + - - -
163A MET* 3.8 4.0 - - + -
181A PHE* 3.3 59.1 - - + -
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Residues in contact with GLN 157 (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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153A GLU* 2.7 61.4 + - + +
154A ALA* 3.9 5.6 - - - +
156A LEU* 1.3 74.0 - - - +
158A ARG* 1.3 57.8 + - - +
160A ALA* 3.0 26.3 + - - +
161A ALA* 4.3 1.2 + - - +
180A VAL* 6.3 2.4 - - - +
181A PHE* 4.2 19.6 + - + +
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Residues in contact with ARG 158 (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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116A GLU* 4.7 9.3 + - - +
154A ALA* 3.2 15.6 + - - +
155A VAL* 3.1 59.7 - - - +
157A GLN* 1.3 78.8 - - - +
159A SER* 1.3 60.2 + - - +
160A ALA 3.2 3.6 + - - -
161A ALA* 4.4 9.5 + - - +
162A HIS* 5.0 2.9 + - - +
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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