Contacts of the helix formed by residues 137 - 150 (chain A) in PDB entry 2O9C
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 PRO 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A THR 4.8 0.2 - - - +
136A GLY* 1.3 83.5 - - - +
138A HIS* 1.3 66.2 + - + +
139A ALA 3.3 0.2 - - - -
140A LEU* 3.4 9.4 + - + +
141A ARG* 3.0 29.1 + - + +
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Residues in contact with HIS 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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136A GLY* 2.9 3.9 - - - -
137A PRO* 1.3 85.0 - - + +
139A ALA* 1.3 68.8 + - - +
141A ARG* 4.0 30.2 + - + -
142A ASN* 2.8 52.5 + - - +
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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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135A THR* 3.5 31.4 - - + -
136A GLY 3.3 4.1 + - - +
138A HIS* 1.3 81.2 - - - +
140A LEU* 1.3 61.9 + - - +
142A ASN* 4.2 2.9 - - - +
143A ALA* 3.2 21.0 + - - +
167A LEU* 3.9 27.1 - - + +
304A THR* 4.5 5.4 - - + -
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Residues in contact with LEU 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 GLY 4.5 0.6 + - - +
137A PRO* 3.4 9.8 + - + +
139A ALA* 1.3 78.2 - - - +
141A ARG* 1.3 67.5 + - - +
143A ALA* 3.2 14.6 + - + +
144A MET* 3.2 38.5 + - + +
167A LEU* 5.7 0.4 - - - -
304A THR* 4.2 19.9 - - + +
307A SER* 3.8 22.4 - - - +
308A LEU* 4.0 39.5 - - + +
311A LEU* 4.7 8.1 - - + -
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Residues in contact with ARG 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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137A PRO* 3.0 19.2 + - + +
138A HIS* 3.8 29.8 + - + +
140A LEU* 1.3 80.3 - - - +
142A ASN* 1.3 84.3 + - - +
144A MET* 3.5 27.1 + - - +
145A PHE* 3.3 39.0 - - + -
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Residues in contact with ASN 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 HIS* 2.8 40.2 + - - +
139A ALA* 4.2 2.5 - - - +
141A ARG* 1.3 101.1 + - - +
143A ALA* 1.3 62.7 + - - +
145A PHE* 3.3 26.5 + - + +
146A ALA* 4.7 1.0 + - - +
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Residues in contact with ALA 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 ALA 3.2 16.5 + - - +
140A LEU* 3.2 10.2 + - + +
142A ASN* 1.3 79.3 - - - +
144A MET* 1.3 63.4 + - - +
145A PHE 3.2 1.3 + - - -
146A ALA* 3.6 11.2 + - - +
147A LEU* 3.6 18.7 + - + +
163A THR* 3.6 28.7 + - + +
167A LEU* 4.8 7.2 - - + -
308A LEU* 4.8 6.7 - - + -
311A LEU* 5.4 1.1 - - + -
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Residues in contact with MET 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 LEU* 3.2 42.2 + - + +
141A ARG* 3.6 18.2 - - - +
142A ASN 3.2 0.6 - - - -
143A ALA* 1.3 78.1 - - - +
145A PHE* 1.3 60.0 + - + +
147A LEU* 3.4 2.5 + - - +
148A GLU* 2.9 30.9 + - + +
311A LEU* 3.5 42.3 - - + +
315A GLN* 5.0 1.0 + - - -
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Residues in contact with PHE 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 ARG* 3.3 52.5 - - + -
142A ASN* 3.3 25.1 - - + +
143A ALA 3.2 1.0 - - - -
144A MET* 1.3 78.9 - - + +
146A ALA* 1.3 62.6 + - - +
148A GLU* 3.2 7.6 + - + +
149A SER* 3.0 22.7 + - - -
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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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142A ASN 4.7 1.0 + - - +
143A ALA* 3.6 6.5 + - - +
144A MET 3.5 0.4 - - - -
145A PHE* 1.3 75.7 - - - +
147A LEU* 1.3 65.7 + - + +
149A SER* 3.3 19.2 + - - +
150A ALA* 3.3 10.7 + - - +
159A VAL* 3.7 28.8 - - + +
163A THR* 5.0 2.5 - - - +
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Residues in contact with LEU 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 ALA* 3.6 15.7 + - + +
144A MET* 3.4 9.8 + - - +
145A PHE 3.2 0.4 - - - -
146A ALA* 1.3 78.3 - - + +
148A GLU* 1.3 62.5 + - - +
149A SER 3.4 0.2 + - - -
150A ALA* 3.4 8.3 + - - +
156A LEU* 3.6 36.4 - - + +
159A VAL* 3.1 29.8 - - + -
160A ALA* 4.1 22.4 - - + +
163A THR* 3.7 14.8 - - + +
308A LEU* 4.8 9.9 - - + -
311A LEU* 4.4 22.7 - - + -
312A LEU* 4.4 13.7 - - + -
315A GLN* 4.1 11.8 + - + +
319A LYS* 5.2 1.0 - - - -
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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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144A MET 2.9 17.6 + - - +
145A PHE* 3.2 7.6 + - + +
147A LEU* 1.3 77.8 - - - +
149A SER* 1.3 59.9 + - - +
150A ALA 3.5 5.5 + - - +
315A GLN* 2.4 37.7 + - - +
319A LYS* 5.2 2.1 + - - -
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Residues in contact with SER 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 PHE 3.0 12.4 + - - -
146A ALA* 3.3 16.3 + - - +
147A LEU 3.3 0.4 - - - -
148A GLU* 1.3 76.7 - - - +
150A ALA* 1.3 65.9 + - - +
151A PRO* 3.2 9.2 - - - +
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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 3.3 11.2 + - - +
147A LEU 3.6 12.1 - - - +
148A GLU 3.3 4.7 - - - +
149A SER* 1.3 76.3 - - - +
151A PRO* 1.3 66.6 - - - +
152A ASN 3.4 0.4 - - - -
155A ALA* 3.9 5.8 - - + +
156A LEU* 3.5 40.2 - - + +
159A VAL* 4.4 6.5 - - + -
319A LYS* 3.1 22.3 + - - -
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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