Contacts of the helix formed by residues 140 - 151 (chain A) in PDB entry 3QOW
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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLU 3.6 4.1 + - - -
139A THR* 1.3 78.6 - - - +
141A PHE* 1.3 64.6 + - - +
142A ASP* 3.7 9.2 + - - +
143A LEU* 3.2 20.7 + - - +
144A VAL* 3.2 20.7 + - - +
299A LEU* 5.4 0.9 - - - +
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Residues in contact with PHE 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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104A THR* 3.5 43.5 - - + -
107A LEU* 4.1 9.4 - - + -
108A ARG* 3.6 62.8 - - + +
111A LEU* 3.9 18.8 - - + -
139A THR 3.9 1.2 + - - -
140A SER* 1.3 71.1 - - - +
142A ASP* 1.3 61.3 + - - +
144A VAL* 3.3 1.4 + - - -
145A ALA* 2.8 33.1 + - + +
172A GLN* 3.3 43.1 + - + -
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Residues in contact with ASP 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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108A ARG* 2.9 35.3 + - - -
140A SER* 3.2 9.0 + - - +
141A PHE* 1.3 79.6 - - - +
143A LEU* 1.3 57.4 + - - +
145A ALA* 3.4 5.8 + - - +
146A GLN* 3.0 26.2 + - - +
299A LEU* 3.7 18.5 - - + +
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Residues in contact with LEU 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 THR* 3.4 26.5 - - + -
140A SER* 3.2 16.2 + - - +
142A ASP* 1.3 74.7 - - - +
144A VAL* 1.3 65.1 + - - +
146A GLN* 3.1 21.6 + - - +
147A MET* 2.9 21.8 + - + +
239A PHE* 4.5 6.3 - - + -
267A VAL* 5.4 2.2 - - + -
296A LEU* 5.1 4.7 - - + +
299A LEU* 3.8 13.1 - - + +
310A VAL 4.2 8.7 - - - +
312A TYR* 3.3 55.9 - - + +
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Residues in contact with VAL 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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139A THR* 3.7 18.2 - - + +
140A SER 3.2 15.9 + - - +
141A PHE* 3.6 1.6 - - - +
143A LEU* 1.3 75.6 - - - +
145A ALA* 1.3 57.1 - - - +
147A MET* 3.0 15.4 + - + +
148A ILE* 2.9 35.7 + - + +
168A GLN* 5.9 0.7 - - + +
169A VAL* 4.1 28.9 - - + -
172A GLN* 3.3 37.7 - - + +
173A VAL* 4.1 16.4 - - + -
239A PHE* 5.5 0.7 - - + -
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Residues in contact with ALA 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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104A THR* 5.2 6.5 - - + -
141A PHE* 2.8 34.3 + - + +
142A ASP* 3.7 6.7 - - - +
144A VAL* 1.3 73.1 - - - +
146A GLN* 1.3 58.2 + - - +
148A ILE* 3.3 8.7 + - + +
149A ASP* 2.8 40.0 + - - +
172A GLN* 3.4 13.4 - - - +
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Residues in contact with GLN 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 ASP 3.0 15.0 + - - +
143A LEU* 3.1 24.9 + - - +
145A ALA* 1.3 76.6 - - - +
147A MET* 1.3 61.8 + - - +
149A ASP* 3.6 8.0 - - + +
150A GLU* 3.0 52.3 + - + +
296A LEU* 4.2 12.7 - - + +
297A SER* 2.8 41.5 + - - +
298A PRO 5.1 0.2 + - - -
299A LEU* 3.7 28.5 - - + +
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Residues in contact with MET 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 LEU* 2.9 15.7 + - + +
144A VAL* 3.4 23.6 - - + +
146A GLN* 1.3 75.8 - - - +
148A ILE* 1.3 58.8 + - + +
150A GLU* 5.1 0.2 - - - -
151A ILE* 2.9 58.2 + - + +
153A MET* 5.2 0.7 - - + -
159A PHE* 3.8 29.4 - - + -
169A VAL* 4.3 2.5 - - + -
173A VAL* 4.1 15.3 - - + -
237A VAL* 5.4 0.4 - - - -
239A PHE* 3.6 32.5 - - + -
267A VAL* 3.8 24.0 - - + -
296A LEU* 4.8 10.9 - - + +
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Residues in contact with ILE 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 VAL* 2.9 22.6 + - + +
145A ALA* 3.6 7.9 - - + +
147A MET* 1.3 77.3 - - + +
149A ASP* 1.3 67.8 + - - +
151A ILE 3.0 19.8 - - - +
152A LYS* 4.5 4.9 - - - +
153A MET* 4.7 6.1 - - + -
172A GLN* 4.1 30.3 - - + +
173A VAL* 4.1 18.8 - - + -
176A ALA* 3.7 32.1 - - + +
177A THR* 3.8 25.1 - - + -
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Residues in contact with ASP 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 ALA* 2.8 28.8 + - - +
146A GLN* 3.3 9.2 + - + +
148A ILE* 1.3 76.1 - - - +
150A GLU* 1.3 63.8 + - + +
152A LYS* 3.4 24.4 + - - +
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Residues in contact with GLU 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 GLN* 3.0 44.3 + - - +
147A MET* 4.4 0.7 - - - +
149A ASP* 1.3 82.9 - - + +
151A ILE* 1.3 66.3 + - + +
152A LYS* 3.3 14.0 + - - +
296A LEU* 3.4 27.4 - - + +
297A SER* 4.8 9.4 + - - -
314A LEU* 6.4 1.3 - - + -
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Residues in contact with ILE 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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147A MET* 2.9 46.6 + - + +
148A ILE 3.0 13.6 - - - +
150A GLU* 1.3 74.0 - - + +
152A LYS* 1.3 60.4 + - - +
153A MET* 3.4 31.3 + - + +
237A VAL* 3.6 22.9 - - + -
265A ARG* 3.8 24.0 - - + +
267A VAL* 4.2 7.4 - - + -
296A LEU* 5.6 4.7 - - + -
314A LEU* 4.2 26.9 - - + -
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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