Contacts of the helix formed by residues 139 - 155 (chain U) in PDB entry 5MQF
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 139 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138U PHE* 3.8 28.5 - - - +
140U LEU* 3.8 30.1 - - - +
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Residues in contact with LEU 140 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139U SER* 3.8 29.4 - - - +
141U HIS* 3.8 25.6 - - - +
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Residues in contact with HIS 141 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140U LEU* 3.8 25.8 - - - +
142U GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141U HIS* 3.8 28.5 - - - +
143U GLN* 3.8 25.6 - - - +
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Residues in contact with GLN 143 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142U GLU* 3.8 29.2 - - - +
144U THR* 3.8 25.6 - - - +
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Residues in contact with THR 144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143U GLN* 3.8 25.8 - - - +
145U VAL* 3.8 28.0 - - - +
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Residues in contact with VAL 145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144U THR* 3.8 25.6 - - - +
146U LEU* 3.8 28.3 - - - +
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Residues in contact with LEU 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145U VAL* 3.8 28.7 - - - +
147U LEU* 3.8 26.0 - - - +
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Residues in contact with LEU 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146U LEU* 3.8 25.4 - - - +
148U LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U LEU* 3.8 29.2 - - - +
149U PHE* 3.8 26.5 - - - +
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Residues in contact with PHE 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U LEU* 3.8 26.0 - - - +
150U LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U PHE* 3.8 29.2 - - - +
151U ASP* 3.8 25.1 - - - +
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Residues in contact with ASP 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U LEU* 3.8 25.1 - - - +
152U HIS* 3.8 29.6 - - - +
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Residues in contact with HIS 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151U ASP* 3.8 29.6 - - - +
153U CYS* 3.8 26.0 - - - +
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Residues in contact with CYS 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152U HIS* 3.8 26.5 - - - +
154U PHE* 3.8 28.9 - - - +
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Residues in contact with PHE 154 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153U CYS* 3.8 28.7 - - - +
155U ASN* 3.8 25.1 - - - +
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Residues in contact with ASN 155 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154U PHE* 3.8 28.9 - - - +
156U SER* 3.8 25.8 - - - +
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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