Contacts of the helix formed by residues 143 - 154 (chain F) in PDB entry 5ZRV
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 GLN 143 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F ILE 2.8 12.7 + - - -
140F SER* 2.8 7.5 + - - +
142F ASN* 1.3 75.4 - - - +
144F ALA* 1.3 64.5 + - - +
145F MET 3.4 0.4 - - - -
146F THR* 3.5 4.2 + - - +
147F THR* 3.2 18.9 + - - -
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ILE 5.6 4.0 - - - -
103F PHE 5.5 7.2 - - - -
140F SER 3.1 10.6 + - - -
141F ALA* 4.9 2.7 - - - +
142F ASN 3.5 3.4 - - - +
143F GLN* 1.3 76.8 - - - +
145F MET* 1.3 58.2 + - - +
147F THR* 3.5 1.0 + - - -
148F GLY* 3.0 25.1 + - - -
162F ALA* 5.3 13.0 - - - +
163F GLY 5.9 2.2 - - - +
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Residues in contact with MET 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ASN* 4.4 10.6 - - - +
143F GLN 3.4 0.2 - - - -
144F ALA* 1.3 75.5 - - - +
146F THR* 1.3 57.6 + - - +
148F GLY* 3.7 1.9 - - - +
149F VAL* 2.9 25.3 + - - -
162F ALA* 5.5 4.6 - - - +
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Residues in contact with THR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ASN 5.1 2.8 + - - -
143F GLN* 3.5 8.7 + - - +
144F ALA 3.2 0.8 - - - -
145F MET* 1.3 75.2 - - - +
147F THR* 1.3 59.9 + - - +
149F VAL* 3.4 1.1 + - - +
150F GLY* 3.0 23.2 + - - -
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Residues in contact with THR 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F GLN 3.2 14.8 + - - -
144F ALA 4.0 1.3 - - - -
146F THR* 1.3 75.8 - - - +
148F GLY* 1.3 57.3 + - - +
150F GLY* 3.4 2.6 + - - +
151F LEU* 2.9 23.6 + - - -
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Residues in contact with GLY 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ALA 3.0 15.6 + - - -
145F MET* 3.7 4.0 - - - -
146F THR 3.2 0.2 - - - -
147F THR* 1.3 75.7 - - - +
149F VAL* 1.3 58.6 + - - +
151F LEU* 3.0 3.4 + - - -
152F ILE* 2.9 24.8 + - - -
160F ILE* 6.1 4.9 - - - -
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Residues in contact with VAL 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F MET 2.9 16.8 + - - -
146F THR* 3.4 2.0 + - - +
148F GLY* 1.3 75.5 - - - +
150F GLY* 1.3 56.9 + - - +
152F ILE* 3.9 2.0 - - - +
153F ALA* 2.9 27.0 + - - -
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Residues in contact with GLY 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F THR 3.0 15.3 + - - -
147F THR* 3.7 4.3 - - - -
149F VAL* 1.3 78.2 - - - +
151F LEU* 1.3 59.9 + - - +
153F ALA* 4.7 0.4 - - - -
154F SER* 3.2 19.1 + - - -
150H GLY* 4.3 25.8 - - - +
151H LEU* 6.1 0.4 - - - -
154H SER* 6.2 2.5 - - - -
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Residues in contact with LEU 151 (chain F).
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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147F THR 2.9 15.8 + - - -
148F GLY* 3.0 5.3 + - - -
150F GLY* 1.3 77.8 - - - +
152F ILE* 1.3 62.6 + - - +
154F SER* 3.9 4.9 + - - -
155F GLY 4.1 4.0 + - - -
156F GLN* 4.4 6.2 + - - -
157F CYS* 4.7 4.9 + - - -
150H GLY* 6.1 0.7 - - - -
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Residues in contact with ILE 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F GLY 2.9 13.2 + - - -
149F VAL* 3.9 2.2 - - - +
151F LEU* 1.3 74.5 - - - +
153F ALA* 1.3 52.5 + - - +
154F SER 3.1 4.5 - - - -
155F GLY* 2.7 29.1 + - - -
156F GLN 4.4 0.5 + - - -
157F CYS 5.3 9.9 - - - +
158F ASP 6.6 0.2 - - - -
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ARG* 5.2 14.1 + - - +
149F VAL 2.9 16.7 + - - -
150F GLY* 4.1 0.7 - - - -
152F ILE* 1.3 74.0 - - - +
154F SER* 1.3 61.1 + - - +
155F GLY* 3.1 1.1 + - - -
153H ALA 5.6 2.0 - - - +
154H SER* 6.0 4.7 - - - -
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Residues in contact with SER 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F GLY 3.2 15.7 + - - -
151F LEU 3.9 3.6 + - - -
152F ILE 3.1 2.0 + - - -
153F ALA* 1.3 76.5 - - - +
155F GLY* 1.3 63.9 + - - +
156F GLN 3.6 1.1 - - - -
150H GLY* 6.1 3.1 - - - -
153H ALA 6.0 4.3 - - - -
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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