Contacts of the helix formed by residues 144 - 155 (chain F) in PDB entry 4Q9U
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 ASP 144 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143F VAL* 1.3 88.1 - - - +
145F PHE* 1.3 63.8 + - - +
146F GLN* 4.0 9.2 - - + +
147F GLU* 3.3 30.4 + - + +
148F ALA* 3.3 5.7 + - - +
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Residues in contact with PHE 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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100F TYR* 5.6 0.4 - - - -
143F VAL 3.5 4.0 + - - -
144F ASP* 1.3 69.5 - - - +
146F GLN* 1.3 64.9 + - + +
148F ALA* 3.1 6.7 + - + +
149F GLN* 2.8 66.4 + - + +
159F PHE* 3.3 25.4 - + - -
160F MET* 5.7 0.7 - - - -
161F GLU* 3.3 44.2 - - + +
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Residues in contact with GLN 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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144F ASP* 3.2 10.0 - - + +
145F PHE* 1.3 83.4 - - + +
147F GLU* 1.3 56.3 + - - +
149F GLN* 3.9 7.1 - - - +
150F SER* 2.9 52.0 + - - +
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Residues in contact with GLU 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 VAL* 3.9 18.2 - - + +
144F ASP* 3.3 23.4 + - + +
145F PHE 3.1 0.2 - - - -
146F GLN* 1.3 77.9 - - - +
148F ALA* 1.3 60.0 + - - +
150F SER* 3.3 5.5 + - - -
151F TYR* 3.0 29.9 + - + +
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Residues in contact with ALA 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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100F TYR* 3.7 26.5 - - + +
108F PHE* 4.9 11.4 - - + -
130F LEU* 5.3 3.1 - - + +
143F VAL* 5.0 1.7 - - + +
144F ASP 3.3 9.0 + - - +
145F PHE* 3.1 11.3 + - + +
147F GLU* 1.3 79.0 - - - +
149F GLN* 1.3 58.2 + - - +
151F TYR* 3.5 8.4 + - - +
152F ALA* 2.9 27.4 + - - +
159F PHE* 4.2 12.6 - - + -
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Residues in contact with GLN 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 PHE* 2.8 53.7 + - + +
146F GLN* 4.0 9.4 - - - +
148F ALA* 1.3 76.7 - - - +
150F SER* 1.3 59.7 + - - +
151F TYR 3.3 0.2 - - - -
152F ALA* 3.8 3.2 - - - +
153F ASP* 2.9 64.4 + - - +
159F PHE* 3.1 30.5 + - - +
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Residues in contact with SER 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 GLN* 2.9 41.9 + - - +
147F GLU* 3.6 6.7 - - - -
149F GLN* 1.3 75.7 - - - +
151F TYR* 1.3 62.2 + - - +
153F ASP* 3.9 2.0 - - - +
154F ASP* 2.8 35.7 + - - +
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Residues in contact with TYR 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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111F ALA 6.0 0.4 - - - -
112F LYS* 3.2 57.3 + - + +
115F VAL* 5.6 9.5 - - + +
116F LYS* 4.0 12.7 + - - +
130F LEU* 5.9 6.5 - - + -
147F GLU* 3.0 14.4 + - + +
148F ALA* 3.5 11.9 - - - +
150F SER* 1.3 75.6 - - - +
152F ALA* 1.3 64.4 + - - +
154F ASP* 3.3 20.6 + - + +
155F ASN* 3.4 31.0 + - + +
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Residues in contact with ALA 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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130F LEU* 5.0 6.7 - - + -
148F ALA 2.9 18.5 + - - +
149F GLN* 3.8 16.4 - - - +
150F SER 3.3 0.2 - - - -
151F TYR* 1.3 80.4 - - - +
153F ASP* 1.3 58.9 + - - +
155F ASN* 3.3 6.5 + - - +
156F SER* 3.0 27.5 + - - -
159F PHE* 4.0 27.1 - - + -
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Residues in contact with ASP 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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149F GLN* 2.9 45.3 + - - +
150F SER* 4.4 2.2 - - - +
152F ALA* 1.3 74.2 - - - +
154F ASP* 1.3 65.7 + - - +
155F ASN 3.1 1.7 + - - -
156F SER* 3.5 17.3 + - - +
159F PHE* 6.1 0.3 - - - +
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Residues in contact with ASP 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 SER* 2.8 32.1 + - - +
151F TYR* 3.3 11.9 - - + +
152F ALA 3.3 0.4 - - - -
153F ASP* 1.3 78.3 - - - +
155F ASN* 1.3 66.9 + - - +
156F SER* 4.0 1.2 + - - -
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Residues in contact with ASN 155 (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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115F VAL* 6.1 4.5 - - + -
119F GLN* 3.8 32.4 + - - +
151F TYR* 3.4 35.2 + - + +
152F ALA* 3.3 6.8 + - - +
153F ASP 3.1 0.4 - - - -
154F ASP* 1.3 88.5 - - - +
156F SER* 1.3 68.3 + - - +
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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