Contacts of the helix formed by residues 144 - 151 (chain F) in PDB entry 4OZH
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 144 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E TYR* 3.7 24.5 - - - +
139E GLN 3.4 26.7 + - - -
140E LEU* 4.0 6.6 - - - +
141E ARG 6.1 0.2 - - - +
217E PRO* 5.4 0.5 - - - +
142F GLU 3.8 0.8 + - - -
143F PRO* 1.3 74.0 - - - +
145F GLU* 1.3 64.6 + - - +
146F ALA* 3.3 20.3 + - - +
147F GLU* 3.3 19.1 + - - +
148F ILE* 3.4 15.7 + - - +
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Residues in contact with GLU 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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143F PRO 3.8 2.4 + - - -
144F SER* 1.3 73.1 + - - +
146F ALA* 1.4 60.8 + - - +
148F ILE* 3.4 24.8 + - - +
149F SER* 3.2 32.6 + - - +
215F GLN* 5.6 1.2 + - - -
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Residues in contact with ALA 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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138E TYR* 3.9 6.8 - - + -
215E PHE* 4.6 5.1 - - + -
217E PRO* 3.7 35.4 - - + -
144F SER* 3.3 11.6 + - - +
145F GLU* 1.4 76.4 - - - +
147F GLU* 1.4 57.0 + - - +
149F SER* 4.0 6.0 - - - -
150F HIS* 3.1 30.8 + - - +
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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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138E TYR* 3.6 43.7 - - + +
140E LEU* 5.2 2.1 - - - +
152E LEU* 4.7 5.0 - - - +
154E THR* 5.2 0.2 - - - -
143F PRO* 4.4 4.0 - - - +
144F SER* 3.3 16.7 + - - +
146F ALA* 1.4 75.5 - - - +
148F ILE* 1.4 58.7 - - + +
151F THR* 3.0 42.2 + - + +
152F GLN 3.6 0.5 + - - -
153F LYS 3.2 19.3 - - - +
154F ALA* 4.2 0.4 - - - -
155F THR* 2.6 46.0 + - - +
208F ARG* 3.3 18.2 + - - +
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Residues in contact with ILE 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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143F PRO* 4.4 8.5 - - + +
144F SER 3.4 21.3 + - - +
145F GLU* 3.4 23.5 + - - +
147F GLU* 1.4 74.2 - - - +
149F SER* 1.3 56.8 + - - +
152F GLN* 3.1 36.4 + - - +
153F LYS 3.8 8.7 - - - +
154F ALA* 4.1 20.6 - - + -
211F ALA* 3.8 14.6 - - + -
214F TRP* 3.7 31.2 - - + +
215F GLN* 3.8 27.1 - - + +
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Residues in contact with SER 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 GLU* 3.2 25.3 + - - +
146F ALA* 4.0 6.5 - - - -
148F ILE* 1.3 78.1 - - - +
150F HIS* 1.3 61.8 + - - +
152F GLN* 4.5 11.6 + - - +
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Residues in contact with HIS 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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134E ASP* 2.8 43.1 + - + +
136E ALA* 5.5 0.7 - - + -
138E TYR* 3.8 20.4 - - - +
215E PHE* 4.5 35.2 - + + +
146F ALA 3.1 19.5 + - - +
147F GLU 4.1 0.2 - - - +
149F SER* 1.3 79.1 - - - +
151F THR* 1.3 63.5 + - - +
152F GLN* 3.5 1.8 + - - +
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Residues in contact with THR 151 (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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134E ASP* 5.4 4.9 + - - +
138E TYR* 4.6 5.4 - - - +
155E ASP* 3.5 18.8 + - - -
147F GLU* 3.0 33.2 + - + +
150F HIS* 1.3 80.5 - - - +
152F GLN* 1.4 67.4 + - - +
153F LYS* 3.1 34.6 + - + +
208F ARG* 3.4 23.3 - - - +
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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