Contacts of the helix formed by residues 152 - 155 (chain F) in PDB entry 4CEV
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 PRO 152 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F GLY 3.4 4.9 - - - +
151F HIS* 1.3 100.6 - - + +
153F ALA* 1.3 63.0 + - - +
155F THR* 3.2 13.7 - - - +
156F GLN* 3.0 38.7 + - + +
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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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68F LEU* 4.0 19.7 - - + -
72F ALA* 3.7 13.4 - - + +
151F HIS* 2.8 28.2 + - + +
152F PRO* 1.3 79.4 - - - +
154F LEU* 1.3 58.6 + - - +
157F ILE* 3.2 25.2 + - - +
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Residues in contact with LEU 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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65F LEU* 4.4 13.5 - - + -
68F LEU* 3.6 31.9 - - + -
71F VAL* 4.5 10.5 - - + -
72F ALA* 4.1 17.5 - - + -
75F ASN* 5.1 0.4 - - - +
103F ILE* 3.6 37.9 - - + +
138F ILE* 4.0 22.9 - - + -
141F MET* 4.8 6.7 - - + -
145F ALA* 4.1 13.9 - - + +
151F HIS* 2.8 15.1 + - + +
153F ALA* 1.3 82.3 - - - +
155F THR* 1.3 62.2 + - - +
156F GLN 3.3 1.8 - - - -
157F ILE* 3.2 19.4 + - + +
163F LYS* 4.5 1.9 + - - -
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Residues in contact with THR 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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145F ALA* 3.6 25.8 - - + +
148F GLY* 3.8 17.0 - - - +
149F PHE 3.8 1.3 - - - -
150F GLY* 3.5 39.1 + - - +
151F HIS 2.9 6.0 + - - +
152F PRO* 3.2 19.9 - - - +
154F LEU* 1.3 76.5 - - - +
156F GLN* 1.3 70.7 + - - +
161F SER* 3.2 14.9 - - - -
163F LYS* 2.8 20.2 + - - +
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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