Contacts of the helix formed by residues 142 - 148 (chain R) in PDB entry 6CNF
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 MET 142 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131R TYR* 4.9 4.5 - - - +
135R ARG* 6.2 2.0 - - - -
141R HIS* 1.3 78.4 - - - +
143R LEU* 1.3 65.6 + - + +
144R ILE* 3.3 30.3 - - + +
145R ASP* 3.2 18.5 + - + +
146R PHE* 2.4 40.7 + - - +
181R PHE* 4.8 8.5 - - + -
185R PHE* 5.8 5.8 - - + -
219R ARG* 2.9 50.0 - - - +
513R PRO* 6.1 2.9 - - + -
514R GLU* 4.2 11.9 - - + -
408S TYR* 3.4 13.7 - - - +
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Residues in contact with LEU 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127R ALA 6.5 0.4 - - - -
131R TYR* 3.5 61.5 - - + +
142R MET* 1.3 81.1 - - + +
144R ILE* 1.3 59.2 + - - +
145R ASP 3.1 0.2 + - - -
146R PHE* 4.5 9.4 - - + -
147R SER* 2.5 43.6 + - - +
154R VAL* 5.1 8.3 - - + +
157R ILE* 5.6 7.6 - - + +
158R GLY* 4.4 25.4 - - - +
161R PHE* 5.4 4.0 - - + -
515R LEU* 5.3 15.7 - - + +
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Residues in contact with ILE 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142R MET* 3.3 18.6 - - + +
143R LEU* 1.3 76.2 - - - +
145R ASP* 1.3 65.6 + - + +
147R SER* 2.7 16.1 + - - -
148R SER* 3.3 11.8 + - - -
153R SER 5.2 0.7 - - - +
154R VAL* 3.4 32.0 - - + +
219R ARG* 4.9 0.2 - - - +
248R SER 5.3 2.9 - - - +
249R HIS* 4.7 16.4 - - + +
406S TYR* 4.7 5.6 - - + -
407S ASN 4.3 6.1 - - - +
408S TYR* 3.2 76.7 - - + +
410S SER 5.8 1.3 - - - +
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Residues in contact with ASP 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94R LEU* 5.6 7.3 - - - +
141R HIS* 5.6 2.4 - - - -
142R MET* 3.2 25.9 + - + +
143R LEU 3.1 0.6 - - - -
144R ILE* 1.3 80.5 - - + +
146R PHE* 1.3 59.4 + - - +
148R SER* 2.6 34.6 + - - -
149R ARG* 4.0 5.7 + - - +
184R HIS* 5.2 10.0 - - - -
185R PHE* 6.1 0.7 - - - -
188R LYS* 5.9 0.3 + - - -
249R HIS* 4.4 22.2 + - - +
406S TYR* 3.7 15.7 + - - -
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Residues in contact with PHE 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90R VAL* 4.9 22.0 - - + -
94R LEU* 3.3 37.9 - - + -
126R ILE* 5.1 0.9 - - + -
127R ALA* 3.4 50.5 - - + -
130R LEU* 3.4 31.6 - - + -
131R TYR* 5.0 8.7 - + + -
141R HIS* 5.5 4.3 - - + -
142R MET 2.4 34.6 + - - +
143R LEU* 3.9 14.1 - - + +
145R ASP* 1.3 67.3 - - - +
147R SER* 1.3 66.2 + - - +
149R ARG* 3.2 27.1 - - + +
157R ILE* 6.2 0.7 - - + -
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Residues in contact with SER 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127R ALA* 5.9 0.7 - - - -
143R LEU* 2.5 30.5 + - - -
144R ILE 2.7 15.1 + - - -
146R PHE* 1.3 81.5 - - - +
148R SER* 1.3 50.9 + - - -
149R ARG* 2.8 12.5 + - - +
150R LEU* 3.1 13.9 + - - +
152R VAL* 3.3 18.8 - - - +
154R VAL* 2.9 31.1 - - - +
157R ILE* 5.0 15.3 - - - +
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Residues in contact with SER 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B LEU* 3.6 11.0 - - - +
144R ILE* 3.4 10.8 - - - -
145R ASP 2.6 21.2 + - - -
147R SER* 1.3 69.8 + - - +
149R ARG* 1.3 55.1 + - - -
150R LEU 2.9 20.9 + - - +
154R VAL* 4.5 9.0 - - - -
406S TYR* 2.8 46.6 + - - -
411S TYR* 4.8 10.5 + - - -
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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