Contacts of the helix formed by residues 200 - 205 (chain A) in PDB entry 2CFZ
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 PHE 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A TYR* 3.4 40.6 - + + -
169A HIS 3.7 4.3 - - - -
170A ALA* 3.6 33.3 - - + +
175A PHE* 3.7 23.6 - + + -
196A ALA* 3.7 20.2 - - + -
197A PRO* 3.0 23.2 + - + +
199A GLY* 1.3 76.9 - - - +
201A MET* 1.3 69.9 + - - +
203A ALA 3.2 1.0 + - - -
204A ALA* 2.8 35.5 + - + +
250A LEU* 3.7 20.4 - - + -
253A PRO* 3.6 19.7 - - + -
256A LEU* 4.5 3.4 - - + +
283A ALA* 3.7 7.6 - - - +
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Residues in contact with MET 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLY 3.4 0.8 - - - -
200A PHE* 1.3 88.4 - - - +
202A GLU* 1.3 68.1 + - - +
204A ALA* 3.5 11.6 + - - +
205A ILE* 3.7 12.3 + - - +
250A LEU* 4.6 10.8 - - + -
252A ALA* 3.9 23.3 - - + +
253A PRO* 3.6 32.3 - - + -
256A LEU* 5.8 1.5 - - + +
537A ALA* 3.6 42.4 - - + +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLY* 3.7 9.1 + - - +
200A PHE 3.4 0.2 - - - -
201A MET* 1.3 79.6 - - - +
203A ALA* 1.3 66.0 + - + +
204A ALA 3.1 0.9 + - - -
205A ILE* 4.1 0.9 - - - +
206A LYS* 2.9 56.5 + - + +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA* 3.6 23.2 - - + +
171A HIS* 5.6 1.2 - - - -
199A GLY 3.1 16.8 + - - +
202A GLU* 1.3 82.9 - - + +
204A ALA* 1.3 63.4 + - - +
205A ILE 3.3 1.4 + - - -
206A LYS* 4.2 6.1 + - - +
207A GLU* 4.8 8.1 + - - +
208A ASN* 4.9 2.1 + - - -
282A PRO* 4.0 35.7 - - + +
283A ALA* 4.0 7.4 - - + +
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA* 3.7 12.8 - - - +
175A PHE* 3.8 31.7 - - + -
200A PHE* 2.8 37.7 + - + +
201A MET 3.7 6.7 - - - +
202A GLU 3.1 0.6 + - - -
203A ALA* 1.3 73.8 - - - +
205A ILE* 1.3 63.7 + - + +
208A ASN* 3.5 15.8 + - - -
250A LEU* 4.3 11.9 - - + -
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 5.2 4.0 - - + -
201A MET 4.0 7.2 - - - +
202A GLU* 3.2 4.3 + - - +
204A ALA* 1.3 88.3 - - + +
206A LYS* 1.3 67.1 + - - +
207A GLU 3.4 2.0 - - - -
208A ASN* 3.2 18.1 + - - +
209A VAL* 3.5 24.6 - - + +
248A LEU* 5.8 0.4 - - + -
250A LEU* 4.3 9.0 - - + -
534A ALA* 3.5 32.3 - - + +
537A ALA* 3.6 31.2 - - + +
538A MET* 3.9 29.6 - - + -
542A LEU* 4.2 3.6 - - + -
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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