Contacts of the helix formed by residues 202 - 213 (chain E) in PDB entry 1PF7
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 THR 202 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E PHE 4.7 4.5 - - - +
201E GLU* 1.3 77.4 - - - +
203E VAL* 1.3 59.8 + - - +
204E ALA* 3.4 8.4 + - - +
205E GLU* 3.0 41.3 + - - +
206E CYS* 2.8 27.9 + - - +
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Residues in contact with VAL 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E THR* 1.3 74.1 - - - +
204E ALA* 1.3 56.6 - - - +
206E CYS* 3.4 8.0 - - - +
207E ARG* 3.0 63.0 + - - +
246E ILE* 3.4 9.6 - - - +
247E MET 3.9 5.8 - - - +
248E ASP* 3.4 22.9 - - + +
251E SER* 3.8 30.1 - - - +
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Residues in contact with ALA 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E THR* 3.1 7.9 + - - +
203E VAL* 1.3 77.2 - - - +
205E GLU* 1.3 65.7 + - + +
207E ARG* 3.2 10.0 + - - +
208E VAL* 3.1 26.4 + - + +
211E LYS* 5.5 0.3 + - - -
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Residues in contact with GLU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PHE 4.4 1.6 - - - +
201E GLU* 3.4 17.8 - - + +
202E THR* 3.0 41.9 + - - +
204E ALA* 1.3 74.5 - - + +
206E CYS* 1.3 66.4 + - - +
208E VAL* 3.0 16.4 + - + +
209E LEU* 3.0 30.5 + - + +
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Residues in contact with CYS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E LEU* 3.7 2.9 - - - +
201E GLU* 4.1 17.4 - - - +
202E THR 2.8 18.4 + - - +
203E VAL* 3.4 7.6 - - - +
205E GLU* 1.3 75.8 - - - +
207E ARG* 1.3 61.2 + - - +
209E LEU* 3.5 10.0 + - - +
210E GLN* 3.2 17.5 + - - +
245E VAL* 3.0 47.1 - - - -
246E ILE* 3.0 32.3 - - + +
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Residues in contact with ARG 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E VAL* 3.0 32.7 + - - +
204E ALA* 3.6 8.7 - - - +
205E GLU 3.1 0.6 - - - -
206E CYS* 1.3 75.7 - - - +
208E VAL* 1.3 59.1 + - - +
210E GLN* 3.3 22.7 + - - +
211E LYS* 2.9 48.7 + - - +
246E ILE* 2.5 30.2 + - - +
247E MET* 2.8 44.6 - - - +
248E ASP* 3.4 20.8 + - - -
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Residues in contact with VAL 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E LEU* 6.1 0.4 - - + -
204E ALA* 3.1 17.5 - - + +
205E GLU* 3.0 14.5 + - + +
207E ARG* 1.3 73.3 - - - +
209E LEU* 1.3 75.9 + - + +
211E LYS* 3.3 18.0 + - + +
212E LEU* 2.9 49.6 + - + +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E LEU* 3.7 13.9 - - + -
138E LEU* 3.9 27.1 - - + -
193E VAL* 3.9 17.5 - - + -
195E VAL* 4.4 7.2 - - + -
201E GLU* 3.9 27.6 - - + -
205E GLU* 3.0 24.0 + - + +
206E CYS* 3.5 8.7 - - - +
208E VAL* 1.3 89.5 - - + +
210E GLN* 1.3 57.8 + - - +
212E LEU* 3.4 11.2 - - + +
214E ALA* 3.0 29.1 + - - +
217E VAL* 4.0 18.8 - - + -
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E LEU* 3.4 22.8 - - + +
122E PRO* 5.7 1.4 - - - +
206E CYS 3.2 4.6 + - - +
207E ARG* 3.3 25.3 - - - +
209E LEU* 1.3 75.8 - - - +
211E LYS* 1.3 62.7 + - + +
212E LEU 3.0 4.7 - - - -
213E GLY* 3.0 17.8 + - - -
214E ALA 3.9 13.8 - - - +
246E ILE* 2.8 60.2 - - - +
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Residues in contact with LYS 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E ALA 5.5 0.2 + - - -
207E ARG* 2.9 44.1 + - - +
208E VAL* 3.4 21.1 - - + +
210E GLN* 1.3 78.2 - - + +
212E LEU* 1.3 66.5 + - + +
213E GLY* 3.1 2.0 + - - -
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ILE* 3.6 23.8 - - + +
138E LEU* 4.6 20.0 - - + -
193E VAL* 5.5 1.1 - - + -
208E VAL* 2.9 40.9 + - + +
209E LEU* 3.4 18.4 - - + +
210E GLN 3.0 0.4 - - - -
211E LYS* 1.3 86.6 - - + +
213E GLY* 1.3 59.2 - - - +
214E ALA* 5.2 0.2 - - + -
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Residues in contact with GLY 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ILE* 4.3 3.1 - - - -
191E THR* 3.7 16.5 + - - +
210E GLN 3.0 12.3 + - - -
211E LYS 3.1 2.0 - - - -
212E LEU* 1.3 81.0 - - - +
214E ALA* 1.3 63.7 + - - +
215E ASP* 3.8 6.2 + - - +
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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