Contacts of the helix formed by residues 409 - 417 (chain A) in PDB entry 1FCZ
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A TRP* 4.2 13.5 - - + +
231A SER* 4.0 16.8 - - - +
232A GLU* 5.2 1.3 - - - +
235A THR* 3.5 23.6 - - + +
407A PRO 3.8 2.7 - - - +
408A MET* 1.3 89.2 - - + +
410A PRO* 1.3 76.5 - - + +
411A LEU 3.4 0.7 - - - +
412A ILE* 3.0 25.9 + - + +
413A ARG* 3.0 17.5 + - - +
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Residues in contact with PRO 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 6.5 0.4 - - + -
408A MET 3.5 3.3 - - - +
409A PRO* 1.3 87.4 - - + +
411A LEU* 1.3 63.1 + - + +
413A ARG* 3.2 12.4 + - + +
414A GLU* 2.9 31.9 + - + +
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Residues in contact with LEU 411 (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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235A THR* 4.1 21.7 + - + +
238A ILE* 3.8 23.2 - - + +
239A ILE* 3.5 37.7 - - + -
409A PRO* 3.4 1.6 - - - +
410A PRO* 1.3 81.6 - - + +
412A ILE* 1.3 63.6 + - - +
414A GLU* 3.4 11.7 + - + +
415A MET* 3.1 22.7 + - - +
451A LMU 4.1 37.9 - - + +
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Residues in contact with ILE 412 (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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227A TRP* 4.8 0.4 - - + -
231A SER* 3.7 28.3 - - - +
234A ALA* 4.1 9.6 - - + -
235A THR* 4.0 7.0 - - - +
238A ILE* 3.9 20.0 - - + -
408A MET* 3.9 12.8 - - + -
409A PRO* 3.0 28.9 + - + +
411A LEU* 1.3 73.2 - - - +
413A ARG* 1.3 65.0 + - - +
415A MET* 3.1 8.5 + - + +
416A LEU* 3.0 38.1 + - + +
450A 156 3.8 36.8 - - + -
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Residues in contact with ARG 413 (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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401A LYS* 6.3 2.9 - - - -
407A PRO* 3.6 26.5 - - - +
408A MET* 3.2 30.9 + - + +
409A PRO 3.0 10.9 + - - +
410A PRO* 3.2 12.3 + - + +
412A ILE* 1.3 77.3 - - - +
414A GLU* 1.3 61.9 + - - +
416A LEU* 3.2 8.4 + - + +
417A GLU* 3.1 24.6 + - - +
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Residues in contact with GLU 414 (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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264A LYS* 2.7 56.7 + - - +
410A PRO* 2.9 19.9 + - + +
411A LEU* 3.5 20.0 - - + +
412A ILE 3.3 0.2 - - - -
413A ARG* 1.3 76.0 - - - +
415A MET* 1.3 63.1 + - - +
416A LEU 3.4 0.2 + - - -
417A GLU* 3.5 10.7 + - - +
451A LMU 4.2 21.0 - - + +
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Residues in contact with MET 415 (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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238A ILE* 4.1 11.4 - - + -
264A LYS 3.4 19.8 - - - +
267A CYS* 3.7 18.8 - - + -
268A LEU* 3.5 44.9 - - + +
271A LEU* 3.6 26.5 - - + -
411A LEU 3.1 10.3 + - - +
412A ILE* 3.1 17.0 + - + +
414A GLU* 1.3 80.9 - - - +
416A LEU* 1.3 66.4 + - + +
417A GLU 3.5 3.6 + - - +
450A 156 4.0 21.1 - - + -
451A LMU 3.8 18.1 - - + +
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Residues in contact with LEU 416 (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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268A LEU* 4.5 7.4 - - + -
394A ALA* 4.4 19.0 - - + +
397A ALA* 3.6 29.2 - - + -
401A LYS* 3.7 16.8 - - - +
408A MET* 4.0 7.4 - - - -
412A ILE* 3.0 37.6 + - + +
413A ARG* 3.2 8.2 + - + +
415A MET* 1.3 83.4 - - + +
417A GLU* 1.3 65.1 + - - +
450A 156 3.9 17.0 - - + -
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Residues in contact with GLU 417 (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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264A LYS* 3.9 28.3 + - - +
413A ARG 3.1 14.3 + - - +
414A GLU* 3.5 16.7 + - - +
415A MET 3.3 4.8 - - - +
416A LEU* 1.3 82.0 - - - +
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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