Contacts of the helix formed by residues 421 - 426 (chain F) in PDB entry 6CP3
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 ALA 421 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165F VAL* 4.2 8.9 - - + +
418F PHE* 3.7 15.6 + - + +
420F VAL* 1.3 74.5 - - - +
422F GLU* 1.3 62.4 + - - +
423F VAL 3.2 3.4 + - - -
424F PHE* 3.4 27.3 + - + +
425F THR* 3.6 15.1 + - + +
600F ADP 3.5 41.7 - - + +
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Residues in contact with GLU 422 (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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418F PHE 3.8 5.5 + - - +
419F ALA* 3.9 18.4 - - - +
420F VAL 3.2 4.3 + - - +
421F ALA* 1.3 77.2 - - - +
423F VAL* 1.3 63.0 + - + +
425F THR* 4.6 0.2 - - - -
426F GLY* 3.0 28.7 + - - -
427F ILE 3.3 25.3 + - - +
428F PRO* 3.6 26.6 - - + +
429F GLY 4.7 2.2 + - - -
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Residues in contact with VAL 423 (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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375B ARG 5.4 4.5 - - - +
378B SER* 4.3 28.4 + - - +
420F VAL 5.1 5.6 - - - +
421F ALA 4.9 0.4 - - - -
422F GLU* 1.3 81.9 - - + +
424F PHE* 1.3 83.9 - - + +
426F GLY* 4.4 3.3 + - - +
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Residues in contact with PHE 424 (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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373B VAL* 4.4 11.4 - - + -
374B SER 3.5 22.4 - - - -
375B ARG* 3.9 25.6 - - + -
393B LYS* 4.6 18.5 - - + +
394B LEU* 5.1 6.8 - - - +
165F VAL* 5.5 6.5 - - + -
420F VAL 5.5 0.7 - - - -
421F ALA* 3.4 29.1 + - + +
422F GLU 3.3 0.4 - - - -
423F VAL* 1.3 93.6 - - + +
425F THR* 1.3 60.8 + - + +
426F GLY 3.6 0.4 - - - -
600F ADP 3.7 54.3 - + + -
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Residues in contact with THR 425 (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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394B LEU* 3.9 29.1 - - + +
345F TYR* 5.9 0.4 - - + -
417F PRO* 4.9 6.4 - - + +
418F PHE 5.7 0.7 + - - -
421F ALA 3.6 16.2 + - - +
422F GLU* 4.2 0.3 + - - -
424F PHE* 1.3 78.9 - - + +
426F GLY* 1.3 63.4 + - - +
427F ILE* 3.3 36.8 + - - +
458F TYR* 5.9 0.2 - - - +
459F MET* 4.5 22.4 - - + -
600F ADP 4.2 21.5 - - + +
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Residues in contact with GLY 426 (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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394B LEU* 5.8 0.9 - - - -
422F GLU* 3.0 17.5 + - - -
423F VAL* 4.4 2.8 + - - -
424F PHE 3.6 1.4 - - - -
425F THR* 1.3 77.6 - - - +
427F ILE* 1.3 60.5 + - - +
428F PRO* 4.0 5.5 - - - +
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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