Contacts of the strand formed by residues 422 - 426 (chain H) in PDB entry 4P0S
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 GLN 422 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392G GLN* 3.8 34.3 + - - +
396G GLY 5.4 1.8 + - - -
397G PHE 4.1 11.9 + - - -
398G PHE* 3.4 23.4 - - - +
399G VAL 3.3 29.8 + - - +
359H LEU 2.9 20.2 + - - +
360H SER* 3.5 15.4 + - - +
361H LEU* 2.8 28.8 + - - +
415H LEU* 6.1 0.7 - - - +
420H GLU 5.2 3.2 + - - -
421H ALA* 1.3 76.0 + - - +
423H ALA* 1.3 69.8 + - - +
424H GLN* 6.1 0.7 - - + +
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Residues in contact with ALA 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G PHE* 3.5 22.1 - - + -
399G VAL 4.1 13.5 - - - +
400G LYS* 4.3 13.6 + - - +
361H LEU* 3.7 10.1 - - + +
363H ILE* 6.4 0.7 - - + -
412H LEU* 4.2 31.6 - - + +
415H LEU* 5.5 6.7 - - + -
421H ALA 5.4 0.2 - - - +
422H GLN* 1.3 84.9 - - - +
424H GLN* 1.3 66.8 + - - +
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Residues in contact with GLN 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G GLN* 4.1 7.1 - - - +
399G VAL 5.4 2.5 - - - +
400G LYS* 4.8 8.3 - - - +
401G ARG* 2.9 32.0 + - - +
360H SER* 6.3 0.2 - - - -
361H LEU 3.6 12.7 + - - +
362H VAL* 4.2 9.9 - - + +
363H ILE* 3.8 21.0 + - - +
412H LEU* 5.5 1.1 - - - -
422H GLN* 6.1 0.6 - - - +
423H ALA* 1.3 79.1 - - - +
425H ILE* 1.3 71.9 + - - +
426H VAL* 4.4 16.6 - - + +
435H PHE* 3.2 46.2 - - - +
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Residues in contact with ILE 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400G LYS* 5.8 3.3 - - - +
321H PHE* 6.2 0.9 - - + -
363H ILE* 4.3 17.0 - - + +
365H ASP* 5.5 2.0 - - + -
369H CYS* 4.0 33.4 - - + +
370H PHE* 4.3 31.7 - - + +
405H ARG* 5.5 1.1 - - - +
408H ALA* 5.9 4.9 - - + -
409H GLU* 3.5 25.4 - - - +
412H LEU* 3.9 25.1 - - + -
424H GLN* 1.3 84.2 + - - +
426H VAL* 1.3 72.3 + - - +
427H GLN* 4.1 1.1 + - + +
431H GLU* 4.1 4.5 - - - +
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Residues in contact with VAL 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H VAL* 3.3 28.9 - - + -
363H ILE 2.8 44.4 + - - +
364H VAL* 3.8 10.8 - - + -
365H ASP* 3.3 13.5 + - - +
424H GLN* 4.1 16.3 + - - +
425H ILE* 1.3 80.1 - - - +
427H GLN* 1.3 62.0 + - - +
428H SER 4.6 5.8 - - - +
431H GLU* 3.3 36.1 - - + +
432H LEU* 4.7 7.2 - - + -
435H PHE* 5.4 6.1 - - + -
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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