Contacts of the strand formed by residues 419 - 425 (chain F) in PDB entry 5IJ7
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 SER 419 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ASP* 5.4 0.4 - - - -
73F SER* 4.7 1.6 - - - -
74F LEU 3.1 9.9 - - - -
75F LYS* 4.3 10.1 - - - +
82F LEU* 4.0 0.9 - - - +
413F ALA 3.8 0.5 - - - +
414F VAL* 3.4 4.9 - - - -
415F CYS* 2.9 32.8 + - - +
417F ASP* 2.7 29.1 + - - -
418F ALA* 1.4 76.9 - - - +
420F ILE* 1.3 63.7 + - - +
421F TRP* 2.8 33.2 + - - -
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Residues in contact with ILE 420 (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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72F ASN 4.0 0.5 - - - +
73F SER* 3.1 8.7 + - - -
74F LEU* 2.8 52.2 + - + +
76F GLU* 3.8 16.6 - - + +
82F LEU* 3.8 15.0 - - + -
99F PHE* 3.9 17.0 - - + -
101F THR* 4.5 2.5 - - - +
110F TYR* 3.4 41.1 - - + +
118F ILE* 4.8 5.2 - - + -
412F ILE* 3.7 29.6 - - + -
413F ALA 3.5 3.6 - - - +
414F VAL* 4.2 5.8 - - + -
418F ALA 4.8 0.2 - - - +
419F SER* 1.3 75.7 - - - +
421F TRP* 1.3 63.0 + - - +
422F ARG 4.2 0.4 - - - -
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Residues in contact with TRP 421 (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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88B ASP* 4.8 4.5 - - + -
89B LEU* 5.0 0.7 - - + -
70F CYS* 3.7 19.3 - - - -
72F ASN 3.6 2.5 - - - -
73F SER* 3.2 36.6 - - - -
392F HIS* 3.7 26.5 - + + -
394F LYS* 3.3 45.3 - - + -
395F CYS* 3.5 27.5 - - + -
411F LEU 3.5 2.3 - - - +
412F ILE* 3.4 8.4 - - - -
413F ALA* 2.8 39.6 + - + +
415F CYS* 3.6 15.9 - - - -
417F ASP* 5.7 1.8 - - - -
419F SER* 2.8 30.6 + - - -
420F ILE* 1.3 76.7 - - - +
422F ARG* 1.3 60.3 + - - +
423F TRP* 3.6 19.9 - + - +
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Residues in contact with ARG 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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70F CYS* 3.4 5.9 - - - -
71F VAL* 2.9 37.3 + - + +
72F ASN 2.8 19.0 + - - +
112F CYS* 4.0 6.0 - - - +
113F HIS 2.8 36.1 + - - +
114F SER* 4.9 1.6 - - - +
116F GLY* 3.1 19.0 + - - +
117F GLU 2.9 19.4 + - - -
118F ILE* 3.7 29.3 - - + +
410F ILE* 3.5 28.2 - - + +
412F ILE* 3.7 18.2 - - + -
420F ILE 4.2 0.6 - - - -
421F TRP* 1.3 70.2 - - - +
423F TRP* 1.3 60.5 + - - +
424F ASP* 2.8 35.5 + - - +
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Residues in contact with TRP 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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68F PHE* 3.6 26.3 - - + -
69F LYS* 3.4 8.3 - - - -
70F CYS* 3.4 46.0 - - + -
372F LEU* 3.6 28.4 - - + +
390F LEU* 3.5 31.2 - - + -
391F THR* 3.2 43.3 - - - -
392F HIS* 4.4 5.2 - - + -
395F CYS* 6.0 4.0 - - + -
410F ILE* 3.7 1.0 - - - -
411F LEU* 2.8 47.1 + - + +
413F ALA* 4.9 0.9 - - + +
421F TRP* 3.6 31.4 - + + +
422F ARG* 1.3 76.8 - - - +
424F ASP* 1.3 65.3 + - - +
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Residues in contact with ASP 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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68F PHE* 3.2 4.0 - - - -
69F LYS* 2.8 43.4 + - + +
71F VAL* 3.3 22.8 - - + +
116F GLY 5.5 0.9 + - - -
409F SER 3.7 2.4 - - - +
410F ILE* 3.7 14.2 - - - +
422F ARG* 2.8 46.9 + - - +
423F TRP* 1.3 73.9 - - - +
425F ARG* 1.3 63.3 + - - +
426F LEU* 3.6 14.5 + - + +
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Residues in contact with ARG 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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67F SER* 3.2 18.2 + - - +
68F PHE* 3.5 33.5 - - + -
362F MET* 3.5 49.1 - - - +
407F ASP 5.7 0.7 - - - -
408F SER* 3.5 22.8 + - - -
409F SER* 2.8 30.3 + - - +
424F ASP* 1.3 71.7 - - - +
426F LEU* 1.3 71.4 + - - +
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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