Contacts of the strand formed by residues 410 - 415 (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 ILE 410 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PHE* 5.1 0.2 - - - -
87F PHE* 3.8 22.4 - - + -
97F LEU* 3.8 18.4 - - + -
112F CYS* 3.7 21.1 - - + -
404F PHE* 3.4 6.8 - - - -
405F SER* 2.9 31.1 + - - +
408F SER 4.4 1.7 - - - -
409F SER* 1.3 89.0 + - - +
411F LEU* 1.3 64.1 + - - +
412F ILE* 4.1 6.3 - - + -
422F ARG* 3.5 50.7 - - + +
423F TRP 3.7 2.0 - - - +
424F ASP* 3.7 13.5 - - - +
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Residues in contact with LEU 411 (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* 4.1 8.5 - - + -
364F ALA* 3.9 20.0 - - + -
372F LEU* 3.8 24.9 - - + -
374F VAL* 3.7 29.6 - - + -
390F LEU* 3.9 8.3 - - + -
402F THR* 3.9 15.7 - - + -
403F SER 3.4 15.5 - - - +
404F PHE* 4.0 25.6 - - + -
410F ILE* 1.3 73.3 - - - +
412F ILE* 1.4 61.5 - - - +
421F TRP 3.5 1.7 - - - +
422F ARG* 3.8 0.3 - - - -
423F TRP* 2.8 46.5 + - + +
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Residues in contact with ILE 412 (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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85F VAL* 3.6 29.5 - - + +
87F PHE* 3.5 28.3 - - + -
99F PHE* 3.8 26.7 - - + -
112F CYS* 4.9 0.2 - - - -
118F ILE* 4.7 0.9 - - + -
402F THR* 3.1 7.6 - - - -
403F SER* 2.8 38.4 + - - +
410F ILE* 4.1 2.5 - - + -
411F LEU* 1.4 75.2 - - - +
413F ALA* 1.3 63.4 + - - +
420F ILE* 3.7 22.2 - - + -
421F TRP 3.4 2.0 - - - +
422F ARG* 3.7 39.5 - - + +
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Residues in contact with ALA 413 (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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372F LEU* 4.2 23.1 - - + -
399F ILE* 3.7 28.0 - - + -
401F GLN 3.6 5.8 - - - -
402F THR* 4.3 2.9 - - + -
412F ILE* 1.3 74.1 - - - +
414F VAL* 1.4 62.8 + - - +
419F SER 3.8 0.9 - - - +
420F ILE* 3.5 3.8 - - - -
421F TRP* 2.8 45.3 + - + +
423F TRP* 4.9 0.2 - - - +
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Residues in contact with VAL 414 (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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82F LEU* 3.6 39.5 - - + +
84F GLY 4.2 12.1 - - - +
85F VAL* 3.4 44.4 - - + -
101F THR* 3.9 11.2 - - - +
399F ILE* 3.3 4.7 - - - -
400F ARG 2.9 25.8 + - - -
401F GLN 3.2 15.2 + - - +
412F ILE* 4.4 2.2 - - + -
413F ALA* 1.4 76.0 - - - +
415F CYS* 1.4 61.4 + - - +
419F SER 3.4 2.9 - - - -
420F ILE* 4.2 8.5 - - + -
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Residues in contact with CYS 415 (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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82F LEU* 3.3 19.4 + - - +
395F CYS* 4.1 7.2 - - - -
397F ALA* 4.0 10.5 - - + -
398F ALA 3.2 9.2 - - - +
399F ILE* 3.6 24.5 - - - -
400F ARG* 5.0 0.2 - - - -
413F ALA 4.9 0.2 - - - -
414F VAL* 1.4 77.7 - - - +
416F ASP* 1.4 59.9 + - - +
417F ASP* 3.1 8.7 - - - +
418F ALA* 3.1 21.0 + - - -
419F SER* 2.9 32.8 + - - +
421F TRP* 3.6 20.4 - - - -
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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