Contacts of the strand formed by residues 485 - 492 (chain C) in PDB entry 2FGJ
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 LEU 485 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473C ILE* 4.1 5.6 - - + -
474C ARG* 3.2 1.9 - - - -
475C PHE* 2.7 42.9 + - + +
483C VAL* 3.6 5.1 - - - +
484C ILE* 1.3 82.3 - - + +
486C ASP* 1.3 60.8 + - - +
488C ILE* 3.5 28.9 - - + -
507C GLY* 4.0 12.1 - - - +
510C THR* 3.7 23.8 - - + -
511C LEU* 4.0 12.6 - - + +
514C LEU* 3.6 31.0 - - + -
676C MET* 3.9 12.1 - - + -
679C GLY* 3.7 18.2 - - - +
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Residues in contact with ASP 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C ILE 3.4 0.9 - - - -
474C ARG* 3.3 35.1 + - - +
483C VAL* 3.9 21.5 - - + +
484C ILE 4.2 1.2 + - - -
485C LEU* 1.3 73.2 - - - +
487C ASN* 1.3 83.4 + - - +
488C ILE* 3.2 8.3 + - - +
679C GLY 3.5 11.4 + - - +
680C LYS* 4.5 22.3 - - + +
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Residues in contact with ASN 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C ASN* 3.0 44.8 + - - +
473C ILE 2.8 10.5 + - - -
474C ARG* 4.6 0.4 - - - +
486C ASP* 1.3 85.1 + - - +
488C ILE* 1.3 61.7 + - - +
489C ASN* 3.4 13.0 + - - +
680C LYS* 5.9 3.0 - - - -
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Residues in contact with ILE 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C PHE* 3.5 23.1 - - + +
472C ASN 3.4 6.8 + - - -
473C ILE* 3.0 32.3 + - + +
485C LEU* 3.5 33.2 - - + -
486C ASP 4.0 6.1 - - - +
487C ASN* 1.3 75.1 - - - +
489C ASN* 1.3 63.7 + - - +
490C LEU* 4.5 0.9 - - + +
511C LEU* 3.7 25.6 - - + -
676C MET* 4.5 6.3 - - + -
679C GLY 3.3 28.0 - - - +
680C LYS* 4.7 2.5 - - - -
681C ILE* 3.9 26.7 - - + +
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Residues in contact with ASN 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C PHE 3.3 6.6 - - - +
471C ARG* 4.0 1.9 - - - -
472C ASN* 3.0 31.1 + - - +
487C ASN* 3.4 31.3 + - - +
488C ILE* 1.3 74.5 - - - +
490C LEU* 1.3 62.0 + - - +
681C ILE* 4.1 10.4 - - - +
684C GLN* 5.1 5.7 + - - +
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Residues in contact with LEU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C ILE 3.6 1.1 - - - +
469C THR* 3.3 4.7 - - - +
470C PHE* 2.7 60.6 + - + +
488C ILE* 4.6 0.9 - - + -
489C ASN* 1.3 73.9 - - - +
491C SER* 1.3 66.6 + - - +
492C ILE* 3.8 26.0 - - + -
500C ILE* 6.0 1.3 - - + -
511C LEU* 4.8 11.7 - - + -
672C ARG* 3.5 28.5 - - - +
674C ILE* 3.6 30.1 - - + -
681C ILE* 4.1 16.8 - - + -
684C GLN* 3.5 12.3 - - - +
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Residues in contact with SER 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C ASP 5.7 2.0 - - - -
468C ILE 3.3 4.9 - - - -
469C THR* 3.8 18.6 + - - +
490C LEU* 1.3 78.4 + - - +
492C ILE* 1.3 57.0 + - - +
493C LYS* 4.1 19.1 - - - -
672C ARG* 2.7 32.2 + - - +
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Residues in contact with ILE 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C ASP* 2.9 6.2 + - - +
468C ILE* 2.8 55.2 + - + +
470C PHE* 5.3 0.2 - - + -
490C LEU* 3.8 30.1 - - + -
491C SER* 1.3 78.5 - - - +
493C LYS* 1.3 67.5 - - - +
496C GLU* 3.8 3.6 - - - +
498C ILE* 3.5 34.5 - - + -
500C ILE* 6.2 0.9 - - + -
515C ILE* 5.2 3.1 - - + -
656C THR* 3.4 31.4 - - + -
658C ILE* 4.0 25.6 - - + -
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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