Contacts of the strand formed by residues 485 - 492 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A ILE* 4.3 5.6 - - + +
474A ARG* 3.1 5.2 - - - -
475A PHE* 2.8 41.2 + - + +
483A VAL* 3.6 5.9 - - - +
484A ILE* 1.3 82.1 - - - +
486A ASP* 1.3 60.6 + - - +
487A ASN 3.9 0.7 - - - -
488A ILE* 4.3 13.2 - - + -
507A GLY* 3.8 23.6 - - - +
510A THR* 4.2 14.6 - - + -
511A LEU* 3.8 35.2 - - + +
514A LEU* 3.7 31.2 - - + -
676A MET* 4.2 16.2 - - + -
679A GLY* 3.6 5.8 - - - +
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Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ARG* 3.4 24.9 + - - +
483A VAL* 4.0 14.1 - - + +
484A ILE 3.9 1.8 + - - +
485A LEU* 1.3 72.5 - - - +
487A ASN* 1.3 79.1 + - - +
488A ILE 3.5 1.4 + - - -
678A LYS 5.5 2.2 - - - +
679A GLY* 3.0 18.8 + - - +
680A LYS* 4.0 25.7 + - + +
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Residues in contact with ASN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ASN* 3.3 42.3 + - - +
473A ILE 2.8 17.1 + - - -
474A ARG* 3.5 8.3 - - + +
486A ASP* 1.3 83.2 + - - +
488A ILE* 1.3 62.5 + - - +
489A ASN* 3.5 11.5 + - - -
523A ASN* 5.8 1.2 - - - +
680A LYS* 5.9 1.5 - - - +
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Residues in contact with ILE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A PHE* 3.7 24.7 - - + +
471A ARG 3.6 2.3 - - - -
472A ASN 3.2 18.7 + - - -
473A ILE* 3.1 38.4 + - + +
485A LEU* 4.3 12.8 - - + -
486A ASP 3.5 3.2 + - - +
487A ASN* 1.3 73.0 - - - +
489A ASN* 1.3 64.7 + - - +
490A LEU* 3.9 9.0 - - + -
511A LEU* 3.1 37.9 - - + -
679A GLY 5.5 3.8 - - - +
680A LYS* 5.9 1.8 - - - +
681A ILE* 3.7 32.8 - - + +
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Residues in contact with ASN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A PHE 3.2 3.8 - - - +
471A ARG* 3.1 15.2 - - + +
472A ASN* 2.7 42.7 + - - +
487A ASN* 3.5 21.4 + - - -
488A ILE* 1.3 71.9 - - - +
490A LEU* 1.3 66.6 - - - +
681A ILE* 4.5 6.0 - - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A ILE 3.5 1.2 - - - +
469A THR* 3.3 5.5 - - - +
470A PHE* 2.8 49.0 + - + +
488A ILE* 3.9 25.8 - - + -
489A ASN* 1.3 77.6 - - - +
491A SER* 1.3 62.2 + - - +
492A ILE* 3.9 24.2 - - + -
511A LEU* 4.5 9.4 - - + -
672A ARG* 3.4 30.7 - - - +
674A ILE* 3.5 30.7 - - + -
681A ILE* 4.3 9.4 - - + -
684A GLN* 4.3 3.4 - - - +
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASP 5.5 3.3 + - - -
468A ILE 3.3 3.4 - - - -
469A THR* 3.5 24.8 + - - +
490A LEU* 1.3 73.0 - - - +
492A ILE* 1.3 56.7 + - - +
493A LYS 4.0 1.3 + - - -
496A GLU* 4.6 0.3 - - - +
672A ARG* 2.5 30.0 + - - +
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASP* 2.8 18.5 + - - +
468A ILE* 2.9 42.4 + - + +
470A PHE* 5.0 4.9 - - + -
490A LEU* 3.9 23.1 - - + -
491A SER* 1.3 75.0 - - - +
493A LYS* 1.3 66.2 + - - +
496A GLU* 4.1 11.7 - - + +
498A ILE* 3.8 22.2 - - + -
500A ILE* 6.1 1.6 - - + -
511A LEU* 5.6 2.7 - - + -
515A ILE* 5.6 0.9 - - + -
656A THR* 3.4 30.2 + - + -
658A ILE* 3.8 23.1 - - + -
672A ARG* 3.7 14.1 - - - +
674A ILE* 5.3 0.2 - - + -
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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