Contacts of the strand formed by residues 485 - 492 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473B ILE* 3.1 2.4 - - + +
474B ARG* 3.0 9.7 - - - +
475B PHE* 2.9 35.5 + - + +
483B VAL* 4.0 2.4 - - - +
484B ILE* 1.3 87.2 - - + +
486B ASP* 1.3 59.7 + - - +
488B ILE* 4.0 13.5 - - + -
507B GLY* 3.9 21.8 - - - +
510B THR* 3.9 27.4 - - + +
511B LEU* 4.0 24.9 - - + -
514B LEU* 3.6 31.2 - - + -
676B MET* 5.5 1.3 - - - -
679B GLY* 3.4 17.7 - - - +
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Residues in contact with ASP 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B ARG* 3.6 24.2 + - - -
483B VAL* 3.7 16.3 - - + +
484B ILE 4.1 1.2 - - - -
485B LEU* 1.3 71.3 - - - +
487B ASN* 1.3 80.4 + - - +
488B ILE* 3.4 2.0 + - - -
678B LYS 5.8 1.1 - - - +
679B GLY 3.5 8.6 + - - +
680B LYS* 3.5 41.9 + - + +
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Residues in contact with ASN 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B ASN* 3.6 24.3 + - - +
473B ILE 3.0 18.7 + - - +
474B ARG* 3.5 9.7 - - + +
485B LEU 3.5 0.2 + - - -
486B ASP* 1.3 83.2 + - - +
488B ILE* 1.3 61.2 + - - +
489B ASN* 3.2 23.2 + - - -
680B LYS* 5.2 4.3 + - - +
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Residues in contact with ILE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B PHE* 3.6 33.5 - - + +
471B ARG 3.9 1.7 - - - -
472B ASN 3.3 7.1 + - - -
473B ILE* 3.1 50.5 + - + +
485B LEU* 4.0 18.8 - - + -
486B ASP 3.4 1.9 + - - +
487B ASN* 1.3 72.3 - - - +
489B ASN* 1.3 66.4 + - - +
490B LEU* 4.3 0.9 - - + -
511B LEU* 3.1 34.3 - - + -
679B GLY 5.0 5.2 - - - +
680B LYS* 5.9 0.9 - - - +
681B ILE* 3.7 30.5 - - + +
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Residues in contact with ASN 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B PHE 3.1 5.4 - - - +
471B ARG* 3.3 9.9 - - + +
472B ASN* 2.8 30.8 + - - +
487B ASN* 3.2 31.1 + - - -
488B ILE* 1.3 74.1 - - - +
490B LEU* 1.3 62.8 + - - +
681B ILE* 4.1 8.3 - - - +
684B GLN* 4.1 9.5 - - - +
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B ILE 3.7 0.6 - - - +
469B THR* 3.5 0.5 - - - -
470B PHE* 2.6 68.2 + - + +
488B ILE* 4.3 0.9 - - + -
489B ASN* 1.3 73.9 - - - +
491B SER* 1.3 73.2 + - - +
492B ILE* 3.8 25.8 - - + -
500B ILE* 5.8 1.6 - - + -
511B LEU* 3.9 24.7 - - + -
672B ARG* 5.2 1.8 - - - +
674B ILE* 3.7 29.4 - - + -
681B ILE* 4.1 13.0 - - + -
684B GLN* 3.3 23.6 - - - +
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Residues in contact with SER 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B ASP 5.2 6.7 + - - -
468B ILE 3.4 4.9 - - - -
469B THR* 3.7 18.2 + - - +
471B ARG* 5.7 0.3 - - - +
490B LEU* 1.3 80.3 + - - +
492B ILE* 1.3 57.5 + - - +
672B ARG* 2.7 40.0 + - - +
684B GLN* 5.1 0.4 + - - -
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B ASP* 3.0 5.4 + - - +
468B ILE* 2.7 58.7 + - + +
470B PHE* 4.8 3.4 - - + -
490B LEU* 3.8 31.6 - - + -
491B SER* 1.3 79.2 - - - +
493B LYS* 1.3 63.5 + - - +
496B GLU* 3.6 8.5 - - + +
498B ILE* 3.4 42.8 - - + -
500B ILE* 6.5 0.7 - - + -
656B THR* 3.7 25.8 - - + -
658B ILE* 4.5 17.0 - - + -
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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