Contacts of the strand formed by residues 462 - 467 (chain B) in PDB entry 5JG8
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 GLU 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B HIS* 5.1 4.2 - - - -
458B THR* 3.1 30.0 - - - +
460B VAL* 3.5 10.1 - - + +
461B ASP* 1.3 81.3 + - - +
463B PHE* 1.3 73.0 + - - +
464B GLU* 6.2 0.2 - - - -
480B PHE* 3.9 2.4 - - - +
481B LEU* 2.8 48.2 + - + +
496B ARG* 4.9 1.4 + - - -
570B PHE* 4.3 4.5 - - + -
574B TYR* 3.7 20.7 + - + -
595B ALA* 4.7 8.7 - - - +
596B GLN* 3.2 32.4 + - - +
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Residues in contact with PHE 463 (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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462B GLU* 1.3 85.5 - - - +
464B GLU* 1.3 72.7 + - - +
465B VAL* 3.8 16.6 - - + -
478B VAL* 3.9 13.9 - - + -
479B ALA 3.2 16.4 - - - +
480B PHE* 4.4 9.4 - - + -
481B LEU* 4.0 4.5 - - - -
553B TRP* 3.5 48.5 - + + -
556B LEU* 4.6 7.2 - - + -
557B VAL* 3.6 32.5 - - + -
560B MET* 6.0 1.8 - - - -
570B PHE* 3.9 23.3 - + - -
595B ALA 5.0 0.3 - - - -
596B GLN* 2.8 33.6 + - + +
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Residues in contact with GLU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PRO* 4.1 6.0 - - - +
428B PRO* 2.4 34.4 - - - +
429B GLY* 4.5 1.4 - - - -
430B HIS* 4.0 22.7 + - - -
462B GLU* 6.2 0.2 - - - -
463B PHE* 1.3 80.7 - - - +
465B VAL* 1.3 65.1 + - - +
466B PHE* 3.9 6.2 - - + -
478B VAL* 3.2 4.2 - - - +
479B ALA* 2.8 39.0 + - + +
481B LEU* 4.2 20.1 - - + +
595B ALA 4.2 7.3 - - - +
596B GLN 3.4 5.2 - - - -
598B SER 3.4 21.3 - - - +
599B ALA* 3.7 13.7 - - + +
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Residues in contact with VAL 465 (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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440B TYR* 3.9 4.5 + - - -
463B PHE* 3.8 23.6 - - + -
464B GLU* 1.3 76.3 - - - +
466B PHE* 1.3 67.4 + - - +
467B TYR* 3.9 20.8 - - + +
475B PRO* 3.8 27.1 - - + -
477B ALA 3.6 10.3 - - - +
478B VAL* 4.4 2.5 - - + +
550B PRO* 4.7 4.9 - - + +
553B TRP* 4.4 10.1 - - + -
554B HIS* 4.6 8.1 - - + +
596B GLN 3.3 15.4 + - - +
597B LEU* 3.7 23.9 - - + +
599B ALA* 3.7 12.7 - - - +
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Residues in contact with PHE 466 (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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428B PRO* 3.8 22.2 - - + -
439B TYR* 3.9 20.6 - + - -
440B TYR* 3.5 26.5 - + + -
443B VAL* 3.1 28.3 - - + -
453B GLN* 4.0 7.6 - - - -
464B GLU* 3.9 7.2 - - + -
465B VAL* 1.3 76.2 - - - +
467B TYR* 1.3 57.1 + - - +
475B PRO* 3.2 6.9 - - - +
476B LEU* 2.7 48.2 + - + -
477B ALA* 2.7 28.2 + - + +
478B VAL 4.5 0.2 - - - -
479B ALA* 4.0 24.0 - - + -
599B ALA* 3.5 23.1 - - + -
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Residues in contact with TYR 467 (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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440B TYR* 2.8 34.7 + - - +
444B ALA* 4.2 2.6 - - - +
465B VAL* 3.9 23.9 - - + +
466B PHE* 1.3 73.7 - - - +
468B ASP* 1.3 66.6 + - - +
469B GLU 3.7 1.0 + - - -
472B LEU* 3.6 34.3 - - + -
473B SER 4.4 2.0 - - - -
474B ARG 3.0 23.8 - - - -
475B PRO* 3.6 9.4 - - + -
476B LEU* 2.9 18.8 - - - +
554B HIS* 2.6 42.9 + + - -
558B TYR* 4.7 0.8 + - - -
597B LEU* 3.1 38.1 - - + +
606B LEU* 4.5 13.0 - - + -
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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