Contacts of the strand formed by residues 472 - 478 (chain B) in PDB entry 2JI8
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 VAL 472 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B CYS* 3.6 52.3 - - + +
439B ALA* 4.1 3.6 - - + -
446B VAL* 3.5 15.9 - - + +
448B ALA* 5.3 0.2 - - + -
465B ILE* 3.8 17.3 - - + -
470B LEU* 2.8 29.2 + - + -
471B PRO* 1.3 76.1 - - - +
473B THR* 1.3 65.1 + - - +
474B VAL* 4.0 16.6 - - + -
509B MET* 4.8 1.0 - - - +
537B LYS 3.7 2.2 + - - +
538B PRO* 3.4 2.1 - - - +
539B CYS 2.9 27.4 + - - +
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B VAL 3.0 12.2 + - - -
447B ILE* 3.3 7.5 - - - +
448B ALA 2.9 23.6 + - - +
471B PRO 5.1 1.7 + - - -
472B VAL* 1.3 73.7 + - - +
474B VAL* 1.3 61.5 + - - +
475B ILE* 3.8 5.1 + - + -
529B LEU* 3.8 24.5 - - + -
532B ALA* 3.4 43.0 + - + +
533B VAL* 3.9 7.1 + - - +
537B LYS 4.9 0.5 + - - -
539B CYS* 3.6 7.4 - - + +
541B ILE* 3.9 18.6 - - + -
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B MET* 3.9 38.4 - - + -
448B ALA* 3.9 5.6 - - + -
450B GLU* 4.1 6.7 - - + -
455B PHE* 4.3 6.1 - - + -
462B LEU* 4.2 9.6 - - + -
465B ILE* 4.6 2.5 - - + -
472B VAL* 4.0 18.2 - - + +
473B THR* 1.3 74.1 - - - +
475B ILE* 1.3 57.0 + - - +
476B ILE* 3.6 27.4 - - + -
509B MET* 5.3 1.1 - - + -
539B CYS 3.0 14.3 + - - +
540B LEU* 3.2 12.3 - - + +
541B ILE 2.7 31.9 + - - +
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Residues in contact with ILE 475 (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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384B VAL* 4.0 23.6 - - + -
447B ILE* 3.7 26.7 - - + -
448B ALA 2.7 16.1 + - - +
449B VAL* 3.6 4.8 - - + -
450B GLU* 2.9 29.3 + - - +
473B THR* 4.5 3.6 - - + +
474B VAL* 1.3 72.6 - - - +
476B ILE* 1.3 62.4 + - - +
477B MET* 3.1 30.5 + - + +
525B LEU* 4.1 14.6 - - + -
529B LEU* 4.1 15.7 - - + -
541B ILE* 3.4 22.7 - - + +
543B ALA* 4.1 8.5 - - + -
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Residues in contact with ILE 476 (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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450B GLU* 3.5 5.8 - - + +
452B ASP* 3.9 26.5 - - + -
455B PHE* 3.5 42.6 - - + -
474B VAL* 3.6 15.7 - - + -
475B ILE* 1.3 71.4 - - - +
477B MET* 1.3 62.4 + - - +
478B ASN* 3.0 10.4 + - + +
505B TYR* 3.8 26.0 - - + -
540B LEU* 3.9 27.6 - - + -
541B ILE 3.0 7.6 + - - +
542B ASN* 4.2 6.5 - - - +
543B ALA* 3.0 27.9 + - - +
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Residues in contact with MET 477 (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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377B TYR* 4.4 14.0 + - + +
380B SER* 4.3 10.5 - - - -
381B LEU* 4.1 23.3 - - + -
384B VAL* 5.7 0.4 - - + -
403B ALA* 3.9 25.4 - - + -
449B VAL* 3.9 16.4 - - + -
450B GLU 2.8 19.3 + - - +
451B GLY* 4.4 1.6 - - - -
452B ASP 3.8 11.1 + - - -
475B ILE* 3.1 37.5 - - + +
476B ILE* 1.3 69.8 - - - +
478B ASN* 1.3 59.0 + - - +
479B ASN* 3.0 19.0 + - - +
525B LEU* 5.2 3.8 - - + -
543B ALA* 3.9 11.0 - - + -
545B ILE* 3.8 26.5 - - + -
1563B TPP 5.1 0.3 + - - -
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Residues in contact with ASN 478 (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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452B ASP* 3.8 11.0 - - - +
476B ILE* 3.0 6.4 + - + +
477B MET* 1.3 66.3 - - - +
479B ASN* 1.3 56.4 + - - +
480B GLY 3.5 12.3 + - - -
501B THR 4.6 0.2 - - - +
502B ARG* 3.1 34.3 + - - +
503B GLY 3.0 35.0 + - - +
505B TYR* 3.6 12.4 - - - -
542B ASN* 3.0 24.7 + - - +
543B ALA 2.9 15.4 + - - +
544B MET* 3.9 8.6 - - - +
545B ILE 3.1 19.3 + - - -
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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