Contacts of the strand formed by residues 470 - 475 (chain A) in PDB entry 5JRS
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 ILE 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A MET* 3.8 0.7 - - - -
432A ILE* 2.9 51.4 + - + -
437A MET* 4.6 1.6 - - - -
439A GLU* 3.8 44.9 + - + +
442A PHE* 4.5 21.1 - - + -
443A ILE* 4.7 4.3 - - + -
463A VAL* 6.3 0.2 - - + -
464A CYS 3.2 10.8 - - - +
465A THR* 3.7 37.5 - - + +
467A GLN 3.7 10.1 - - - +
468A ARG* 4.7 3.1 - - + +
469A PRO* 1.3 74.8 - - - +
471A PHE* 1.3 62.5 + - - +
472A ILE* 5.8 0.2 - - + -
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Residues in contact with PHE 471 (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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399A PRO* 6.1 2.9 - - + -
404A PHE* 3.8 24.0 - + - -
417A LYS* 6.0 1.6 - - + -
429A ILE* 3.4 29.4 - - + -
430A LYS 3.3 4.0 - - - -
431A MET* 3.3 45.8 - - + -
432A ILE* 4.8 0.2 - - - -
463A VAL* 3.2 7.6 - - - +
464A CYS* 2.8 46.3 + - + +
469A PRO* 3.4 23.3 - - + -
470A ILE* 1.3 73.4 - - - +
472A ILE* 1.3 63.5 + - - +
473A ILE* 4.0 8.3 - - + -
602B THR* 3.8 26.0 - - + -
603B ASN* 5.6 1.1 - - - -
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Residues in contact with ILE 472 (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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428A ALA 3.7 1.6 - - - +
429A ILE* 3.6 2.1 - - - -
430A LYS* 2.8 48.4 + - + +
432A ILE* 3.7 29.8 - - + -
437A MET* 4.2 2.2 - - + -
442A PHE* 3.5 39.5 - - + -
449A MET* 6.2 1.6 - - + -
460A LEU* 3.3 30.7 - - + -
462A GLY 3.8 3.4 - - - +
463A VAL* 4.5 1.1 - - + -
470A ILE* 5.8 0.7 - - + -
471A PHE* 1.3 74.6 - - - +
473A ILE* 1.3 59.5 + - - +
474A THR* 4.0 11.7 - - + -
542A LEU* 4.1 22.0 - - + -
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Residues in contact with ILE 473 (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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397A ILE* 3.7 30.7 - - + -
402A LEU* 3.5 24.0 - - + -
421A TRP* 5.1 0.9 - - + -
427A VAL* 3.8 35.4 - - + -
428A ALA 3.4 2.0 - - - -
429A ILE* 3.5 31.4 - - + -
460A LEU* 3.5 1.7 - - - +
461A TYR* 2.8 28.0 + - + -
462A GLY 2.9 16.7 + - - +
463A VAL 4.6 0.2 - - - +
464A CYS* 4.0 16.8 - - - -
471A PHE* 4.0 2.5 - - + -
472A ILE* 1.3 74.7 - - - +
474A THR* 1.3 66.4 + - - +
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Residues in contact with THR 474 (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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427A VAL* 3.4 8.5 - - - +
428A ALA* 2.8 45.0 + - - +
430A LYS* 3.8 31.3 - - + +
458A VAL* 3.9 11.2 - - + +
459A GLN 3.3 13.7 - - - +
460A LEU* 4.2 7.9 - - + -
461A TYR* 3.6 7.2 - - - -
472A ILE* 4.0 10.5 - - + -
473A ILE* 1.3 80.0 - - - +
475A GLU* 1.3 68.1 + - - +
4000A 6MV 3.6 6.1 + - - -
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Residues in contact with GLU 475 (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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457A LEU 3.6 8.1 - - - +
458A VAL* 3.7 7.3 - - + +
459A GLN* 2.9 44.5 + - + +
461A TYR* 3.5 28.2 - - + +
474A THR* 1.3 73.6 + - - +
476A TYR* 1.3 70.0 + - - +
477A MET* 3.9 14.1 - - - +
530A ASN* 5.4 1.0 + - - +
536A LYS* 2.9 32.5 + - - -
4000A 6MV 2.9 22.9 + - - -
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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