Contacts of the strand formed by residues 468 - 475 (chain A) in PDB entry 6X70
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A HIS* 2.6 34.1 + - + +
361A ILE 3.2 16.4 - - - +
362A ASP* 3.4 20.0 - - + +
448A PHE* 3.9 3.7 - - - -
449A TYR* 3.1 5.9 + - - -
464A ILE* 2.9 40.5 + - + +
465A SER* 2.9 19.8 + - - +
466A ILE 3.7 0.2 - - - -
467A ASP* 1.3 81.7 - - - +
469A ALA* 1.3 60.8 + - - +
518A ARG* 5.5 0.3 - - - -
521A LEU* 4.8 2.9 - - - +
12P G 3.4 31.8 + - - +
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Residues in contact with ALA 469 (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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359A PHE 3.9 0.9 - - - +
360A HIS* 3.7 2.7 - - - -
361A ILE* 2.9 35.7 + - + +
448A PHE* 4.0 12.5 - - + -
449A TYR* 3.9 22.2 - - + -
452A LEU* 4.1 12.1 - - + -
461A ILE* 4.8 1.1 - - + -
462A LEU 3.3 13.7 - - - +
464A ILE* 4.1 2.5 - - - +
468A GLU* 1.3 75.4 - - - +
470A VAL* 1.3 64.0 + - - +
471A CYS* 4.0 9.0 - - - -
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Residues in contact with VAL 470 (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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358A ILE* 3.9 14.4 - - + -
359A PHE 3.9 2.7 - - - -
360A HIS* 3.5 36.3 - - + +
460A LEU 4.0 0.7 - - - +
461A ILE* 3.9 0.3 - - - -
462A LEU* 2.8 59.7 + - + +
464A ILE* 3.6 20.2 - - + -
469A ALA* 1.3 72.7 - - - +
471A CYS* 1.3 58.7 + - - +
472A VAL* 4.2 6.4 + - + +
514A LEU* 3.8 28.7 - - + -
610A ILE* 6.2 0.2 - - + -
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Residues in contact with CYS 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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357A ILE 3.9 0.5 - - - +
358A ILE* 3.7 1.8 - - - -
359A PHE* 2.8 48.5 + - + +
361A ILE* 4.1 14.8 - - + -
452A LEU* 4.2 11.2 - - - -
458A PHE* 3.5 43.8 - - + -
460A LEU 3.5 3.8 - - - -
461A ILE* 4.2 11.2 - - - -
469A ALA* 4.1 17.5 - - - -
470A VAL* 1.3 77.1 - - - +
472A VAL* 1.3 61.2 + - - +
473A ARG 4.1 0.2 + - - -
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Residues in contact with VAL 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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350A ILE* 4.0 20.9 - - + -
356A TYR* 3.9 24.9 - - + -
357A ILE 3.7 4.7 - - - +
358A ILE* 4.2 12.6 - - + -
458A PHE* 3.4 4.7 - - - -
459A ASN* 2.7 32.9 + - - -
460A LEU* 2.7 39.7 + - + +
462A LEU* 4.6 2.7 - - + -
470A VAL* 4.4 6.5 - - + +
471A CYS* 1.3 77.5 - - - +
473A ARG* 1.3 58.1 + - - +
474A ILE 4.1 0.4 - - - +
611A LEU* 3.6 26.0 - - + -
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Residues in contact with ARG 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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356A TYR* 3.2 3.6 - - - -
357A ILE* 2.8 42.9 + - + +
359A PHE* 4.3 16.8 - - + -
457A ILE* 3.0 43.1 + - - +
458A PHE* 4.5 3.8 - - + -
459A ASN* 3.5 3.4 - - - +
471A CYS 4.1 0.2 + - - -
472A VAL* 1.3 74.4 - - - +
474A ILE* 1.3 71.1 + - - +
475A ILE* 3.7 19.3 + - + +
485A LEU* 6.2 3.8 - - - +
486A ASN* 5.3 1.9 + - - -
489A LEU* 3.4 37.0 - - - +
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Residues in contact with ILE 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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348A THR 5.7 0.4 - - - +
349A LYS 4.9 3.4 - - - +
350A ILE* 3.7 26.7 - - + -
354A ASP* 3.7 41.7 - - + +
355A THR 3.5 9.6 - - - +
356A TYR* 4.3 3.8 - - + +
459A ASN* 2.5 40.8 + - + +
473A ARG* 1.3 78.4 - - - +
475A ILE* 1.3 72.6 - - - +
476A PRO* 3.6 12.9 - - + +
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Residues in contact with ILE 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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355A THR* 2.8 36.4 + - + +
356A TYR* 4.7 0.4 - - - -
357A ILE* 3.5 39.7 - - + +
473A ARG* 4.0 28.3 - - + +
474A ILE* 1.3 84.3 - - - +
476A PRO* 1.3 77.6 - - + +
477A ASP* 3.5 8.1 + - - +
479A ILE* 4.2 15.5 - - + +
481A ASN* 4.7 15.5 - - + +
486A ASN* 5.7 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