Contacts of the strand formed by residues 456 - 464 (chain A) in PDB entry 4I1R
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 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A VAL 3.4 8.8 + - - +
407A TYR* 3.7 40.8 - - + -
408A GLY 3.0 21.5 + - - +
454A THR* 3.2 6.7 - - - -
455A GLY* 1.4 78.2 - - - +
457A ASN* 1.3 70.2 + - - +
458A VAL* 4.1 15.0 - - + -
485A ASN* 3.5 17.5 - - - +
487A VAL* 3.7 20.6 - - + -
525A ILE* 3.9 11.2 - - + -
554A LEU* 3.8 13.7 - - + -
558A ARG* 3.8 20.0 - - + +
559A ALA 4.0 8.7 - - - +
560A LEU* 4.5 5.2 - - + -
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Residues in contact with ASN 457 (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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398A PHE* 4.1 8.1 - - - -
402A LEU* 3.5 26.0 - - - +
408A GLY 3.4 4.7 - - - +
449A MET* 3.1 45.2 - - - +
454A THR* 3.8 14.4 - - - +
456A LEU* 1.3 77.9 - - - +
458A VAL* 1.3 64.7 + - - +
459A PHE* 3.9 0.6 + - - +
484A ALA 4.0 7.0 - - - +
485A ASN 3.3 6.7 + - - +
486A ILE* 3.3 20.6 - - + +
487A VAL* 2.9 27.5 + - - +
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Residues in contact with VAL 458 (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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408A GLY 2.8 15.5 + - - +
409A LEU* 3.4 19.1 - - + +
410A LEU* 2.7 34.1 + - - +
449A MET* 5.3 0.2 - - - +
456A LEU* 4.1 21.3 - - + -
457A ASN* 1.3 77.5 - - - +
459A PHE* 1.3 59.1 + - - +
460A LEU* 3.8 30.3 - - + -
487A VAL* 3.6 12.3 - - + +
525A ILE* 4.2 23.1 - - + -
529A LEU* 5.1 0.7 - - + -
560A LEU* 4.1 19.7 - - + -
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Residues in contact with PHE 459 (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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410A LEU* 3.5 28.9 - - + -
412A TYR* 5.3 0.7 - - + -
425A MET* 4.5 6.5 - - - -
442A VAL* 3.7 21.3 - - + -
445A ILE* 3.7 39.5 - - + -
446A LEU* 3.4 25.1 - - + -
449A MET* 3.7 18.2 - - + -
457A ASN* 3.9 3.0 + - - +
458A VAL* 1.3 72.1 - - - +
460A LEU* 1.3 60.1 + - - +
461A LEU* 3.4 28.9 - - + -
486A ILE* 4.9 1.8 - - + -
487A VAL 2.9 11.2 + - - +
488A PHE* 3.5 18.6 - + + -
489A GLY 2.8 32.5 + - - +
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Residues in contact with LEU 460 (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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369A LEU* 5.4 2.9 - - + -
409A LEU* 4.6 15.7 - - + -
410A LEU 2.7 17.6 + - - +
411A TYR* 3.7 20.9 - - + -
412A TYR 3.0 24.0 + - - -
458A VAL* 3.8 26.2 - - + -
459A PHE* 1.3 72.5 - - - +
461A LEU* 1.3 66.6 + - - +
489A GLY* 3.4 22.7 - - - +
511A PHE* 3.8 18.4 - - + -
515A LEU* 3.7 32.1 - - + -
519A LEU* 5.6 2.0 - - + -
525A ILE* 6.5 0.2 - - + -
529A LEU* 4.2 14.4 - - + -
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Residues in contact with LEU 461 (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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411A TYR* 5.1 1.3 - - - -
412A TYR* 3.5 24.0 - - + -
425A MET* 3.9 11.9 - - - -
442A VAL* 3.7 20.9 - - + -
459A PHE* 3.4 27.6 - - + -
460A LEU* 1.3 77.9 - - - +
462A ASP* 1.3 58.3 + - - +
463A MET* 3.6 10.8 - - + -
488A PHE* 3.6 26.0 - - + -
489A GLY 2.9 7.8 + - - +
490A TYR* 3.5 32.8 - - + -
491A ALA* 2.8 34.5 + - - +
511A PHE* 5.1 2.8 - - - -
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Residues in contact with ASP 462 (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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365A ASP* 4.1 9.7 - - - +
411A TYR* 2.7 31.7 + - + +
412A TYR 2.8 12.8 + - - +
413A ALA* 4.0 1.3 - - + -
414A GLY 3.2 13.4 + - - -
460A LEU 4.3 0.2 - - - -
461A LEU* 1.3 71.6 - - - +
463A MET* 1.3 57.9 + - - +
491A ALA* 3.8 8.0 - - - +
493A CYS 3.8 15.9 + - - +
494A GLN* 2.8 29.6 + - - +
509A GLY* 5.3 3.1 - - - -
511A PHE* 3.4 36.5 + - + +
512A MET 4.4 3.6 + - - -
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Residues in contact with MET 463 (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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412A TYR* 3.3 33.2 - - - -
414A GLY 3.3 6.5 - - - -
416A GLY* 3.7 19.1 - - - -
417A TYR 5.1 0.4 - - - +
423A SER* 4.7 2.2 - - - -
424A PHE 3.2 31.4 - - - +
425A MET* 4.0 4.0 - - + +
442A VAL* 4.0 20.4 - - + -
461A LEU* 3.8 19.1 - - + -
462A ASP* 1.3 72.7 - - - +
464A CYS* 1.3 61.7 + - - +
466A LYS* 6.2 2.5 - - + +
490A TYR* 3.8 25.8 - - + +
491A ALA 3.3 9.9 + - - +
492A THR* 3.6 30.3 - - + +
493A CYS 3.8 2.4 + - - -
494A GLN* 3.9 3.9 - - - +
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Residues in contact with CYS 464 (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 LEU* 3.9 16.6 - - + -
414A GLY 3.0 13.4 + - - +
415A HIS* 3.7 28.8 + - - +
416A GLY* 3.0 23.3 + - - +
463A MET* 1.3 74.9 - - - +
465A ARG* 1.3 83.7 + - - +
466A LYS 3.4 4.5 + - - -
492A THR 5.6 0.7 - - - -
494A GLN* 3.7 27.6 - - + +
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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