Contacts of the strand formed by residues 488 - 498 (chain B) in PDB entry 3B76
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 SER 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413B ASN* 4.1 5.5 + - - -
414B ILE 3.1 6.7 - - - -
415B GLN* 3.3 29.8 + - - -
416B LYS* 4.9 1.8 - - - -
466B ASP* 4.3 6.5 - - - +
486B SER* 3.2 19.9 + - - -
487B SER* 1.3 84.8 + - - +
489B ILE* 1.3 63.7 + - - +
490B VAL* 5.7 1.4 - - - +
602B EDO 4.2 7.3 + - - -
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Residues in contact with ILE 489 (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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412B VAL 3.6 1.6 - - - +
413B ASN* 3.5 1.3 - - - +
414B ILE* 2.8 53.4 + - + +
416B LYS* 4.6 9.0 - - + -
422B LEU* 3.8 40.2 - - + -
465B VAL* 3.8 13.9 - - + -
466B ASP* 3.6 15.9 - - - +
481B LEU 4.5 3.4 - - - +
482B LEU* 4.2 11.0 - - + +
486B SER* 5.9 0.9 - - - -
488B SER* 1.3 76.3 - - - +
490B VAL* 1.3 66.5 + - - +
491B LEU* 3.7 30.3 - - + -
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Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 3.8 26.5 - - + -
412B VAL 3.4 5.8 - - - +
413B ASN* 3.6 25.8 - - + +
464B ASN* 3.8 1.2 - - - +
465B VAL* 3.5 4.3 - - - -
466B ASP* 2.9 44.7 + - - +
467B GLY 5.8 0.4 - - - +
488B SER* 5.7 1.1 - - - +
489B ILE* 1.3 73.3 - - - +
491B LEU* 1.3 66.4 + - - +
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Residues in contact with LEU 491 (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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410B LYS 3.7 0.9 - - - +
411B VAL* 3.4 3.9 - - - +
412B VAL* 2.7 43.4 + - + +
414B ILE* 5.0 4.7 - - + -
422B LEU* 4.9 1.6 - - + -
424B MET* 4.3 13.7 - - + -
450B ILE* 4.1 25.8 - - + -
456B ILE* 4.4 19.1 - - + -
462B LEU* 5.1 8.1 - - + -
464B ASN 3.5 2.5 - - - +
465B VAL* 3.7 30.7 - - + -
482B LEU* 3.7 14.6 - - + -
489B ILE* 3.7 26.7 - - + -
490B VAL* 1.3 78.1 - - - +
492B LYS* 1.3 61.8 + - - +
493B ALA 4.1 0.2 - - - -
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Residues in contact with LYS 492 (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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409B GLU* 3.9 23.5 + - + +
410B LYS 3.3 10.3 - - - +
411B VAL* 3.6 24.5 - - + -
462B LEU* 3.8 3.5 - - - +
463B LEU* 2.8 47.8 + - + -
464B ASN* 2.9 33.9 + - + +
469B GLU* 5.9 1.1 - - - +
491B LEU* 1.3 73.1 - - - +
493B ALA* 1.3 58.0 + - - +
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Residues in contact with ALA 493 (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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409B GLU* 3.1 5.5 - - - +
410B LYS* 2.9 46.8 + - + +
456B ILE* 3.7 28.7 - - + -
460B ASP* 4.1 7.9 - - + -
461B ILE 3.2 11.9 - - - +
462B LEU* 4.1 9.4 - - + -
463B LEU* 4.3 4.9 - - - -
491B LEU 4.1 0.4 - - - -
492B LYS* 1.3 74.8 - - - +
494B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 494 (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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435A TRP* 3.8 31.2 - - + +
437A LEU* 4.4 1.8 - - + -
407B MET* 3.9 43.5 - - + -
408B HIS 3.6 11.2 - - - +
409B GLU* 3.8 23.8 - - + +
459B GLY 4.6 0.9 - - - +
460B ASP* 3.5 3.9 - - - -
461B ILE* 2.7 63.7 + - + +
463B LEU* 4.1 13.4 - - + +
493B ALA* 1.3 74.0 - - - +
495B GLU* 1.3 60.5 + - - +
496B VAL* 4.3 1.8 + - + +
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Residues in contact with GLU 495 (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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407B MET* 3.2 4.1 - - - -
408B HIS* 2.9 66.8 + - + +
410B LYS* 2.8 32.2 + - - +
457B LYS* 4.0 18.0 + - - +
460B ASP* 3.5 20.0 - - - +
494B LEU* 1.3 74.3 - - - +
496B VAL* 1.3 74.2 + - - +
497B LYS* 3.4 4.0 + - - -
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Residues in contact with VAL 496 (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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427A ALA* 3.6 25.8 - - + -
428A GLY* 6.0 0.2 - - - -
437A LEU* 6.1 1.3 - - + -
440A TYR* 5.4 11.0 - - + -
442A ILE* 3.7 27.0 - - + +
406B SER 3.7 7.0 - - - +
407B MET* 4.3 20.9 - - + +
459B GLY 5.8 1.2 + - - -
461B ILE* 5.8 7.2 - - + -
494B LEU* 4.3 2.4 + - + +
495B GLU* 1.3 81.0 - - - +
497B LYS* 1.3 58.7 + - - +
498B GLU 3.5 23.3 - - - +
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Residues in contact with LYS 497 (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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442A ILE* 5.3 1.7 - - - +
406B SER* 2.9 20.6 + - - +
408B HIS* 3.5 28.9 - - + +
495B GLU* 3.4 6.2 + - - +
496B VAL* 1.3 73.2 - - - +
498B GLU* 1.3 60.0 + - + +
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Residues in contact with GLU 498 (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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442A ILE* 4.0 6.3 - - - -
404B PHE* 5.1 2.0 - - + +
405B GLN* 3.2 9.1 - - - +
406B SER* 3.0 40.6 + - - +
496B VAL* 3.4 10.0 - - - +
497B LYS* 1.3 81.5 - - + +
499B GLY* 1.3 61.3 + - - +
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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