Contacts of the strand formed by residues 486 - 495 (chain A) in PDB entry 3FO5
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 GLN 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A 1PE 5.2 0.2 - - - +
475A THR* 3.3 6.2 - - - -
476A SER* 2.8 42.0 + - - +
477A PRO 5.5 1.9 - - - +
479A LEU* 4.8 6.2 - - - +
485A PRO* 1.3 76.2 - - - +
487A ASP* 1.3 58.8 + - - +
488A PHE* 3.8 22.6 - - + -
522A TYR* 4.1 1.9 - - - -
523A ARG* 3.1 46.3 + - + +
524A ARG 4.7 0.8 - - - -
525A GLY* 3.7 24.2 - - - +
553A GLY* 4.1 22.7 - - - +
554A VAL* 3.4 23.2 - - - +
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Residues in contact with ASP 487 (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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473A HIS* 2.7 30.1 + - + +
474A VAL 3.1 13.9 - - - +
475A THR* 4.2 2.5 - - + -
486A GLN* 1.3 73.9 - - - +
488A PHE* 1.3 64.6 + - - +
518A GLU* 5.7 0.9 - - - -
519A THR* 5.3 3.0 + - - +
522A TYR* 3.6 30.0 - - + +
523A ARG 2.9 2.2 + - - -
524A ARG* 2.9 42.4 + - - +
525A GLY 2.8 28.2 + - - -
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Residues in contact with PHE 488 (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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2A 1PE 3.7 39.5 - - - -
472A TYR 3.8 0.2 - - - +
473A HIS* 3.4 8.8 - - - -
474A VAL* 2.8 40.3 + - + +
476A SER* 4.2 12.1 - - - -
486A GLN* 3.8 41.7 - - + -
487A ASP* 1.3 77.2 - - - +
489A VAL* 1.3 64.0 + - - +
490A ILE* 3.6 20.4 - - + -
510A SER* 4.5 2.0 - - - +
524A ARG* 4.2 2.0 - - - +
525A GLY* 3.4 36.1 - - - +
526A GLU* 3.6 11.4 - - - -
527A THR 4.4 1.8 - - - -
551A THR* 3.8 21.5 - - + -
554A VAL* 5.0 0.2 - - + -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A VAL* 5.7 1.1 - - + -
471A ILE* 3.8 22.4 - - + -
472A TYR 3.4 5.2 - - - +
473A HIS* 3.9 11.9 - - + -
488A PHE* 1.3 77.6 - - - +
490A ILE* 1.3 63.3 + - - +
510A SER* 3.2 9.5 + - - -
511A VAL* 2.9 48.6 + - + +
512A THR* 5.0 0.9 - - - -
513A LEU* 4.1 17.0 - - + -
516A HIS* 3.9 14.1 - - + +
524A ARG* 3.7 33.8 - - - +
525A GLY 5.1 0.4 + - - -
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Residues in contact with ILE 490 (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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2A 1PE 4.0 20.9 - - - +
446A LEU* 4.6 7.9 - - + -
456A TYR* 4.1 8.7 - - - +
470A ALA 3.6 1.2 - - - +
471A ILE* 3.1 7.7 - - - -
472A TYR* 2.8 43.6 + - + +
474A VAL* 4.0 21.3 - - + -
488A PHE* 3.6 26.5 - - + -
489A VAL* 1.3 79.6 - - - +
491A LEU* 1.3 74.9 + - - +
492A ALA 3.8 0.4 + - - +
508A LEU* 3.8 27.4 - - + -
509A ARG 3.6 6.5 - - - +
510A SER* 4.3 8.7 - - - +
511A VAL* 4.3 0.2 - - - -
527A THR* 4.6 5.2 - - + -
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Residues in contact with LEU 491 (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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379A TRP* 3.8 33.9 - - + -
387A LEU* 3.9 27.4 - - + +
388A SER* 4.1 11.4 - - - +
391A ASN* 3.1 29.2 + - + +
465A VAL* 4.7 1.1 - - + -
469A ASP* 4.5 2.0 - - + -
470A ALA 3.6 14.8 - - - +
471A ILE* 4.0 10.5 - - + +
490A ILE* 1.3 74.4 - - - +
492A ALA* 1.3 64.8 + - - +
493A SER* 3.7 7.6 - - - +
508A LEU* 3.3 3.5 - - - -
509A ARG* 2.9 31.3 + - + +
511A VAL* 3.8 21.0 - - + +
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Residues in contact with ALA 492 (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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444A SER 5.3 4.5 - - - +
446A LEU* 4.5 3.8 - - + -
468A ASP 3.8 0.5 - - - +
469A ASP* 3.2 5.7 - - - +
470A ALA* 2.8 34.1 + - + +
472A TYR* 3.8 28.5 - - + -
490A ILE* 3.8 0.8 + - + -
491A LEU* 1.3 72.0 - - - +
493A SER* 1.3 61.8 + - - +
494A ARG* 4.2 0.4 - - - -
506A ILE* 5.2 6.1 - - + -
507A ALA 3.2 4.9 - - - -
508A LEU* 3.3 22.2 - - + -
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Residues in contact with SER 493 (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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388A SER* 3.3 18.0 + - - -
391A ASN* 2.9 21.1 + - - -
392A VAL* 3.7 22.8 - - - +
468A ASP 3.5 0.4 - - - -
469A ASP* 2.9 24.1 + - - -
491A LEU* 3.7 3.3 - - - +
492A ALA* 1.3 73.8 + - - +
494A ARG* 1.3 61.1 + - - +
495A ARG* 4.0 0.9 - - - -
505A VAL 3.6 1.7 - - - +
506A ILE* 3.6 1.6 - - - -
507A ALA* 2.8 36.7 + - - +
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Residues in contact with ARG 494 (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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440A PHE* 3.5 29.5 + - + -
441A LEU* 4.1 22.2 + - - +
444A SER* 3.0 40.4 + - - -
467A GLU* 3.5 20.8 + - - +
468A ASP* 2.8 45.6 + - - +
492A ALA 4.2 0.4 - - - -
493A SER* 1.3 74.0 - - - +
495A ARG* 1.3 83.9 + - - +
505A VAL 3.2 5.2 - - - +
506A ILE* 4.3 5.4 - - + -
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Residues in contact with ARG 495 (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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385A VAL 5.4 0.4 + - - -
388A SER* 3.6 21.8 - - - -
389A TYR* 4.4 3.8 - - - +
392A VAL* 3.7 33.9 - - + +
396A LYS* 5.9 2.2 - - - +
440A PHE* 3.5 7.8 - - - -
468A ASP* 3.6 8.3 + - - +
469A ASP* 3.1 40.2 + - - -
493A SER 4.0 1.0 - - - -
494A ARG* 1.3 106.0 + - - +
496A LYS* 1.3 69.2 + - - +
503A PRO 4.4 0.3 - - - +
504A TYR* 3.4 3.1 - - - -
505A VAL* 2.8 43.2 + - + +
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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