Contacts of the strand formed by residues 457 - 466 (chain A) in PDB entry 1F9O
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 PHE 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A LYS 3.1 16.4 - - - +
451A PHE* 3.8 13.9 - - + -
452A ASN* 3.7 4.8 + - - +
456A THR* 1.3 81.0 + - - +
458A GLN* 1.3 77.0 + - - +
459A ILE* 4.2 7.2 - - + -
493A THR* 2.8 44.2 + - + -
495A LEU* 4.4 1.8 - - + -
498A ALA* 3.7 26.0 - - + -
524A LEU* 3.8 20.9 - - + -
527A ALA* 3.7 21.8 - - + -
528A MET* 3.7 33.4 - - + -
532A TYR* 3.6 20.3 + + - -
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Residues in contact with GLN 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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448A GLU 4.2 0.2 - - - +
449A ILE* 3.8 0.9 - - - +
450A LYS* 2.9 47.6 + - + +
452A ASN* 4.7 10.7 + - - +
457A PHE* 1.3 81.1 - - - +
459A ILE* 1.3 70.9 + - - +
491A TYR* 3.9 38.0 + - + +
492A GLY* 3.2 13.5 - - - +
493A THR* 4.4 3.9 + - - +
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Residues in contact with ILE 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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412A PHE* 4.2 11.0 - - + -
448A GLU 4.1 3.1 - - - -
449A ILE* 4.3 13.7 - - + -
457A PHE* 4.2 15.5 - - + -
458A GLN* 1.3 81.0 - - - +
460A PRO* 1.3 83.0 - - + +
491A TYR* 3.3 6.2 - - - -
492A GLY* 3.0 29.5 + - - +
494A ASP* 4.1 9.4 - - + +
497A CYS* 4.0 14.8 - - + +
498A ALA* 3.6 37.7 - - + +
501A LEU* 4.2 21.1 - - + -
524A LEU* 4.7 2.5 - - + -
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Residues in contact with PRO 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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412A PHE* 3.3 39.2 - - + +
444A TRP* 5.0 4.3 - - + -
445A ILE* 3.9 20.0 - - + -
448A GLU* 3.6 32.8 - - + +
459A ILE* 1.3 96.3 - - + +
461A SER* 1.3 59.8 + - - +
463A ILE* 4.5 7.9 - - + -
488A VAL* 4.0 17.5 - - + -
490A ASN 4.1 2.0 - - - +
491A TYR* 3.8 14.8 - - + -
494A ASP* 6.0 1.6 - - - +
497A CYS* 5.6 0.3 - - - +
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Residues in contact with SER 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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410A THR 3.7 1.4 - - - +
411A TRP* 3.7 10.2 - - - -
412A PHE* 2.9 28.0 + - - +
460A PRO* 1.3 76.0 - - - +
462A THR* 1.3 65.4 + - - +
490A ASN* 2.9 21.1 + - - -
491A TYR 3.9 15.0 - - - -
492A GLY* 4.0 6.6 - - - -
494A ASP* 5.7 6.9 + - - +
1C V3P 4.1 24.1 - - - -
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Residues in contact with THR 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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410A THR* 3.2 15.9 + - - +
461A SER* 1.3 80.6 + - - +
463A ILE* 1.3 70.6 + - - +
488A VAL* 3.8 1.0 - - - +
489A VAL* 2.9 41.6 + - + +
490A ASN* 3.2 30.8 + - - +
1C V3P 3.6 26.4 + - - +
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Residues in contact with ILE 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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409A ASN* 3.7 19.7 - - - +
410A THR* 2.8 37.8 + - - +
411A TRP 4.5 2.5 - - - +
412A PHE* 4.3 22.9 - - + +
415A GLN* 4.1 17.9 - - + +
444A TRP* 5.1 4.3 - - + -
460A PRO* 4.5 19.5 - - + -
462A THR* 1.3 83.5 - - - +
464A ASP* 1.3 63.7 + - - +
465A TRP* 4.0 21.5 - - + +
486A VAL* 4.2 13.5 - - + -
487A LYS 3.3 11.4 - - - +
488A VAL* 4.3 10.1 - - + -
489A VAL* 3.8 3.7 - - - +
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Residues in contact with ASP 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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399A GLU* 4.4 7.6 - - - +
410A THR* 5.2 5.6 - - - +
463A ILE* 1.3 76.7 - - - +
465A TRP* 1.3 88.9 + - - +
486A VAL* 3.5 3.8 - - - +
487A LYS* 2.7 44.2 + - + +
489A VAL* 3.7 18.3 - - + +
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Residues in contact with TRP 465 (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 SER* 4.0 18.6 - - - -
369A ALA* 3.6 16.4 - - + -
370A ILE 3.2 32.8 - - - -
371A ALA* 4.0 13.9 - - + -
397A TYR* 5.0 3.8 - - - +
399A GLU* 3.9 42.2 + - + +
400A ASN* 5.4 2.9 - - - -
409A ASN* 3.1 37.0 + - - +
410A THR* 5.5 1.6 - - + -
415A GLN* 4.0 1.3 - - - -
463A ILE* 4.0 16.5 - - + +
464A ASP* 1.3 98.3 + - - +
466A GLU* 1.3 68.0 + - - +
467A GLY 5.6 0.4 - - - +
484A LEU* 4.4 11.9 - - + -
485A HIS 3.4 20.2 - - - -
486A VAL* 3.7 24.0 - - + -
487A LYS* 5.1 2.9 - - - -
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Residues in contact with GLU 466 (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 GLU* 5.0 1.6 - - - -
465A TRP* 1.3 78.3 - - - +
467A GLY* 1.3 67.3 + - - +
483A ASN 3.6 1.6 - - - +
484A LEU* 3.5 3.0 - - - +
485A HIS* 2.9 48.7 + - + +
487A LYS* 2.9 35.2 + - - +
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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