Contacts of the helix formed by residues 453 - 469 (chain A) in PDB entry 5F0L
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A ILE 3.9 2.6 + - - -
452A VAL* 1.3 77.9 - - - +
454A GLN* 1.3 59.0 + - - +
455A ASP* 3.5 3.6 - - - -
456A GLN* 3.0 25.2 + - - +
457A VAL* 2.8 32.1 + - - +
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Residues in contact with GLN 454 (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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453A SER* 1.3 78.6 + - - +
455A ASP* 1.3 69.5 + - - +
457A VAL* 3.4 21.8 + - - +
458A ASP* 3.5 11.1 + - - +
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Residues in contact with ASP 455 (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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416A LEU 5.3 0.7 - - - -
417A LYS* 5.4 11.6 - - + +
453A SER* 3.5 1.9 - - - -
454A GLN* 1.3 81.8 - - - +
456A GLN* 1.3 62.0 + - + +
458A ASP* 3.4 9.8 - - - +
459A SER* 3.2 23.5 + - - -
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Residues in contact with GLN 456 (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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413A LEU* 2.8 46.9 - - - +
416A LEU* 4.1 9.5 - - + +
417A LYS* 3.6 46.5 - - + +
451A ILE 5.5 0.2 + - - -
452A VAL* 3.2 14.4 - - + -
453A SER* 3.0 32.9 + - - +
455A ASP* 1.3 77.7 - - + +
457A VAL* 1.3 62.8 + - - +
458A ASP 3.3 1.1 - - - -
459A SER* 3.4 15.0 + - - -
460A ILE* 3.4 22.3 + - - +
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Residues in contact with VAL 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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452A VAL* 3.3 26.4 - - + +
453A SER 2.8 25.0 + - - +
454A GLN* 3.4 17.2 + - - +
456A GLN* 1.3 70.5 - - - +
458A ASP* 1.3 63.1 + - - +
459A SER 3.5 0.2 + - - -
460A ILE* 3.5 15.2 + - - +
461A MET* 3.7 18.3 + - + +
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Residues in contact with ASP 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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454A GLN 3.5 8.5 + - - +
455A ASP* 3.4 13.0 - - - +
456A GLN 3.3 0.2 - - - -
457A VAL* 1.3 82.7 - - - +
459A SER* 1.3 58.0 + - - +
461A MET* 3.6 6.6 + - - +
462A ASN* 2.7 58.4 + - - -
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Residues in contact with SER 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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416A LEU* 2.8 46.0 + - - -
418A LEU 5.4 0.3 + - - -
422A HIS* 5.4 0.5 - - - -
455A ASP 3.2 13.1 + - - -
456A GLN* 3.6 10.0 - - - -
457A VAL 3.3 0.8 - - - -
458A ASP* 1.3 79.2 - - - +
460A ILE* 1.3 61.4 + - - +
462A ASN* 3.3 8.7 + - - +
463A LEU* 3.1 26.7 + - - +
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Residues in contact with ILE 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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416A LEU* 4.0 21.8 - - + -
441A LEU* 3.9 18.6 - - + -
444A VAL* 5.7 11.2 - - + -
452A VAL* 3.8 30.1 - - + -
456A GLN 3.4 18.3 + - - +
457A VAL* 3.5 7.6 + - - +
458A ASP 3.4 0.6 - - - -
459A SER* 1.3 75.5 - - - +
461A MET* 1.3 63.3 + - + +
463A LEU* 3.3 10.2 + - - +
464A VAL* 3.1 32.0 + - + +
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Residues in contact with MET 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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457A VAL* 3.7 15.9 + - + +
458A ASP* 3.6 8.6 + - - +
459A SER 3.4 0.4 - - - -
460A ILE* 1.3 80.6 - - + +
462A ASN* 1.3 58.8 + - - +
464A VAL* 3.2 21.3 + - + +
465A SER* 2.9 29.6 + - - -
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Residues in contact with ASN 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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422A HIS* 3.2 38.7 + - + +
458A ASP* 2.7 42.4 + - - -
459A SER* 3.5 10.8 - - - +
461A MET* 1.3 78.2 - - - +
463A LEU* 1.3 59.8 + - - +
465A SER* 2.6 22.5 + - - -
466A THR* 3.3 4.5 + - - -
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Residues in contact with LEU 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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416A LEU* 3.5 31.0 - - + -
421A PHE* 4.9 6.1 - - + -
422A HIS* 3.7 22.4 - - + +
425A PHE* 4.2 22.4 - - + -
437A SER* 3.4 14.6 - - - +
440A VAL* 3.7 29.8 - - + -
441A LEU* 3.9 24.0 - - + +
444A VAL* 6.0 0.2 - - + -
459A SER* 3.1 15.8 + - - +
460A ILE* 3.5 7.6 - - - +
461A MET 3.2 0.2 - - - -
462A ASN* 1.3 74.0 - - - +
464A VAL* 1.3 63.1 + - - +
466A THR* 3.0 16.0 + - - -
467A LEU* 3.3 8.7 + - - +
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A LEU* 3.9 22.2 - - + -
460A ILE* 3.1 24.4 + - + +
461A MET* 3.2 23.8 + - + +
463A LEU* 1.3 74.6 - - - +
465A SER* 1.3 62.8 + - - +
467A LEU* 3.1 16.7 + - + +
468A ILE* 3.1 33.7 + - + +
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Residues in contact with SER 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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422A HIS* 5.0 0.5 - - - -
461A MET 2.9 12.5 + - - -
462A ASN* 2.6 32.0 + - - +
464A VAL* 1.3 76.3 - - - +
466A THR* 1.3 58.6 + - - +
468A ILE* 4.5 5.2 - - - -
469A GLN* 3.2 53.8 + - - +
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Residues in contact with THR 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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422A HIS* 3.6 29.8 + - + +
425A PHE* 4.7 8.8 - - + -
430A TYR* 5.7 1.9 - - - -
433A ARG* 4.1 36.9 - - - +
434A LYS* 4.4 1.7 + - - +
437A SER* 2.8 23.9 + - - -
462A ASN 3.3 5.9 + - - +
463A LEU* 3.0 10.0 + - - -
465A SER* 1.3 80.5 + - - +
467A LEU* 1.3 61.5 + - - +
468A ILE 3.8 0.2 + - - -
469A GLN* 4.2 12.3 + - - -
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Residues in contact with LEU 467 (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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430A TYR* 5.9 0.3 - - - -
434A LYS* 3.1 61.7 + - + +
437A SER* 3.7 9.2 + - - -
438A CYS* 4.3 17.3 - - + +
441A LEU* 4.0 21.8 - - + -
463A LEU 3.3 13.2 + - - +
464A VAL* 3.1 13.9 + - + +
466A THR* 1.3 78.6 + - - +
468A ILE* 1.3 66.8 + - + +
469A GLN 5.1 0.3 - - - -
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Residues in contact with ILE 468 (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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430A TYR* 4.5 3.5 + - - -
434A LYS* 4.4 9.3 + - - +
464A VAL* 3.1 34.0 + - + +
465A SER* 3.9 4.5 - - - +
467A LEU* 1.3 84.3 - - + +
469A GLN* 1.3 87.4 + - + +
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Residues in contact with GLN 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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430A TYR* 3.3 33.5 + - - -
433A ARG* 6.6 0.2 - - - -
465A SER* 3.2 34.6 + - - +
466A THR* 4.2 12.1 - - - -
468A ILE* 1.3 97.8 - - + +
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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