Contacts of the helix formed by residues 481 - 496 (chain A) in PDB entry 5K9S
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 ASN 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A THR* 3.6 22.2 - - + +
438A GLN* 3.8 8.1 - - - +
479A HIS* 3.2 31.9 + - + +
480A GLU* 1.3 83.6 - - - +
482A GLU* 1.3 60.7 + - - +
483A SER* 2.5 39.8 + - - -
484A VAL* 3.1 7.1 + - + +
485A TYR* 3.5 20.6 + - - +
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Residues in contact with GLU 482 (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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480A GLU 3.6 2.8 + - - +
481A ASN* 1.3 76.6 + - - +
483A SER* 1.3 64.9 + - - +
484A VAL 3.2 1.3 - - - -
485A TYR* 2.9 45.2 + - - +
486A LYS* 3.0 38.9 + - - +
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Residues in contact with SER 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLN* 2.7 28.1 + - - -
481A ASN* 2.5 23.2 + - - -
482A GLU* 1.3 75.4 - - - +
484A VAL* 1.3 60.8 + - - +
486A LYS* 3.3 18.8 - - - +
487A ALA* 3.0 27.3 + - - +
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 4.3 2.7 - - + -
437A ILE* 4.0 26.7 - - + -
438A GLN* 3.6 29.6 - - + +
441A LEU* 4.0 9.1 - - + +
476A LEU* 4.2 14.6 - - + -
479A HIS* 3.4 46.7 - - + +
481A ASN* 3.1 10.5 + - + +
483A SER* 1.3 76.6 + - - +
485A TYR* 1.3 63.1 + - - +
487A ALA* 3.3 0.9 + - - +
488A SER* 3.0 26.9 + - - -
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Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU 4.6 6.0 + - - -
477A GLN* 3.3 54.7 + - + +
479A HIS 4.6 3.4 - - - +
481A ASN 3.5 14.2 + - - +
482A GLU* 2.9 30.8 + - - +
484A VAL* 1.3 82.1 - - - +
486A LYS* 1.3 66.8 + - + +
488A SER* 3.2 12.9 + - - -
489A LEU* 3.2 30.4 + - + +
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Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLU* 3.0 45.7 + - - +
483A SER* 3.3 19.9 - - - +
485A TYR* 1.3 84.0 - - + +
487A ALA* 1.3 66.8 + - - +
489A LEU* 3.5 6.1 + - - +
490A ASN* 3.1 24.3 + - - +
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Residues in contact with ALA 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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441A LEU* 3.9 22.9 - - + -
442A ASP* 5.6 4.3 - - - +
483A SER 3.0 20.6 + - - +
484A VAL 3.3 2.7 + - - +
486A LYS* 1.3 79.2 - - + +
488A SER* 1.3 62.8 + - - +
490A ASN* 3.2 8.9 + - - +
491A LEU* 3.2 26.4 + - + +
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Residues in contact with SER 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LEU* 4.1 4.0 - - - +
473A ILE* 3.6 28.7 - - - +
476A LEU* 3.5 28.4 - - - +
477A GLN* 3.9 10.1 + - - +
484A VAL 3.0 18.3 + - - -
485A TYR 3.2 7.6 + - - -
487A ALA* 1.3 77.6 - - - +
489A LEU* 1.3 57.1 + - - +
491A LEU* 3.3 6.3 + - - +
492A ILE* 3.0 34.5 + - - +
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLN* 4.1 24.0 - - + +
485A TYR* 3.2 42.7 + - + +
486A LYS* 3.8 6.1 - - - +
487A ALA 3.2 0.4 - - - -
488A SER* 1.3 74.9 + - - +
490A ASN* 1.3 66.6 + - - +
492A ILE* 4.0 7.5 - - + +
493A GLU* 3.0 52.5 + - + +
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Residues in contact with ASN 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A SER* 5.1 6.7 + - - -
486A LYS 3.1 14.3 + - - +
487A ALA* 3.2 12.5 + - - +
489A LEU* 1.3 81.6 - - - +
491A LEU* 1.3 70.2 + - - +
493A GLU* 3.9 3.1 - - - +
494A LYS* 2.9 54.6 + - - +
495A TYR* 4.8 1.2 + - - -
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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
----------------------------------------------------------
441A LEU* 4.1 31.0 - - + +
444A ILE* 3.9 20.9 - - + -
445A SER* 4.1 21.8 - - - +
448A PHE* 4.0 14.6 - - + -
473A ILE* 4.5 16.6 - - + -
487A ALA* 3.2 15.0 + - + +
488A SER* 3.7 5.8 - - - +
490A ASN* 1.3 83.8 - - - +
492A ILE* 1.3 58.6 + - - +
495A TYR* 2.9 54.1 + - + -
496A PHE* 3.2 15.3 - - + -
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Residues in contact with ILE 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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470A LEU* 4.7 7.6 - - + -
473A ILE* 3.7 19.7 - - + +
474A GLU* 3.5 40.8 - - + +
477A GLN* 5.8 5.8 - - + +
488A SER 3.0 20.0 + - - +
489A LEU* 4.0 7.2 - - + +
490A ASN 3.3 0.2 - - - -
491A LEU* 1.3 77.2 - - - +
493A GLU* 1.3 67.5 + - + +
496A PHE* 3.0 47.2 + - + +
497A SER* 3.3 1.4 + - - +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 3.0 44.8 + - + +
490A ASN* 4.2 3.6 - - - +
492A ILE* 1.3 82.0 - - + +
494A LYS* 1.3 61.0 + - - +
497A SER* 2.8 24.1 + - - +
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Residues in contact with LYS 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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449A GLN* 6.5 0.2 - - - -
452A GLU* 3.3 18.3 + - - -
490A ASN* 2.9 35.5 + - - +
493A GLU* 1.3 80.3 - - - +
495A TYR* 1.3 100.0 + - + +
497A SER* 5.4 1.0 - - - -
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Residues in contact with TYR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A SER* 4.8 4.6 + - - -
448A PHE* 3.3 58.1 - + + +
449A GLN* 4.6 5.2 + - - +
452A GLU* 2.9 30.0 + - + -
457A THR* 4.1 20.0 - - + +
461A SER* 3.2 19.5 + - - -
490A ASN* 4.8 1.5 + - - -
491A LEU* 2.9 43.7 + - + +
494A LYS* 1.3 109.1 - - + +
496A PHE* 1.3 65.9 + - + +
497A SER 3.7 2.8 + - - -
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Residues in contact with PHE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PHE* 3.8 21.5 - + - -
461A SER* 3.1 35.9 - - - -
464A ILE* 4.1 22.9 - - + -
470A LEU* 3.5 46.2 - - + -
473A ILE* 4.7 7.9 - - + -
491A LEU* 3.2 26.9 - - + -
492A ILE* 3.0 31.8 + - + +
495A TYR* 1.3 85.1 - - + +
497A SER* 1.3 58.8 + - - +
498A VAL 5.2 0.3 - - - +
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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