Contacts of the helix formed by residues 485 - 495 (chain D) in PDB entry 1S77
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 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481D PHE* 2.7 51.0 + - + +
482D ILE* 3.0 8.1 + - - +
484D GLU* 1.3 83.3 + - - +
486D HIS* 1.3 68.1 - - - +
487D GLU* 3.3 2.5 - - - -
488D ASN* 2.9 37.6 + - - +
489D ILE* 3.0 14.4 + - + +
501D TRP* 3.6 25.3 - - + -
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Residues in contact with HIS 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ILE 3.0 8.1 + - - -
483D GLU* 3.1 15.9 + - - +
484D GLU 3.5 0.8 - - - -
485D ASN* 1.3 80.2 - - - +
487D GLU* 1.3 85.3 + - + +
489D ILE* 3.1 5.7 + - - +
490D MET* 3.0 46.9 + - + +
518D TYR* 2.9 25.2 + - - +
522D GLN* 3.7 30.7 - - + -
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Residues in contact with GLU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D ASN 3.3 1.2 - - - -
486D HIS* 1.3 98.0 + - + +
488D ASN* 1.3 62.9 + - - +
490D MET* 4.2 10.2 - - - +
491D ALA* 3.0 25.6 + - - +
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Residues in contact with ASN 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D ASN* 2.9 28.7 + - - +
487D GLU* 1.3 77.7 - - - +
489D ILE* 1.3 63.4 + - - +
491D ALA* 3.1 8.5 + - - +
492D CYS* 3.0 27.0 + - - -
501D TRP* 3.3 42.9 + - + +
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Residues in contact with ILE 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ILE* 3.4 56.3 - - + +
485D ASN* 3.0 12.9 + - + +
486D HIS* 3.4 6.7 - - - +
488D ASN* 1.3 74.8 - - - +
490D MET* 1.3 57.3 + - - +
491D ALA 3.2 0.2 + - - -
492D CYS* 3.3 4.4 + - - +
493D ALA* 2.9 26.9 + - - +
501D TRP* 3.8 16.8 - - + -
511D PHE* 4.4 0.7 - - + -
514D PHE* 3.9 8.3 - - + -
515D CYS* 3.5 37.9 - - - +
518D TYR* 3.7 25.1 - - + -
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Residues in contact with MET 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D HIS* 3.0 42.7 + - + +
487D GLU* 3.9 13.0 - - - +
489D ILE* 1.3 75.0 - - - +
491D ALA* 1.3 53.7 + - - +
493D ALA* 3.3 6.0 + - - +
494D LYS* 2.7 36.8 + - - +
518D TYR* 3.9 8.1 - - - -
519D ALA* 3.8 22.9 - - + -
522D GLN* 3.5 40.4 - - + -
523D HIS* 4.0 17.7 - - + +
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Residues in contact with ALA 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D GLU* 3.0 20.0 + - - +
488D ASN* 3.2 10.8 - - - +
490D MET* 1.3 72.6 - - - +
492D CYS* 1.3 61.2 + - - +
493D ALA 3.0 1.3 - - - -
494D LYS* 3.2 5.4 + - - +
495D SER 2.8 27.7 + - - -
499D ASN* 3.1 33.9 - - + +
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Residues in contact with CYS 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D ASN 3.0 19.0 + - - +
489D ILE 3.7 6.5 - - - +
491D ALA* 1.3 75.6 - - - +
493D ALA* 1.3 58.1 + - - +
496D PRO* 3.1 31.2 - - - +
499D ASN* 3.3 26.5 - - - -
501D TRP* 3.7 22.4 - - - -
502D TRP* 3.5 36.3 - - + -
512D LEU* 4.0 5.7 - - + +
515D CYS* 4.2 13.5 - - + -
516D PHE* 4.4 0.2 - - - -
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Residues in contact with ALA 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D ILE 2.9 13.6 + - - +
490D MET 3.3 9.0 - - - +
492D CYS* 1.3 78.8 - - - +
494D LYS* 1.3 62.6 + - - +
496D PRO* 3.9 2.6 - - - +
515D CYS* 3.7 12.7 - - - +
516D PHE* 3.6 27.5 - - + -
519D ALA* 3.3 33.0 - - + -
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Residues in contact with LYS 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D MET* 2.7 20.7 + - - +
491D ALA* 3.6 6.7 - - - +
493D ALA* 1.3 76.2 - - - +
495D SER* 1.3 69.6 + - - +
496D PRO* 3.8 3.6 - - - +
499D ASN* 5.4 0.7 - - - +
523D HIS* 4.5 20.5 + - - -
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Residues in contact with SER 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D ALA 2.8 13.5 + - - -
492D CYS 3.7 2.0 - - - -
494D LYS* 1.3 87.2 + - - +
496D PRO* 1.3 58.2 - - - +
497D LEU* 3.3 6.3 - - - -
498D GLU* 2.9 33.0 + - - -
499D ASN* 2.6 40.5 + - - +
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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