Contacts of the helix formed by residues 473 - 484 (chain D) in PDB entry 3KSA
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 473 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460D ILE* 2.9 39.7 - - + -
469D ASP 3.4 9.5 + - - +
470D ILE 2.7 15.6 + - - +
471D LEU 4.6 0.4 - - - -
472D LYS* 1.3 70.2 - - - +
474D GLU* 1.3 67.5 + - - +
475D GLU* 3.2 1.8 + - + +
476D ILE 3.4 2.3 + - - -
477D ASN* 3.2 19.9 + - - +
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Residues in contact with GLU 474 (chain D).
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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472D LYS 3.6 5.4 + - - +
473D ASN* 1.3 72.2 - - - +
475D GLU* 1.3 58.5 + - - +
477D ASN* 3.1 6.4 + - - +
478D THR* 2.8 38.9 + - + +
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Residues in contact with GLU 475 (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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455D LEU* 4.7 19.2 - - + +
456D ARG* 4.9 13.9 - - + +
459D VAL* 5.5 11.4 - - + -
460D ILE* 5.4 6.5 - - + -
473D ASN* 3.2 2.0 + - - +
474D GLU* 1.3 78.6 - - - +
476D ILE* 1.3 62.1 + - + +
478D THR* 2.7 20.5 + - - -
479D MET* 3.3 17.7 + - + +
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Residues in contact with ILE 476 (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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459D VAL* 4.1 18.4 - - + -
460D ILE* 3.3 31.1 - - + +
462D THR* 4.3 7.9 - - + -
470D ILE* 4.1 18.6 - - + +
471D LEU* 4.8 1.3 - - + -
473D ASN 3.4 5.1 + - - +
475D GLU* 1.3 76.8 - - - +
477D ASN* 1.3 61.7 + - - +
479D MET* 3.1 13.3 + - - +
480D ILE* 2.8 49.3 + - + +
518D LEU* 5.6 0.2 - - + -
521D PHE* 3.6 47.1 - - + -
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Residues in contact with ASN 477 (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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471D LEU* 3.8 18.3 + - - +
472D LYS 5.7 0.2 - - - -
473D ASN 3.2 12.3 + - - +
474D GLU* 3.1 11.2 + - - +
476D ILE* 1.3 75.2 - - - +
478D THR* 1.3 63.6 + - - +
480D ILE* 3.1 12.8 + - + +
481D TYR* 3.0 23.6 + - - +
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Residues in contact with THR 478 (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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415D LYS 5.4 9.6 - - - +
453D LEU* 4.9 13.5 - - - +
454D PRO 5.6 0.7 + - - -
455D LEU* 5.2 1.2 - - - +
474D GLU* 2.8 19.9 + - + +
475D GLU* 2.7 26.9 + - - -
477D ASN* 1.3 74.3 - - - +
479D MET* 1.3 61.1 + - - +
481D TYR* 3.4 5.5 + - - +
482D THR* 2.9 34.5 + - - +
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Residues in contact with MET 479 (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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431D LEU* 4.0 24.9 - - + -
453D LEU* 4.6 6.3 - - + +
455D LEU* 3.2 39.9 - - + -
459D VAL* 5.0 2.2 - - + -
475D GLU* 3.8 7.0 - - + +
476D ILE* 3.1 23.2 + - + +
478D THR* 1.3 82.9 + - - +
480D ILE* 1.3 66.9 + - + +
482D THR* 3.2 5.1 + - - -
483D ILE* 3.1 41.7 + - + +
518D LEU* 3.3 23.1 - - + -
521D PHE* 4.1 23.8 - - + -
522D PHE* 4.5 7.0 - - - -
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Residues in contact with ILE 480 (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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471D LEU* 4.3 11.0 - - + -
476D ILE* 2.8 39.2 + - + +
477D ASN* 3.1 9.2 + - - +
479D MET* 1.3 76.1 - - - +
481D TYR* 1.3 61.5 + - - +
483D ILE* 3.4 5.9 + - - +
484D GLY 3.2 22.9 + - - +
486D GLY* 3.8 21.6 + - - +
487D VAL* 3.4 37.0 - - + +
521D PHE* 4.2 12.3 - - + -
526D MET* 5.7 7.8 - - + +
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Residues in contact with TYR 481 (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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477D ASN 3.0 12.1 + - - +
478D THR* 3.7 9.2 - - - +
480D ILE* 1.3 76.3 - - - +
482D THR* 1.3 63.4 + - + +
483D ILE 3.0 1.8 + - - -
484D GLY* 3.2 12.7 + - - -
497D ASN* 4.9 1.6 + - - -
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Residues in contact with THR 482 (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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416D LEU* 4.7 25.6 - - + -
429D LEU* 4.0 20.1 - - - +
453D LEU* 4.6 18.7 - - + +
478D THR* 2.9 22.2 + - - +
479D MET* 3.2 7.8 + - - -
481D TYR* 1.3 74.9 - - + +
483D ILE* 1.3 60.1 + - - +
497D ASN* 3.5 8.8 + - - +
498D TYR* 3.0 25.1 + - - -
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Residues in contact with ILE 483 (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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429D LEU* 4.1 15.7 - - + -
431D LEU* 5.5 0.2 - - + -
479D MET* 3.1 34.9 + - + +
480D ILE 3.9 3.1 - - - +
481D TYR 3.0 0.6 - - - -
482D THR* 1.3 85.4 - - - +
484D GLY* 1.3 56.8 + - - +
485D ALA* 3.6 6.0 + - + +
491D PHE* 5.7 0.2 - - + -
496D ALA* 3.5 2.1 - - - +
497D ASN* 2.7 35.9 + - + +
498D TYR* 4.4 3.6 - - + +
501D ILE* 3.9 30.5 - - + -
522D PHE* 4.7 8.7 - - + -
526D MET* 3.3 41.3 - - + -
529D LEU* 4.9 0.7 - - + -
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Residues in contact with GLY 484 (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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480D ILE 3.2 7.1 + - - +
481D TYR* 3.2 13.3 + - - -
483D ILE* 1.3 75.1 - - - +
485D ALA* 1.3 54.5 + - - -
486D GLY* 2.5 23.9 + - - -
496D ALA* 3.8 12.3 - - - -
497D ASN* 4.2 3.1 - - - +
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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