Contacts of the helix formed by residues 470 - 483 (chain D) in PDB entry 2G4C
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 LYS 470 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466D MET* 3.0 26.9 - - - +
467D HIS* 2.7 30.2 + - + +
469D SER* 1.3 85.5 - - - +
471D LEU* 1.3 57.6 + - - +
472D LYS 3.7 0.9 - - - -
473D ASP* 4.3 12.1 - - + +
474D PHE* 3.2 21.1 + - - +
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Residues in contact with LEU 471 (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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385D LEU* 5.1 0.2 - - + -
402D LEU* 4.1 24.0 - - + -
406D LEU* 4.8 9.2 - - + -
439D PHE* 5.9 0.2 - - + -
441D VAL* 3.7 37.9 - - + -
453D ILE* 4.4 9.2 - - + -
455D LEU* 3.5 32.1 - - + -
466D MET* 4.2 11.9 - - + -
467D HIS 3.7 4.0 + - - +
468D ILE* 4.9 8.7 - - - +
469D SER 3.5 0.6 - - - -
470D LYS* 1.3 77.2 - - - +
472D LYS* 1.3 57.7 + - - +
474D PHE* 3.4 4.8 - - + +
475D LEU* 2.8 57.2 + - + +
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Residues in contact with LYS 472 (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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405D GLU* 3.9 24.9 + - - +
406D LEU* 3.6 28.4 - - + +
409D ASN* 3.6 33.5 + - - +
411D ILE* 4.6 3.8 - - + -
469D SER 4.7 12.1 - - - +
471D LEU* 1.3 77.5 - - - +
473D ASP* 1.3 89.5 + - + +
475D LEU* 4.1 6.3 - - - -
476D ILE* 2.8 36.9 + - - +
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Residues in contact with ASP 473 (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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469D SER 5.2 1.1 - - - +
470D LYS* 4.3 17.8 - - + +
471D LEU 3.4 0.2 - - - -
472D LYS* 1.3 91.5 - - + +
474D PHE* 1.3 68.3 + - - +
476D ILE* 3.4 5.3 + - - +
477D LYS* 3.0 34.7 + - - +
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Residues in contact with PHE 474 (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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439D PHE* 3.3 48.0 - + - -
455D LEU* 4.2 12.6 - - + -
462D MET* 5.4 6.3 - - + -
464D GLU* 5.8 5.4 - - - -
466D MET* 3.6 21.1 - - + -
470D LYS 3.2 20.5 + - - +
471D LEU* 3.4 6.5 + - + +
472D LYS 3.2 0.2 - - - -
473D ASP* 1.3 83.0 + - - +
475D LEU* 1.3 64.3 + - + +
477D LYS* 2.7 11.0 + - + +
478D TYR* 2.7 52.0 + + + +
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Residues in contact with LEU 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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382D LYS* 5.1 2.0 - - + +
383D VAL* 4.5 14.6 - - + -
406D LEU* 4.3 10.5 - - + -
411D ILE* 3.7 34.5 - - + -
438D LEU* 6.3 0.9 - - + -
439D PHE* 3.4 41.5 - - + -
471D LEU* 2.8 48.3 + - + +
472D LYS* 3.5 6.5 - - - +
474D PHE* 1.3 79.3 - - + +
476D ILE* 1.3 56.8 - - - +
478D TYR* 3.1 4.9 + - - +
479D ILE* 3.0 39.6 + - + +
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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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409D ASN* 3.8 39.0 - - + +
411D ILE* 3.6 18.2 - - + -
472D LYS* 2.8 34.2 + - - +
473D ASP* 4.0 4.9 - - - +
475D LEU* 1.3 71.0 - - - +
477D LYS* 1.3 59.2 + - + +
479D ILE* 4.6 5.7 - - + +
480D SER* 2.9 29.8 + - - -
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Residues in contact with LYS 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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473D ASP* 3.0 26.0 + - - +
474D PHE* 2.7 16.8 + - + +
476D ILE* 1.3 74.2 - - + +
478D TYR* 1.3 63.4 + - - +
479D ILE 3.2 1.3 - - - -
480D SER* 3.8 10.1 + - - +
481D SER* 2.5 36.5 + - - +
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Residues in contact with TYR 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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376D PRO* 3.7 28.9 - - + +
438D LEU* 4.7 9.6 - - + +
439D PHE* 3.4 37.7 - + + -
459D ASP* 3.1 24.4 + - - +
462D MET* 5.5 6.3 - - + -
474D PHE* 2.7 29.0 + + + +
475D LEU* 3.4 13.9 - - - +
477D LYS* 1.3 79.3 - - - +
479D ILE* 1.3 65.4 + - + +
481D SER* 3.6 2.9 - - - -
482D ALA* 3.2 28.1 + - + +
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Residues in contact with ILE 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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376D PRO* 4.9 6.1 - - + -
377D CYS* 4.4 25.6 - - + +
382D LYS* 3.4 42.6 - - + -
410D GLY 6.0 0.2 - - - +
411D ILE* 5.3 10.8 - - + -
438D LEU* 4.8 9.6 - - + -
475D LEU* 3.0 21.4 + - + +
476D ILE* 4.6 4.7 - - - +
478D TYR* 1.3 84.3 - - + +
480D SER* 1.3 54.1 + - - +
481D SER 2.6 16.5 + - - -
482D ALA 4.7 0.2 - - - +
483D LYS* 2.9 32.6 + - + +
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Residues in contact with SER 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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476D ILE* 2.9 28.2 + - - -
477D LYS* 3.7 13.1 + - - +
478D TYR 3.6 0.2 - - - -
479D ILE* 1.3 74.3 - - - +
481D SER* 1.3 61.6 + - - +
483D LYS* 4.6 10.2 - - - +
484D ASN* 4.6 14.4 + - - +
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Residues in contact with SER 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 LYS* 2.5 27.1 + - - +
478D TYR* 3.6 4.5 - - - -
479D ILE 2.6 7.1 + - - -
480D SER* 1.3 75.6 + - - +
482D ALA* 1.3 55.1 + - - -
483D LYS 2.7 13.7 + - - -
484D ASN* 2.7 26.0 + - - +
485D VAL* 3.5 9.7 - - - +
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Residues in contact with ALA 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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265D LYS* 5.5 0.9 - - - +
375D HIS* 3.3 21.1 + - + +
376D PRO* 3.9 28.9 - - + -
478D TYR* 3.2 19.3 + - + +
479D ILE 4.7 0.2 - - - +
481D SER* 1.3 78.7 - - - +
483D LYS* 1.3 60.1 + - - +
485D VAL* 4.1 17.4 + - - +
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Residues in contact with LYS 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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113D GLU* 4.0 21.2 + - - +
116D THR* 5.6 2.8 + - - -
265D LYS* 3.9 23.7 + - + +
266D PHE* 5.1 1.5 - - + -
375D HIS* 4.3 0.4 - - - -
376D PRO* 5.7 0.2 - - - +
377D CYS* 3.6 34.5 - - + -
479D ILE* 2.9 25.7 + - + +
480D SER* 4.6 6.5 - - - +
481D SER 2.7 1.2 + - - +
482D ALA* 1.3 81.8 - - - +
484D ASN* 1.3 85.3 + - - +
485D VAL 3.4 4.7 + - - -
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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