Contacts of the helix formed by residues 471 - 485 (chain D) in PDB entry 6T8G
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 GLY 471 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470D SER* 1.3 81.1 - - - +
472D LYS* 1.3 66.7 + - - +
474D VAL* 3.9 3.9 - - - +
475D GLY 3.4 9.0 + - - -
652D PHE* 3.2 23.0 - - - -
676D GLY* 4.9 1.4 - - - -
801D ADP 3.2 41.9 + - - -
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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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464D VAL* 4.5 8.4 - - + +
465D ALA 4.3 6.7 - - - +
466D GLY* 4.2 21.3 - - - +
468D THR* 5.6 1.1 - - - -
470D SER* 3.8 3.1 - - - +
471D GLY* 1.3 75.6 - - - +
473D SER* 1.3 63.6 + - - +
475D GLY* 3.1 13.5 + - - -
476D VAL* 3.2 16.9 + - - +
595D ASP* 4.0 7.2 + - - +
596D GLU* 2.4 32.3 + - - -
629D ALA* 3.7 15.8 - - + +
630D THR 3.1 31.2 - - - +
631D GLN* 3.1 28.4 - - + +
652D PHE* 3.9 11.5 - - + -
801D ADP 2.9 18.2 + - - +
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Residues in contact with SER 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D LYS* 1.3 72.5 - - - +
474D VAL* 1.3 57.7 + - - -
476D VAL* 3.5 11.5 - - - +
477D ASN* 2.9 35.7 + - - -
503D GLU* 3.3 36.7 + - - +
595D ASP* 3.3 14.7 + - - -
801D ADP 2.5 35.6 + - - -
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Residues in contact with VAL 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D GLY 3.9 7.4 - - - +
472D LYS 3.2 0.2 - - - -
473D SER* 1.3 77.0 - - - +
475D GLY* 1.3 55.6 + - - +
477D ASN* 3.3 11.9 + - - +
478D ALA* 2.9 26.2 + - - +
693D GLY* 6.5 0.4 - - - -
694D ALA 4.4 15.0 - - - +
695D PHE* 4.2 22.2 - - + -
696D VAL* 4.0 11.0 - - - +
801D ADP 3.1 58.4 + - + +
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Residues in contact with GLY 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D GLY 3.4 7.0 + - - -
472D LYS 3.1 8.0 + - - -
474D VAL* 1.3 79.5 - - - +
476D VAL* 1.3 57.8 + - - +
478D ALA* 3.3 8.5 + - - +
479D MET* 2.9 38.5 + - - +
652D PHE* 4.7 1.6 - - - -
678D MET* 4.2 22.1 - - - +
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Residues in contact with VAL 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D VAL* 5.5 6.5 - - + -
472D LYS 3.2 15.2 + - - +
473D SER* 3.5 14.6 - - - +
474D VAL 3.2 0.2 - - - -
475D GLY* 1.3 73.2 - - - +
477D ASN* 1.3 60.8 + - - +
479D MET* 3.2 8.9 + - - +
480D LEU* 2.9 43.5 + - + +
503D GLU* 4.9 5.4 - - - +
504D LEU* 4.6 17.7 - - + -
593D VAL* 5.4 7.0 - - + -
595D ASP* 5.0 15.0 - - + +
627D ILE* 5.3 13.9 - - + -
628D LEU 5.4 1.1 - - - +
629D ALA* 4.9 16.2 - - + -
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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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473D SER* 2.9 26.1 + - - +
474D VAL* 3.6 10.3 - - - +
476D VAL* 1.3 75.9 - - - +
478D ALA* 1.3 57.5 + - - +
480D LEU 3.3 0.2 + - - -
481D LEU* 3.0 35.9 + - - +
503D GLU* 3.0 29.5 + - - +
504D LEU* 5.0 1.2 - - - +
506D ILE* 6.1 0.6 - - - +
507D TYR* 3.3 25.5 + - - +
696D VAL* 3.9 17.0 + - + +
697D SER 5.6 1.0 + - - -
698D ASP* 4.9 10.3 + - - -
701D VAL* 4.4 14.7 - - + +
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Residues in contact with ALA 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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423D PHE* 4.4 10.2 - - + -
442D ALA 4.4 12.6 - - - +
443D LEU* 5.5 4.7 - - + +
474D VAL 2.9 14.3 + - - +
475D GLY* 3.4 12.1 - - - +
476D VAL 3.2 0.2 - - - -
477D ASN* 1.3 78.1 - - - +
479D MET* 1.3 54.4 + - + +
481D LEU* 3.5 3.9 + - - +
482D SER* 2.6 38.2 + - - -
678D MET* 5.9 1.3 - - + -
693D GLY* 6.2 0.7 - - - -
694D ALA* 4.5 14.6 - - + +
696D VAL* 3.9 13.2 - - + +
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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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441D LEU* 3.6 37.1 - - + +
442D ALA 5.6 0.2 - - - -
443D LEU* 3.8 26.2 - - + -
462D LEU* 3.7 26.7 - - + -
464D VAL* 4.5 11.4 - - + -
475D GLY* 2.9 23.3 + - - +
476D VAL* 3.2 9.8 + - + +
478D ALA* 1.3 76.3 - - - +
480D LEU* 1.3 64.9 + - + +
482D SER* 3.2 5.5 + - - -
483D ILE* 3.0 32.0 + - - +
627D ILE* 4.0 26.5 - - + -
650D ILE* 4.8 4.5 - - + -
678D MET* 4.7 7.9 - - + -
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Residues in contact with LEU 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 VAL* 2.9 36.3 + - + +
477D ASN 3.3 0.2 + - - -
478D ALA 3.3 0.2 - - - -
479D MET* 1.3 84.3 - - + +
481D LEU* 1.3 59.3 + - - +
483D ILE* 3.2 9.4 + - + +
484D LEU* 2.9 34.7 + - + +
494D LEU* 3.7 41.1 - - + -
496D MET* 3.9 10.5 - - + -
504D LEU* 4.8 1.6 - - + -
507D TYR* 3.4 37.2 - - + +
591D VAL* 6.4 0.2 - - + -
593D VAL* 4.2 24.5 - - + -
627D ILE* 6.3 0.7 - - + -
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Residues in contact with LEU 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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321D LEU* 5.0 1.8 - - + -
423D PHE* 4.2 18.4 - - + -
477D ASN 3.0 25.2 + - - +
478D ALA* 4.1 3.1 - - - +
480D LEU* 1.3 73.9 - - - +
482D SER* 1.3 60.9 + - - +
484D LEU* 4.2 7.2 - - + +
485D PHE* 3.0 58.9 + - + -
507D TYR* 3.5 23.3 - - + +
696D VAL* 3.7 23.6 - - + -
700D GLU* 4.7 9.2 - - + +
701D VAL* 3.7 20.0 - - + -
704D VAL* 4.1 19.5 - - + -
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Residues in contact with SER 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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423D PHE* 4.0 9.9 - - - -
427D LEU* 5.4 1.8 - - - -
432D TYR* 3.9 19.0 + - - -
440D PRO* 3.4 31.0 - - - +
441D LEU* 4.0 2.2 - - - -
442D ALA* 3.3 38.1 + - - +
478D ALA 2.6 23.8 + - - -
479D MET 3.5 4.5 - - - -
480D LEU 3.2 0.4 - - - -
481D LEU* 1.3 77.7 - - - +
483D ILE* 1.3 61.5 + - - +
485D PHE* 4.2 1.1 + - - -
486D LYS 4.2 0.5 + - - -
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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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438D THR 4.9 0.7 - - - +
439D VAL* 3.7 39.3 - - + -
440D PRO* 3.8 10.7 - - - +
441D LEU* 4.0 10.5 - - + -
456D LEU* 5.2 1.8 - - + -
479D MET 3.0 21.7 + - - +
480D LEU* 3.4 16.2 - - + +
482D SER* 1.3 76.9 - - - +
484D LEU* 1.3 65.7 + - + +
486D LYS* 3.0 11.4 + - - +
487D SER* 2.3 35.6 + - - +
492D ALA* 4.1 17.5 - - + -
494D LEU* 4.9 16.2 - - + -
512D HIS* 6.3 0.7 - - + +
591D VAL* 5.0 9.6 - - + -
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Residues in contact with LEU 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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315D LEU* 4.7 0.3 - - - +
316D PRO* 4.6 1.2 - - - +
480D LEU* 2.9 25.8 + - + +
481D LEU* 3.1 8.0 + - + +
483D ILE* 1.3 80.2 - - + +
485D PHE* 1.3 62.2 + - + +
486D LYS 3.3 1.0 + - - -
487D SER* 3.8 6.7 + - - +
494D LEU* 4.5 9.0 - - + -
507D TYR* 4.7 20.0 - - + -
510D ILE* 4.5 17.0 - - + -
512D HIS* 3.5 36.1 - - + +
704D VAL* 3.8 26.2 - - + -
705D VAL* 6.2 0.4 - - + -
708D TRP* 3.3 39.6 + - + +
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Residues in contact with PHE 485 (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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315D LEU* 4.6 16.0 - - - +
316D PRO* 4.1 28.9 - - + -
317D PRO 3.7 20.9 - - - -
318D LEU* 4.1 18.4 - - + -
320D LEU* 5.6 4.7 - - + -
321D LEU* 3.7 27.6 - - + -
423D PHE* 4.4 0.9 - + - -
427D LEU* 4.2 17.7 - - + -
432D TYR* 3.5 16.8 + - + +
481D LEU* 3.0 42.1 + - + +
482D SER 4.2 0.2 + - - -
483D ILE 3.2 0.6 + - - -
484D LEU* 1.3 78.0 - - + +
486D LYS* 1.3 60.5 + - - +
487D SER 3.8 0.4 - - - -
704D VAL* 3.7 31.4 - - + -
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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