Contacts of the helix formed by residues 471 - 487 (chain B) in PDB entry 6T8O
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B SER* 1.3 82.1 + - - +
472B LYS* 1.3 61.7 + - - +
474B VAL* 4.2 2.6 - - - +
475B GLY* 2.9 27.4 + - - -
652B PHE* 3.8 24.0 - - - -
674B GLY 4.3 2.7 + - - -
675B HIS* 5.0 1.1 - - - -
676B GLY 5.3 1.6 - - - -
801B ADP 3.3 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B VAL* 3.8 19.3 - - + -
465B ALA* 3.9 5.8 - - - +
466B GLY* 2.4 45.2 + - - +
470B SER* 4.8 3.4 - - - +
471B GLY* 1.3 75.2 - - - +
473B SER* 1.3 61.0 + - - +
475B GLY* 3.1 1.6 + - - -
476B VAL* 2.9 38.5 + - + +
595B ASP* 4.5 9.0 - - - +
629B ALA* 4.9 2.9 - - + -
630B THR 2.3 38.4 + - - +
631B GLN* 3.4 25.8 + - - +
652B PHE* 4.1 11.6 - - + -
801B ADP 2.7 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B LYS* 1.3 70.9 - - - +
474B VAL* 1.3 56.7 + - - -
476B VAL* 3.4 6.3 + - - +
477B ASN* 2.8 41.3 + - - -
503B GLU* 3.4 31.7 + - - +
504B LEU* 5.3 4.6 - - - +
595B ASP* 4.5 5.8 + - - -
631B GLN* 4.4 2.4 + - - -
801B ADP 2.4 55.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLY 4.2 2.2 - - - +
473B SER* 1.3 76.7 - - - +
475B GLY* 1.3 58.6 + - - +
477B ASN* 3.3 10.3 + - - +
478B ALA* 2.9 26.5 + - - +
694B ALA 4.3 6.5 - - - +
695B PHE* 4.3 3.1 - - + -
696B VAL* 3.6 38.1 - - + +
801B ADP 3.2 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 5.5 0.7 - - - +
471B GLY 2.9 21.4 + - - -
472B LYS 3.5 0.9 - - - -
474B VAL* 1.3 78.8 - - - +
476B VAL* 1.3 56.2 + - - +
478B ALA* 3.2 8.4 + - - +
479B MET* 2.9 40.4 + - - +
652B PHE* 5.0 8.3 - - - -
693B GLY* 6.5 0.7 - - - -
694B ALA 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B VAL* 4.6 18.6 - - + -
472B LYS* 2.9 23.0 + - + +
473B SER* 4.0 6.5 - - - +
475B GLY* 1.3 73.0 - - - +
477B ASN* 1.3 61.0 + - - +
479B MET* 3.3 8.8 + - + +
480B LEU* 2.9 47.0 + - + +
504B LEU* 4.5 19.5 - - + -
593B VAL* 5.2 5.2 - - + -
595B ASP* 5.7 2.9 - - - +
627B ILE* 4.9 15.9 - - + -
629B ALA* 4.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B SER* 2.8 32.7 + - - +
474B VAL* 3.6 9.1 - - - +
476B VAL* 1.3 77.9 - - - +
478B ALA* 1.3 56.3 + - - +
481B LEU* 2.9 36.2 + - - +
503B GLU* 5.7 2.2 + - - -
504B LEU* 3.7 12.1 - - - +
506B ILE* 5.1 3.9 - - - +
507B TYR* 2.5 38.7 + - - +
696B VAL* 3.8 14.3 - - + +
698B ASP* 5.3 5.5 + - - -
701B VAL* 4.4 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.1 19.8 - - + -
442B ALA 4.6 7.2 - - - +
443B LEU* 5.9 3.8 - - + +
474B VAL 2.9 14.7 + - - +
475B GLY* 3.2 11.0 + - - +
477B ASN* 1.3 75.3 - - - +
479B MET* 1.3 59.0 + - + +
481B LEU* 3.5 5.8 + - - +
482B SER* 2.9 32.0 + - - -
694B ALA* 4.2 18.6 - - + +
696B VAL* 4.2 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU* 3.5 24.0 - - + +
442B ALA 5.2 0.4 - - - -
443B LEU* 3.8 31.4 - - + -
462B LEU* 3.7 33.7 - - + -
464B VAL* 4.5 10.3 - - + -
475B GLY* 2.9 23.0 + - - +
476B VAL* 3.6 11.9 - - + +
478B ALA* 1.3 76.6 - - - +
480B LEU* 1.3 59.7 + - + +
482B SER* 3.1 7.4 + - - -
483B ILE* 2.9 30.4 + - - +
627B ILE* 4.3 20.4 - - + -
650B ILE* 4.5 18.8 - - + -
652B PHE* 5.8 2.0 - - + -
678B MET* 5.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B VAL* 2.9 36.3 + - + +
477B ASN 4.1 2.2 - - - +
479B MET* 1.3 79.2 - - + +
481B LEU* 1.3 58.2 + - - +
483B ILE* 3.2 13.5 + - + +
484B LEU* 2.9 32.1 + - + +
494B LEU* 4.3 24.5 - - + +
496B MET* 3.8 24.7 - - + -
504B LEU* 4.8 2.2 - - + -
507B TYR* 3.6 33.2 - - + +
591B VAL* 5.2 3.6 - - + -
593B VAL* 4.3 23.8 - - + -
627B ILE* 5.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 4.6 5.2 - - + -
423B PHE* 4.5 10.3 - - + -
477B ASN 2.9 25.4 + - - +
478B ALA* 3.9 4.3 - - - +
480B LEU* 1.3 75.2 - - - +
482B SER* 1.3 59.2 + - - +
484B LEU* 3.5 20.1 - - + -
485B PHE* 2.8 63.8 + - + -
507B TYR* 3.5 21.5 - - + +
696B VAL* 3.8 26.5 - - + -
700B GLU 4.9 3.8 - - - +
701B VAL* 4.5 14.1 - - + +
704B VAL* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.0 6.6 - - - -
427B LEU* 4.9 0.4 - - - +
432B TYR* 3.4 23.9 + - - -
440B PRO* 3.4 31.7 - - - +
441B LEU* 3.8 2.7 - - - -
442B ALA* 3.0 38.5 + - - +
478B ALA 2.9 18.6 + - - -
479B MET 3.1 9.4 + - - -
481B LEU* 1.3 75.3 - - - +
483B ILE* 1.3 62.4 + - - +
485B PHE* 5.1 0.4 - - - -
486B LYS 4.1 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B VAL* 3.8 40.8 - - + +
440B PRO 3.8 12.3 - - - +
441B LEU* 3.9 11.7 - - + -
456B LEU* 5.2 3.1 - - + -
479B MET 2.9 13.6 + - - +
480B LEU* 3.3 20.9 - - + +
482B SER* 1.3 79.0 - - - +
484B LEU* 1.3 60.5 + - - +
486B LYS* 4.8 0.3 - - - +
487B SER* 3.4 24.4 + - - +
492B ALA* 4.9 11.7 - - + +
493B ARG 5.5 0.2 - - - +
494B LEU* 4.0 29.6 - - + -
512B HIS* 5.1 4.6 + - + -
591B VAL* 5.0 11.0 - - + -
627B ILE* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 2.9 19.6 + - + +
481B LEU* 2.9 22.8 + - + +
483B ILE* 1.3 78.6 - - + +
485B PHE* 1.3 63.7 + - - +
486B LYS 3.2 1.7 + - - -
487B SER 3.2 17.5 - - - +
494B LEU* 5.1 5.2 - - + -
507B TYR* 5.0 9.6 - - + -
510B ILE* 4.4 24.5 - - + -
512B HIS* 3.4 37.0 - - + +
704B VAL* 4.0 24.2 - - + -
705B VAL* 5.6 2.0 - - + -
708B TRP* 3.3 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.7 15.4 - - - +
316B PRO* 4.4 22.3 - - + +
317B PRO 3.7 22.2 - - - -
318B LEU* 3.9 21.2 - - + +
320B LEU* 5.6 0.9 - - + -
321B LEU* 3.9 19.5 - - + -
423B PHE* 4.1 10.1 - + - -
427B LEU* 3.8 18.6 - - + -
432B TYR* 3.4 19.4 - - + +
481B LEU* 2.8 55.5 + - + +
482B SER* 4.1 0.6 + - - -
483B ILE 3.6 0.2 - - - -
484B LEU* 1.3 74.8 - - + +
486B LYS* 1.3 59.2 + - - +
704B VAL* 3.6 28.3 - - + -
708B TRP* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.6 13.3 - - - +
432B TYR* 3.0 46.1 + - + +
433B ASP* 4.1 7.1 + - - +
435B HIS* 3.8 24.2 + - - +
437B SER 3.3 23.6 - - - +
438B THR* 4.2 5.4 - - - +
440B PRO* 3.7 29.6 - - + -
482B SER 4.1 6.2 + - - +
483B ILE 3.9 0.8 + - - -
484B LEU 3.2 0.6 - - - -
485B PHE* 1.3 81.5 - - - +
487B SER* 1.3 65.2 + - - +
488B THR* 4.1 1.9 + - - +
491B GLU* 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 6.3 0.4 - - - -
438B THR* 2.3 43.6 + - - -
483B ILE 3.4 13.1 + - - +
484B LEU 3.2 12.0 - - - +
486B LYS* 1.3 79.9 - - - +
488B THR* 1.3 67.7 + - - +
491B GLU* 4.6 9.1 + - - -
492B ALA* 3.8 18.2 - - - +
512B HIS* 3.0 16.6 + - - -
708B TRP* 3.6 6.8 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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