Contacts of the helix formed by residues 471 - 485 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F SER* 1.3 80.1 + - - +
472F LYS* 1.3 61.5 + - - +
473F SER 3.5 0.7 - - - -
474F VAL* 3.8 2.7 - - - +
475F GLY 2.9 22.9 + - - -
652F PHE* 3.5 14.1 - - - -
676F GLY 4.5 0.4 - - - -
801F ADP 3.3 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F VAL* 3.8 20.0 - - + -
465F ALA* 4.6 2.5 - - - +
466F GLY 4.4 9.9 - - - +
470F SER* 3.8 4.5 + - - +
471F GLY* 1.3 75.8 - - - +
473F SER* 1.3 57.1 + - - +
475F GLY* 3.2 2.6 + - - -
476F VAL* 3.0 31.9 + - + +
595F ASP* 3.4 33.1 + - - +
596F GLU* 3.4 10.8 + - - -
629F ALA* 4.2 7.4 - - + +
630F THR 3.3 37.7 - - - +
631F GLN* 4.0 7.4 - - - +
652F PHE* 4.1 14.8 - - + -
801F ADP 2.7 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F LYS* 1.3 75.8 + - - +
474F VAL* 1.3 57.2 + - - -
476F VAL* 3.4 8.7 + - - +
477F ASN* 2.9 37.1 + - - -
503F GLU* 3.3 43.7 - - - +
595F ASP* 4.1 13.8 + - - -
801F ADP 2.6 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F GLY 3.5 2.0 + - - +
472F LYS 3.2 0.6 - - - -
473F SER* 1.3 76.5 - - - +
475F GLY* 1.3 59.9 + - - +
477F ASN* 3.4 9.2 + - - +
478F ALA* 2.9 27.2 + - - +
693F GLY 6.1 0.4 - - - -
694F ALA 3.8 16.6 - - - +
695F PHE* 4.3 6.3 - - + -
696F VAL* 3.8 24.0 - - - +
801F ADP 3.6 66.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 475 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443F LEU* 5.4 1.0 - - - +
464F VAL* 6.5 0.2 - - - -
471F GLY 2.9 15.7 + - - -
472F LYS 3.2 3.5 + - - -
474F VAL* 1.3 76.8 - - - +
476F VAL* 1.3 57.7 + - - +
478F ALA* 3.2 8.5 + - - +
479F MET* 3.0 40.9 + - - +
652F PHE* 4.3 14.1 - - - -
678F MET* 5.3 5.8 - - - -
693F GLY* 6.2 2.0 - - - -
694F ALA 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F VAL* 5.0 7.4 - - + -
472F LYS* 3.0 19.2 + - + +
473F SER* 3.8 8.3 - - - +
474F VAL 3.3 0.2 - - - -
475F GLY* 1.3 75.0 - - - +
477F ASN* 1.3 57.5 + - - +
479F MET* 3.3 10.6 + - - +
480F LEU* 2.9 45.6 + - + +
504F LEU* 4.2 20.9 - - + -
593F VAL* 5.0 5.4 - - + -
594F VAL 5.6 2.9 - - - +
595F ASP* 5.0 6.3 - - + +
627F ILE* 4.8 19.7 - - + +
629F ALA* 4.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 477 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473F SER* 2.9 27.7 + - - +
474F VAL* 3.7 8.4 - - - +
475F GLY 3.3 0.2 - - - -
476F VAL* 1.3 77.3 - - - +
478F ALA* 1.3 56.8 + - - +
481F LEU* 2.9 34.8 + - - +
503F GLU* 4.3 20.2 + - - +
504F LEU* 3.9 10.7 - - - +
506F ILE* 5.3 1.9 - - - +
507F TYR* 2.9 36.4 + - - +
696F VAL* 3.9 15.2 + - + +
698F ASP* 5.6 3.4 + - - -
701F VAL* 4.5 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F PHE* 3.9 18.8 - - + -
442F ALA 4.4 9.4 - - - +
443F LEU* 5.6 3.4 - - + +
474F VAL 2.9 17.6 + - - +
475F GLY* 3.2 8.5 + - - +
477F ASN* 1.3 74.7 - - - +
479F MET* 1.3 60.1 + - + +
481F LEU 3.5 1.0 + - - -
482F SER* 2.8 32.8 + - - -
694F ALA* 4.1 16.8 - - + +
696F VAL* 3.6 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 479 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F LEU* 3.6 22.4 - - + +
442F ALA 5.0 0.9 - - - -
443F LEU* 3.8 31.0 - - + -
462F LEU* 3.7 25.1 - - + -
464F VAL* 4.0 18.4 - - + -
475F GLY* 3.0 25.9 + - - +
476F VAL* 3.6 9.9 - - + +
478F ALA* 1.3 76.9 - - - +
480F LEU* 1.3 60.3 + - + +
482F SER* 3.2 7.6 + - - -
483F ILE* 3.0 31.0 + - - +
627F ILE* 3.7 34.1 - - + -
650F ILE* 4.4 9.2 - - + -
652F PHE* 6.0 1.1 - - + -
678F MET* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476F VAL* 2.9 25.9 + - + +
477F ASN 4.0 0.2 - - - +
478F ALA 3.3 0.2 - - - -
479F MET* 1.3 79.7 - - + +
481F LEU* 1.3 59.7 + - - +
483F ILE* 3.2 9.8 + - + +
484F LEU* 2.9 34.2 + - + +
494F LEU* 4.1 30.1 - - + -
496F MET* 4.0 11.4 - - + -
504F LEU* 3.9 15.0 - - + -
507F TYR* 3.6 37.7 - - + +
591F VAL* 5.4 0.9 - - + -
593F VAL* 3.7 30.1 - - + -
627F ILE* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F LEU* 4.4 8.1 - - + -
423F PHE* 3.8 18.6 - - + -
477F ASN 2.9 26.8 + - - +
480F LEU* 1.3 74.0 - - - +
482F SER* 1.3 60.7 + - - +
484F LEU* 4.2 7.9 - - + +
485F PHE* 3.0 56.2 + - + +
507F TYR* 3.3 26.9 - - + +
696F VAL* 3.8 21.8 - - + -
700F GLU 4.4 12.8 - - - +
701F VAL* 3.8 18.4 - - + +
704F VAL* 4.5 11.2 - - + -
705F VAL* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 482 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F PHE* 4.2 6.3 - - - -
427F LEU* 5.2 1.3 - - - -
432F TYR* 3.2 25.1 + - - -
440F PRO* 3.4 27.9 - - - +
441F LEU* 3.8 2.2 - - - -
442F ALA* 3.0 40.7 + - - +
478F ALA 2.8 18.9 + - - -
479F MET 3.2 10.9 + - - -
481F LEU* 1.3 77.0 - - - +
483F ILE* 1.3 61.6 + - - +
486F LYS 4.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 483 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438F THR 5.0 0.8 - - - +
439F VAL* 3.7 29.2 - - + -
440F PRO* 3.5 20.9 - - - +
441F LEU* 3.8 11.9 - - + -
456F LEU* 5.0 5.8 - - + -
479F MET 3.0 15.9 + - - +
480F LEU* 3.5 17.5 - - + +
481F LEU 3.2 0.2 - - - -
482F SER* 1.3 76.6 - - - +
484F LEU* 1.3 65.7 + - + +
485F PHE 3.3 0.9 + - - -
486F LYS* 3.4 10.4 + - - +
487F SER* 3.4 15.0 + - - +
492F ALA* 4.1 25.1 - - + +
494F LEU* 4.2 24.9 - - + -
512F HIS* 5.5 1.1 + - + -
591F VAL* 5.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F PRO* 4.8 0.2 - - - +
480F LEU* 2.9 25.3 + - + +
481F LEU* 3.3 10.9 + - + +
483F ILE* 1.3 78.5 - - + +
485F PHE* 1.3 61.2 + - - +
486F LYS 3.5 0.2 + - - -
487F SER 4.4 3.8 - - - +
494F LEU* 4.2 13.0 - - + -
496F MET* 5.7 0.7 - - + -
507F TYR* 4.7 18.4 - - + -
510F ILE* 4.1 21.1 - - + -
512F HIS* 3.4 42.8 - - + +
704F VAL* 4.9 11.4 - - + -
705F VAL* 5.1 7.0 - - + -
708F TRP* 3.2 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 485 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F LEU* 4.1 11.5 - - - +
316F PRO* 4.3 26.1 - - + +
317F PRO 3.8 19.3 - - - -
318F LEU* 3.6 30.6 - - + +
320F LEU* 5.5 1.3 - - + -
321F LEU* 3.7 24.2 - - + -
423F PHE* 3.9 4.9 - + - -
427F LEU* 3.7 13.7 - - + -
432F TYR* 3.4 18.5 + - + +
481F LEU* 3.0 48.8 + - + +
482F SER 4.0 0.2 + - - -
483F ILE 3.3 0.6 - - - -
484F LEU* 1.3 78.5 - - - +
486F LYS* 1.3 59.0 + - - +
704F VAL* 3.5 30.3 - - + -
----------------------------------------------------------
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