Contacts of the helix formed by residues 539 - 553 (chain F) in PDB entry 6V3O
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 ALA 539 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F GLU* 3.3 34.8 - - + +
537F ALA* 5.5 1.4 - - - +
538F THR* 1.3 84.0 + - - +
540F PRO* 1.3 75.5 - - + +
541F SER* 3.2 3.3 + - - +
542F ASP* 3.0 20.5 + - - +
543F VAL* 4.0 5.0 + - - +
565F PHE* 5.0 3.0 - - - -
577F SER* 4.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 540 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F GLU* 3.8 6.5 - - + +
487F GLN* 3.6 24.5 - - + +
539F ALA* 1.3 89.1 - - + +
541F SER* 1.3 60.2 + - - +
543F VAL* 3.1 15.0 + - + +
544F LEU* 3.1 18.2 + - + +
577F SER* 3.6 35.2 - - - +
580F ARG* 4.5 10.5 - - + -
581F LEU* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478F TYR* 3.9 16.2 - - - -
483F GLU* 2.4 40.0 + - - -
486F ARG* 4.0 16.1 + - - -
487F GLN* 4.6 3.7 - - - +
490F LEU* 3.7 14.7 - - - +
539F ALA* 4.0 2.3 - - - +
540F PRO* 1.3 75.3 - - - +
542F ASP* 1.3 62.8 + - - +
544F LEU* 4.4 4.3 - - - +
545F ALA* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 542 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459F SER* 3.7 28.7 + - - -
460F GLU* 5.1 2.3 - - - +
462F HIS* 5.1 1.6 + - - +
463F THR* 4.6 13.0 - - - +
486F ARG* 5.0 4.5 + - - -
534F ILE* 3.3 23.2 - - + +
537F ALA* 4.6 4.7 - - + -
538F THR* 2.5 44.0 + - - +
539F ALA* 3.0 11.4 + - - +
540F PRO 3.2 0.8 - - - -
541F SER* 1.3 82.3 + - - +
543F VAL* 1.3 61.7 + - + +
545F ALA* 3.8 5.6 + - - +
546F VAL* 3.7 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 543 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534F ILE* 3.7 12.1 - - + -
537F ALA* 5.8 0.2 - - + -
539F ALA 4.8 5.2 - - - +
540F PRO* 3.1 9.0 + - + +
542F ASP* 1.3 77.4 - - + +
544F LEU* 1.3 66.2 + - - +
546F VAL* 3.2 14.2 + - - +
547F GLU* 3.2 11.8 + - + +
561F VAL* 3.5 27.2 - - + +
563F PRO* 4.0 34.3 - - + -
581F LEU* 4.1 22.4 - - + -
587F TYR* 3.7 24.7 - - + +
595F GLN* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487F GLN* 4.8 13.0 - - + -
490F LEU* 4.0 19.7 - - + +
491F LEU* 4.0 30.3 - - + -
494F LEU* 4.1 22.7 - - + +
540F PRO* 3.1 19.4 + - + +
541F SER* 4.8 2.7 - - - -
543F VAL* 1.3 76.2 - - - +
545F ALA* 1.3 63.0 + - - +
547F GLU* 3.2 6.6 + - + +
548F LEU* 3.0 23.9 + - - +
581F LEU* 4.0 13.0 - - + -
584F VAL* 5.7 4.7 - - + -
586F TRP* 4.8 3.1 - - + -
587F TYR* 4.0 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 545 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F HIS* 4.8 12.3 - - + -
463F THR* 5.7 3.6 - - + -
466F ILE* 3.6 26.0 - - + +
478F TYR* 4.1 11.0 - - + +
490F LEU* 4.0 6.9 - - + +
541F SER 2.8 18.7 + - - +
542F ASP* 3.9 7.4 - - - +
543F VAL 3.2 0.2 - - - -
544F LEU* 1.3 77.9 - - - +
546F VAL* 1.3 56.5 + - - +
548F LEU* 3.5 3.0 + - - +
549F LEU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 546 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F HIS* 3.4 43.3 - - + +
518F PHE* 4.2 11.0 - - + -
532F TYR* 3.7 27.8 - - + -
534F ILE* 3.8 11.9 - - + -
542F ASP 3.7 12.3 + - - +
543F VAL 3.2 8.3 + - - +
545F ALA* 1.3 74.7 - - - +
547F GLU* 1.3 60.3 + - - +
549F LEU* 4.3 4.9 - - - +
550F GLN* 2.7 33.2 + - + +
561F VAL* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F LEU* 4.3 5.3 - - + +
543F VAL 3.2 15.0 + - - +
544F LEU* 3.2 12.8 + - - +
546F VAL* 1.3 76.9 - - - +
548F LEU* 1.3 61.0 + - - +
550F GLN* 3.5 16.6 + - - +
551F ARG* 3.3 21.3 + - - +
559F LEU 4.4 2.5 - - - +
560F PRO* 5.8 0.2 - - - +
561F VAL* 3.2 30.1 + - + +
586F TRP* 4.0 22.0 - - + -
587F TYR* 3.5 16.8 - - + -
590F ARG* 2.8 45.6 + - - +
591F ILE* 4.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466F ILE* 4.6 8.7 - - + -
489F TRP* 4.1 9.0 - - + -
490F LEU* 3.8 24.5 - - + -
493F GLU* 4.0 18.6 - - + -
494F LEU* 3.7 25.3 - - + +
500F LEU* 3.9 22.9 - - + -
544F LEU 3.0 13.1 + - - +
545F ALA* 3.6 8.3 - - - +
547F GLU* 1.3 76.3 - - - +
549F LEU* 1.3 62.1 + - + +
551F ARG* 3.1 22.8 + - - +
552F GLU* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F HIS* 4.1 46.4 - - + +
465F VAL* 3.6 27.8 - - + -
466F ILE* 4.2 15.7 - - + -
469F ILE* 4.4 9.9 - - + -
501F LEU* 5.8 2.0 - - + -
514F VAL* 4.9 1.6 - - + -
515F ILE* 6.0 1.1 - - + -
518F PHE* 4.0 22.2 - - + -
545F ALA 3.0 21.2 + - - +
546F VAL* 3.8 3.1 - - - +
548F LEU* 1.3 78.2 - - + +
550F GLN* 1.3 62.8 + - - +
552F GLU* 4.5 7.0 - - + +
553F CYS* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 550 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518F PHE* 3.8 24.1 - - + -
521F LEU* 5.2 1.0 - - + +
532F TYR* 5.4 1.8 - - + -
546F VAL* 2.7 23.8 + - + +
547F GLU* 3.5 22.3 + - - +
549F LEU* 1.3 74.5 - - - +
551F ARG* 1.3 60.5 + - - +
553F CYS 3.4 0.5 + - - -
554F GLY 3.4 3.1 + - - -
555F VAL* 3.0 46.7 + - + +
558F PRO* 3.3 16.2 - - + +
559F LEU* 2.5 59.7 + - - +
561F VAL* 3.9 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 551 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493F GLU* 2.9 26.3 + - - +
494F LEU* 2.9 37.9 + - - +
496F GLY 4.1 9.5 + - - -
497F LYS* 5.8 0.8 - - - -
498F ARG 4.8 7.9 + - - +
547F GLU 3.3 10.1 + - - +
548F LEU* 3.1 17.0 + - - +
550F GLN* 1.3 79.0 - - - +
552F GLU* 1.3 80.0 + - - +
554F GLY* 3.1 18.7 + - - -
555F VAL 4.3 8.2 + - - +
558F PRO* 6.5 0.2 - - - -
586F TRP* 4.5 6.9 - - - +
590F ARG* 4.7 16.2 - - - +
503G PRO* 5.3 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 552 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498F ARG 4.9 0.6 - - - -
499F PRO* 3.2 13.3 - - - +
500F LEU* 2.5 47.3 + - + +
501F LEU* 3.8 27.2 + - + +
548F LEU* 2.9 35.0 + - + +
549F LEU* 3.9 8.1 - - + +
551F ARG* 1.3 107.1 + - - +
553F CYS* 1.3 60.2 + - - +
554F GLY 3.4 0.7 - - - -
503G PRO* 5.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 553 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501F LEU* 5.5 6.7 - - - -
515F ILE* 4.0 30.7 - - - -
518F PHE* 3.5 36.8 - - + +
519F HIS* 3.3 28.0 - - + -
522F ALA* 4.2 6.6 - - - +
549F LEU* 3.0 27.5 + - - +
550F GLN 3.9 2.5 - - - +
551F ARG 3.2 0.2 - - - -
552F GLU* 1.3 78.3 - - - +
554F GLY* 1.3 60.5 + - - +
555F VAL* 3.6 0.9 - - + -
----------------------------------------------------------
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