Contacts of the helix formed by residues 493 - 506 (chain D) in PDB entry 4JVG
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 GLN 493 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D PHE* 4.1 26.0 - - + -
491D THR* 3.8 7.7 + - - +
492D PRO* 1.3 83.1 - - + +
494D GLN* 1.3 66.2 + - + +
496D GLN* 2.9 22.2 + - - +
497D ALA 3.2 6.1 + - - -
600D VAL* 5.4 0.7 - - - +
601D LYS* 4.7 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 494 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D PHE* 4.0 16.4 - - + -
485D LEU* 3.3 46.8 - - + +
487D VAL* 3.9 26.5 - - - +
488D THR 4.5 1.0 + - - -
490D PRO* 3.0 18.1 - - + +
491D THR* 2.7 50.0 + - + +
493D GLN* 1.3 72.9 - - + +
495D LEU* 1.3 53.9 + - - +
496D GLN 2.6 15.6 + - - -
497D ALA* 3.0 13.8 + - - +
498D PHE* 3.2 12.6 + - - +
525D LEU* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D PRO* 4.7 14.1 - - + +
491D THR 2.8 19.2 + - - +
492D PRO* 3.7 10.5 - - + +
493D GLN 3.3 0.4 - - - -
494D GLN* 1.3 71.0 - - - +
496D GLN* 1.3 69.9 + - - +
498D PHE* 4.3 16.8 - - + -
499D LYS* 3.3 44.5 + - + +
525D LEU* 4.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D PRO 3.2 10.6 + - - +
493D GLN* 2.9 12.7 + - - +
494D GLN 2.6 6.3 + - - -
495D LEU* 1.3 92.8 - - - +
497D ALA* 1.3 64.4 + - - +
498D PHE 2.7 5.8 + - - -
499D LYS* 3.0 23.2 + - - +
500D ASN* 2.6 60.5 + - - +
600D VAL* 4.7 4.7 - - + -
601D LYS* 4.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 497 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D PHE* 4.0 34.5 - - + +
485D LEU* 5.9 3.8 - - + -
493D GLN 3.2 3.2 + - - -
494D GLN* 3.0 7.0 + - - +
496D GLN* 1.3 75.5 - - - +
498D PHE* 1.3 55.3 + - - +
500D ASN* 3.7 2.0 + - - +
501D GLU* 2.9 32.9 + - - +
599D THR 5.1 0.2 - - - +
600D VAL* 3.9 25.4 - - + +
801D B96 3.8 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 498 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D LEU* 5.3 9.6 - - + +
494D GLN 3.2 14.2 + - - +
495D LEU* 4.4 15.9 - - + +
496D GLN 2.7 4.2 + - - -
497D ALA* 1.3 70.0 - - - +
499D LYS* 1.3 69.7 + - + +
500D ASN 2.8 5.7 + - - -
501D GLU* 2.8 12.0 + - - -
502D VAL* 3.0 25.8 + - + +
519D TYR* 3.8 28.7 - + + -
520D SER 4.0 5.6 - - - -
521D THR* 4.3 9.6 - - + -
525D LEU* 3.8 38.1 - - + -
526D ALA 3.4 31.4 - - - -
527D ILE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 499 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D LEU* 3.3 48.5 + - + +
496D GLN* 3.0 23.5 + - - +
498D PHE* 1.3 82.3 - - + +
500D ASN* 1.3 61.7 + - - +
502D VAL* 4.7 3.9 - - - +
503D GLY* 3.3 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 500 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D GLN* 2.6 56.9 + - - +
497D ALA* 3.7 6.7 - - - +
498D PHE 2.8 0.4 + - - -
499D LYS* 1.3 73.1 + - - +
501D GLU* 1.3 63.7 + - - +
503D GLY* 3.6 6.4 + - - -
504D VAL* 3.6 14.2 + - - +
600D VAL* 3.3 23.0 - - + +
601D LYS* 4.0 20.2 + - - +
801D B96 4.4 9.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 501 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D LYS* 3.0 22.9 + - - +
497D ALA* 2.9 17.6 + - - +
498D PHE 2.8 7.9 + - - -
500D ASN* 1.3 68.7 - - - +
502D VAL* 1.3 66.3 + - - +
503D GLY 3.1 1.6 - - - -
504D VAL* 3.0 3.8 - - - +
505D LEU* 2.9 39.2 + - + +
527D ILE* 3.2 26.1 - - + +
801D B96 2.6 78.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 502 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D PHE* 3.0 33.9 + - + +
499D LYS* 4.7 2.7 - - - +
501D GLU* 1.3 75.8 - - - +
503D GLY* 1.3 53.5 + - - +
505D LEU* 4.7 4.3 - - - -
506D ARG* 2.8 47.9 + - + +
516D PHE* 4.1 11.4 - - + -
519D TYR* 3.4 52.0 - - + -
527D ILE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 503 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D LYS 3.3 16.7 + - - -
500D ASN 3.9 2.5 - - - -
501D GLU 3.1 1.4 - - - -
502D VAL* 1.3 79.3 - - - +
504D VAL* 1.3 55.9 + - - +
506D ARG* 3.1 15.0 - - - +
507D LYS* 3.1 31.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 504 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D ASN 3.6 13.3 + - - +
501D GLU 3.0 10.8 - - - +
503D GLY* 1.3 71.6 - - - +
505D LEU* 1.3 65.9 + - - +
506D ARG 3.1 1.6 - - - -
507D LYS* 2.6 37.9 + - - +
508D THR* 3.6 4.3 + - - +
572D ILE* 3.4 39.9 - - + -
801D B96 3.7 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C ARG* 3.4 10.4 + - - -
501D GLU* 2.9 44.7 + - + +
502D VAL 4.3 0.9 - - - +
504D VAL* 1.3 74.6 - - + +
506D ARG* 1.3 60.0 + - - +
507D LYS 3.0 2.9 + - - -
508D THR* 2.8 32.7 + - - +
513D ILE* 5.2 1.8 - - + -
514D LEU* 4.6 11.2 - - + +
516D PHE* 3.8 35.2 - - + +
527D ILE* 4.5 3.8 - - + -
529D THR* 5.1 4.3 - - + -
801D B96 3.7 53.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 506 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ASP* 3.0 48.7 + - - +
450C TRP* 3.5 16.4 - - - +
509C ARG* 2.8 23.6 + - - +
448D ASP* 4.6 16.8 + - - +
450D TRP* 2.9 45.4 - - + +
502D VAL* 2.8 33.8 + - + +
503D GLY* 3.1 18.4 - - - +
505D LEU* 1.3 76.2 - - - +
507D LYS* 1.3 57.7 + - + +
516D PHE* 3.7 19.2 - - + -
519D TYR* 5.3 5.7 + - - -
----------------------------------------------------------
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