Contacts of the helix formed by residues 509 - 526 (chain D) in PDB entry 6E7P
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 VAL 509 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 6.0 1.6 - - + -
428D PHE* 4.0 12.9 - - + -
432D VAL* 3.8 37.2 - - + -
435D ILE* 6.3 2.2 - - + -
504D LEU* 3.5 13.1 + - + +
505D PHE* 3.5 39.9 + - + +
508D MET* 1.3 83.3 - - + +
510D LEU* 1.3 66.3 + - - +
511D SER 3.2 1.3 - - - -
512D LEU* 3.2 16.9 + - - +
513D PHE* 3.7 15.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 510 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LEU* 6.4 1.1 - - + -
514A ILE* 6.3 1.6 - - + -
506C ILE* 4.4 13.0 - - + +
507C TYR* 3.6 34.5 - - + -
510C LEU* 6.5 0.7 - - + -
468D ILE 5.9 1.6 - - - +
505D PHE 2.8 17.2 + - - +
506D ILE* 3.4 35.0 + - + +
509D VAL* 1.3 74.0 - - - +
511D SER* 1.3 61.8 + - - +
513D PHE* 3.3 16.4 + - + +
514D ILE* 3.4 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 511 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PHE* 3.0 30.6 + - - +
514A ILE* 3.9 12.9 - - - +
517A ILE* 3.7 22.1 - - - +
518A THR* 5.1 1.2 + - - -
506D ILE 4.0 7.2 + - - -
507D TYR* 3.6 14.5 + - - -
508D MET 4.7 3.1 - - - -
509D VAL 3.2 2.0 - - - +
510D LEU* 1.3 76.2 - - - +
512D LEU* 1.3 59.4 + - - +
514D ILE* 3.5 11.0 + - - +
515D ALA* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 4.6 20.0 - - + +
417A THR* 4.6 17.0 - - + -
418A LEU* 3.6 21.5 - - + -
517A ILE* 3.7 23.6 - - + -
521A TYR* 4.9 3.4 - - + -
428D PHE* 3.7 28.7 - - + -
508D MET 3.3 24.7 - - - +
509D VAL 3.2 10.7 + - - +
511D SER* 1.3 78.0 - - - +
513D PHE* 1.3 56.2 + - - +
515D ALA* 2.8 8.0 + - + -
516D LEU* 2.7 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 513 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TYR* 3.7 58.6 - + + +
511C SER* 3.1 16.6 + - - +
425D VAL* 3.9 38.4 - - + -
428D PHE* 3.4 33.2 - + + -
429D CYS* 4.8 15.9 - - + -
432D VAL* 5.1 4.7 - - + -
509D VAL* 3.7 19.2 + - + -
510D LEU* 3.3 12.6 + - + +
512D LEU* 1.3 76.9 - - - +
514D ILE* 1.3 56.5 + - + +
516D LEU* 4.3 5.4 - - + +
517D ILE* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 514 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 3.8 46.7 - - + -
518A THR* 5.1 2.5 - - - +
510C LEU* 6.4 1.1 - - + -
511C SER* 3.9 16.8 - - - +
514C ILE* 3.9 41.5 - - + -
510D LEU* 3.4 30.3 + - + +
511D SER* 3.9 6.3 - - - +
512D LEU 3.1 0.8 - - - -
513D PHE* 1.3 79.5 - - + +
515D ALA* 1.3 61.0 + - - +
517D ILE* 3.7 1.9 + - - +
518D THR* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 515 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 4.5 7.6 - - + +
518A THR* 3.8 34.8 + - - +
521A TYR* 4.2 16.0 - - + -
511D SER 3.0 16.6 + - - +
512D LEU* 2.8 12.6 + - + +
514D ILE* 1.3 76.5 - - - +
516D LEU* 1.3 60.1 + - - +
518D THR* 3.8 3.3 - - - -
519D GLY* 2.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.8 21.1 - - + -
521A TYR* 3.4 39.2 - - + +
421D ALA* 5.0 2.0 - - + +
424D SER* 3.7 39.3 - - - +
425D VAL* 4.5 14.4 - - + +
428D PHE* 4.6 9.2 - - + -
512D LEU* 2.7 31.2 + - + +
513D PHE* 4.8 8.1 - - + +
515D ALA* 1.3 72.8 - - - +
517D ILE* 1.3 62.7 + - + +
519D GLY* 3.3 2.1 + - - -
520D ALA* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 517 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TYR 4.5 4.0 - - - +
508C MET* 4.8 12.8 - - + +
511C SER* 3.8 26.7 - - - +
512C LEU* 3.7 34.3 - - + -
515C ALA* 4.6 2.5 - - + -
417D THR* 4.7 7.0 - - + +
418D LEU* 5.3 4.3 - - + -
421D ALA* 3.7 25.6 - - + -
425D VAL* 4.3 18.2 - - + -
513D PHE 3.3 18.2 - - - +
514D ILE 3.7 1.9 + - - +
515D ALA 3.3 0.4 - - - -
516D LEU* 1.3 74.1 - - + +
518D THR* 1.3 61.1 + - - +
520D ALA* 3.2 4.0 + - - +
521D TYR* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 518 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 4.8 18.2 - - + -
511C SER 5.1 0.2 + - - -
514C ILE* 5.2 1.7 - - - +
515C ALA* 3.8 25.4 + - + +
518C THR* 4.9 18.1 - - + -
514D ILE* 3.0 24.3 + - - +
515D ALA* 3.9 5.6 - - - -
517D ILE* 1.3 79.4 - - - +
519D GLY* 1.3 61.1 + - - +
521D TYR* 3.2 12.6 + - + +
522D ASP* 3.3 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 519 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A TYR* 4.3 18.7 - - - -
522A ASP* 5.8 2.5 - - - -
525A LYS* 5.2 6.3 + - - -
515D ALA 2.8 19.1 + - - -
516D LEU 3.3 3.1 + - - -
518D THR* 1.3 76.6 - - - +
520D ALA* 1.3 57.5 + - - +
522D ASP* 4.2 7.6 + - - +
523D THR* 3.5 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D THR* 4.5 5.5 - - + +
420D VAL* 4.3 15.3 - - + +
421D ALA* 3.9 26.2 - - + -
516D LEU 2.8 17.1 + - - +
517D ILE 3.8 3.8 - - - +
519D GLY* 1.3 74.5 - - - +
521D TYR* 1.3 63.6 + - - +
522D ASP 3.2 2.0 - - - -
523D THR* 2.6 25.6 + - - +
524D ILE* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 521 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C SER* 5.7 0.5 + - - -
512C LEU* 4.9 5.8 - - + -
515C ALA* 4.3 23.8 - - + -
516C LEU* 3.5 33.7 - - + +
519C GLY* 4.5 15.4 - - - -
413D ILE* 4.8 13.1 - - + +
414D LEU* 4.5 9.7 - - + +
417D THR* 4.0 27.3 - - + +
517D ILE* 2.8 17.1 + - + +
518D THR* 3.2 9.3 + - + +
520D ALA* 1.3 75.3 - - - +
522D ASP* 1.3 69.6 + - - +
524D ILE* 3.4 16.0 - - + +
525D LYS* 3.5 39.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 522 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ASP* 5.7 1.4 - - - +
519C GLY* 6.0 2.1 - - - -
518D THR* 3.3 22.5 + - - +
519D GLY* 4.4 8.3 - - - +
520D ALA 3.2 0.6 - - - -
521D TYR* 1.3 87.8 - - - +
523D THR* 1.3 62.9 + - + +
525D LYS* 3.8 6.5 + - - +
526D HIS* 3.3 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 523 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LYS* 5.1 12.3 - - - +
420D VAL* 4.7 6.6 - - - +
519D GLY 3.5 17.5 - - - +
520D ALA* 2.6 25.2 + - - +
522D ASP* 1.3 80.1 - - + +
524D ILE* 1.3 63.5 + - - +
525D LYS 3.5 0.2 + - - -
526D HIS 3.6 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 524 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D ILE* 3.3 44.8 - - + +
416D ALA* 3.5 19.5 - - + +
417D THR* 3.4 32.1 - - - +
420D VAL* 5.1 8.7 - - + -
520D ALA 3.9 9.2 - - - +
521D TYR* 3.4 21.5 - - + +
523D THR* 1.3 82.9 + - - +
525D LYS* 1.3 63.6 + - + +
526D HIS 3.8 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 525 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C GLY* 5.4 5.0 + - - +
523C THR* 5.2 11.5 - - - +
413D ILE* 5.3 8.7 - - + -
521D TYR* 3.5 50.9 - - + +
522D ASP* 4.2 4.5 - - - +
524D ILE* 1.3 83.5 - - + +
526D HIS* 1.3 104.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 526 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D ASP* 3.3 21.7 + - + +
523D THR* 3.7 15.1 - - - +
524D ILE 3.5 0.9 - - - +
525D LYS* 1.3 129.1 + - + +
----------------------------------------------------------
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