Contacts of the helix formed by residues 466 - 487 (chain B) in PDB entry 6TD2
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 THR 466 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B SER* 3.5 19.1 - - - +
464B ASN 5.2 1.1 - - - +
465B TYR* 1.3 74.7 - - - +
467B THR* 1.3 66.4 + - - +
468B GLU* 3.8 16.0 + - - +
469B GLU* 2.9 47.5 + - - +
470B ARG* 3.0 11.8 + - - +
515B LEU* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B TYR 4.0 0.6 + - - -
466B THR* 1.3 73.9 - - - +
468B GLU* 1.3 72.9 + - - +
470B ARG* 3.2 33.4 + - - +
471B ILE* 3.1 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B THR* 3.9 14.3 + - - +
467B THR* 1.3 87.1 + - - +
469B GLU* 1.3 57.9 + - - +
471B ILE* 3.3 13.6 + - + +
472B PHE* 2.8 30.2 + - - +
515B LEU* 4.3 25.0 - - + +
602B EDO 3.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B HIS* 2.9 32.9 + - + +
434B ALA* 3.7 2.8 - - - -
435B SER* 2.7 49.1 + - - -
453B PHE* 3.9 14.3 - - + -
458B PRO* 3.7 5.2 - - - +
465B TYR* 3.6 18.1 - - + -
466B THR* 2.9 34.8 + - - +
468B GLU* 1.3 75.7 - - - +
470B ARG* 1.3 59.2 + - - +
472B PHE* 3.7 7.3 - - - +
473B ALA* 2.9 29.5 + - - +
515B LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B PRO* 3.8 27.9 - - - +
459B LEU* 4.2 20.8 - - + +
466B THR 3.0 10.6 + - - +
467B THR* 3.2 34.1 + - - +
469B GLU* 1.3 75.5 - - - +
471B ILE* 1.3 72.6 + - - +
473B ALA* 3.1 4.7 + - - +
474B GLN* 3.1 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B THR* 3.1 22.0 + - + +
468B GLU* 3.3 15.0 + - + +
470B ARG* 1.3 88.9 - - - +
472B PHE* 1.3 63.0 + - - +
474B GLN* 3.3 13.1 + - - +
475B ARG* 3.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PHE* 3.5 33.0 - + - -
432B HIS* 3.9 13.0 - + + -
453B PHE* 4.1 18.8 - + - -
468B GLU 2.8 19.8 + - - +
469B GLU* 3.7 4.3 - - - +
470B ARG 3.2 0.2 - - - -
471B ILE* 1.3 72.6 - - - +
473B ALA* 1.3 64.3 + - - +
475B ARG* 3.2 31.8 + - - +
476B LEU* 3.1 46.9 + - + +
513B LEU* 3.9 2.5 - - + -
514B ASN* 3.1 39.0 - - - -
515B LEU* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B PHE* 3.6 22.7 - - + +
456B GLY* 4.4 2.9 - - - -
458B PRO* 3.5 25.4 - - + -
459B LEU* 4.1 10.3 - - + -
469B GLU 2.9 18.2 + - - +
470B ARG 3.6 4.3 - - - +
472B PHE* 1.3 76.9 - - - +
474B GLN* 1.3 59.0 + - - +
476B LEU* 3.1 7.1 + - - +
477B MET* 2.9 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 5.0 14.6 - - + +
142B GLU* 4.6 2.5 - - - +
459B LEU* 3.9 23.8 - - + +
470B ARG* 3.1 47.6 + - - +
471B ILE* 3.8 10.6 - - - +
473B ALA* 1.3 76.8 - - - +
475B ARG* 1.3 61.9 + - - +
477B MET* 3.5 10.3 + - - +
478B LYS* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE* 3.1 19.4 + - - +
472B PHE* 3.4 34.4 - - + +
474B GLN* 1.3 77.0 - - - +
476B LEU* 1.3 61.8 + - + +
478B LYS* 3.2 8.4 + - + +
479B TYR* 3.1 58.0 + - + +
512B SER 4.9 0.4 + - - -
513B LEU* 5.0 1.2 - - - +
514B ASN 3.4 30.5 + - - +
515B LEU 3.9 12.1 + - - -
516B LYS 3.5 11.9 + - - -
517B PRO* 4.8 5.0 - - - +
518B LEU* 4.0 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PHE* 3.5 26.2 - - + -
453B PHE* 3.6 25.4 - - + +
454B ILE* 3.9 17.5 - - + -
472B PHE* 3.1 29.9 + - + +
473B ALA 3.1 4.7 + - - +
475B ARG* 1.3 72.6 - - - +
477B MET* 1.3 68.4 + - - +
479B TYR* 3.0 10.7 + - + -
480B TRP* 3.0 32.6 + - + +
513B LEU* 3.6 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 3.5 34.1 - - + +
138B LEU* 3.6 20.4 - - + +
141B VAL* 3.8 24.7 - - + -
142B GLU* 4.3 9.2 - - + +
454B ILE 3.4 23.8 + - - +
456B GLY* 3.5 26.2 - - - -
459B LEU* 4.4 12.6 - - - -
473B ALA 2.9 19.6 + - - +
474B GLN* 3.8 8.5 - - - +
476B LEU* 1.3 75.6 - - - +
478B LYS* 1.3 51.5 + - - +
480B TRP* 3.4 2.9 + - - +
481B THR* 2.7 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 2.9 38.2 + - - +
474B GLN 3.2 13.2 + - - +
475B ARG* 3.5 11.2 - - + +
476B LEU 3.1 0.8 - - - -
477B MET* 1.3 75.1 - - - +
479B TYR* 1.3 61.5 + - + +
481B THR* 3.5 5.2 - - - -
482B ASN* 2.8 50.0 + - - +
485B ARG* 4.8 4.2 - - - +
491B ASP* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 5.7 0.2 - - - -
475B ARG* 3.1 53.5 + - + +
476B LEU* 3.0 25.6 + - + +
478B LYS* 1.3 75.6 - - + +
480B TRP* 1.3 71.6 + + + +
483B PHE* 2.9 29.2 + - - +
489B PRO* 3.2 36.1 - - + +
490B ASN* 5.5 4.9 - - - -
491B ASP* 5.6 2.5 - - + -
500B TRP* 4.1 11.7 - + + -
513B LEU* 3.8 23.8 - - + -
518B LEU* 3.3 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.8 13.0 - - + +
138B LEU* 5.7 2.9 - - + -
198B THR* 5.8 0.5 - - - +
200B PHE* 3.8 18.8 - + - -
226B VAL* 3.6 15.9 - - + +
228B GLN* 2.9 28.7 + - + -
327B LEU* 3.8 18.2 - - + -
428B TYR* 3.7 38.8 - + - -
454B ILE* 3.4 48.3 - - + +
476B LEU* 3.0 24.0 + - + +
477B MET* 4.0 4.0 - - - +
479B TYR* 1.3 89.2 - - + +
481B THR* 1.3 62.6 + - + +
483B PHE* 3.1 10.3 + - - +
484B ALA* 2.9 26.0 + - - +
500B TRP* 4.7 4.9 - + - -
513B LEU* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.7 9.4 - - + -
138B LEU* 3.9 16.4 - - + -
142B GLU* 3.4 29.9 + - + -
144B ALA* 4.7 14.1 - - + -
477B MET 2.7 24.5 + - - +
478B LYS* 3.4 4.5 + - - -
480B TRP* 1.3 71.8 - - - +
482B ASN* 1.3 67.6 + - - +
484B ALA* 3.0 9.3 + - - +
485B ARG* 2.9 52.4 + - - +
603B EDO 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LYS* 2.8 49.9 + - - +
479B TYR* 3.9 2.7 - - - +
481B THR* 1.3 73.0 + - - +
483B PHE* 1.3 57.6 + - - +
485B ARG* 2.7 28.2 + - - +
486B THR* 2.2 38.9 + - - +
488B ASP 3.5 12.1 - - - +
489B PRO 3.9 6.2 + - - +
490B ASN 4.3 7.4 - - - +
491B ASP* 3.8 22.9 + - - +
492B PRO* 3.8 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B THR* 4.4 4.9 - - + -
224B ARG* 3.3 18.1 - - + -
225B ALA 3.1 29.4 - - - -
226B VAL* 3.5 23.6 - - + -
325B GLN* 3.6 21.5 - - + -
326B VAL 3.6 16.8 - - - -
327B LEU* 3.8 12.3 - - + -
426B TYR* 4.5 3.6 - + - -
479B TYR 2.9 16.1 + - - +
480B TRP* 3.1 10.7 + - - +
482B ASN* 1.3 77.8 - - - +
484B ALA* 1.3 59.2 + - - +
487B GLY* 2.6 66.5 + - - -
488B ASP 3.7 6.9 + - - -
489B PRO* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 4.6 9.0 - - + -
114B VAL 4.9 0.7 - - - +
115B LEU* 3.6 31.2 - - + -
196B SER* 3.5 5.7 + - - -
198B THR* 3.2 27.5 + - + +
224B ARG* 2.6 28.8 + - - -
480B TRP 2.9 11.5 + - - +
481B THR* 3.0 7.6 + - - +
483B PHE* 1.3 77.0 - - - +
485B ARG* 1.3 59.2 + - + +
603B EDO 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 4.1 23.3 - - + -
142B GLU* 2.9 41.2 + - - -
196B SER* 4.6 1.8 + - - -
224B ARG* 4.7 6.1 + - - -
478B LYS* 4.8 4.0 - - - +
481B THR* 2.9 29.9 + - - +
482B ASN* 2.7 41.7 + - - +
484B ALA* 1.3 76.4 - - - +
486B THR* 1.3 67.8 + - + +
603B EDO 3.3 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 4.5 6.2 + - - -
325B GLN* 4.2 9.0 + - - -
482B ASN* 2.2 33.7 + - - +
485B ARG* 1.3 91.2 - - + +
487B GLY* 1.3 57.8 + - - +
488B ASP* 2.9 24.4 + - - +
490B ASN 5.3 0.3 + - - -
492B PRO* 6.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 3.6 4.3 - - - +
325B GLN* 3.8 28.2 - - - +
424B ARG* 4.7 3.9 - - - -
426B TYR* 3.3 14.2 - - - -
483B PHE* 2.6 49.0 + - - -
486B THR* 1.3 71.6 - - - +
488B ASP* 1.3 56.7 + - - +
----------------------------------------------------------
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