Contacts of the helix formed by residues 461 - 473 (chain B) in PDB entry 6IWQ
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 461 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 3.6 7.6 - - + +
412B TRP* 2.7 53.8 - - + +
413B GLY* 4.1 3.1 - - - -
459B SER* 2.6 21.1 + - - +
460B PRO* 1.3 77.6 - - + +
462B LEU* 1.3 60.9 + - - +
463B LYS 2.9 2.5 - - - -
464B ASN* 2.5 42.3 + - - +
465B TYR* 2.9 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B SER* 2.5 31.6 - - - +
459B SER* 2.6 13.0 - - - +
461B THR* 1.3 76.1 + - - +
463B LYS* 1.3 58.1 + - - -
465B TYR* 3.4 11.5 + - + +
466B VAL* 3.3 21.1 + - - +
480B PHE* 4.4 6.1 - - + -
484B ARG* 3.4 45.3 - - + +
486B GLU* 4.6 11.9 - - + +
487B SER* 4.0 21.3 - - - -
490B LEU* 3.3 28.5 - - + -
655B HIS* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLY 5.9 0.7 - - - +
410B GLN* 4.1 23.9 - - + +
456B VAL* 4.3 20.8 + - - +
457B GLY* 4.6 9.7 - - - -
458B SER 2.6 10.2 + - - +
460B PRO* 3.3 16.6 - - + +
461B THR 2.8 1.2 + - - -
462B LEU* 1.3 75.7 - - - +
464B ASN* 1.3 64.2 + - - +
466B VAL* 3.7 4.7 + - - +
467B ARG* 3.4 26.3 + - - +
490B LEU* 4.3 15.3 - - + +
491B PRO* 2.7 30.6 - - - +
492B TYR* 4.1 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLY 4.0 2.3 - - - +
409B LEU* 3.7 19.8 - - + +
410B GLN* 2.8 53.7 + - - +
413B GLY* 2.9 29.1 - - - +
414B GLY 4.2 1.3 - - - +
460B PRO 3.6 7.8 - - - +
461B THR* 2.5 24.0 + - - +
463B LYS* 1.3 73.0 - - - +
465B TYR* 1.3 64.8 + - - +
466B VAL 3.2 0.2 - - - -
467B ARG* 3.2 5.4 + - - +
468B VAL* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B SER 4.1 6.3 - - - -
360B MET* 4.0 36.5 + - + -
361B LEU* 4.5 9.1 - - + +
412B TRP* 4.2 20.3 - - - -
413B GLY* 4.1 3.4 + - - -
414B GLY* 3.5 34.5 - - - -
417B PHE* 5.5 1.3 - + - -
461B THR* 2.9 21.4 + - - -
462B LEU* 3.4 17.7 + - + +
464B ASN* 1.3 76.5 - - - +
466B VAL* 1.3 62.6 + - - +
468B VAL* 3.3 4.3 + - - +
469B VAL* 3.0 29.2 + - - +
480B PHE* 3.8 15.3 - + + -
484B ARG* 3.7 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B LEU 3.3 15.9 + - - +
463B LYS* 4.1 5.4 - - - +
464B ASN 3.2 0.8 - - - -
465B TYR* 1.3 76.5 - - - +
467B ARG* 1.3 64.0 + - - +
469B VAL* 3.8 2.0 - - - +
470B GLU* 2.9 25.4 + - + +
480B PHE* 3.9 15.0 - - + -
481B TYR* 3.5 21.8 - - + +
487B SER* 3.7 36.1 - - - +
490B LEU* 4.4 8.1 - - + +
492B TYR* 3.3 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASP* 3.0 45.6 + - - +
408B GLY* 3.5 32.8 - - - +
409B LEU* 4.5 5.8 - - + -
463B LYS* 3.4 17.2 + - - +
464B ASN* 3.2 11.0 + - - +
466B VAL* 1.3 80.0 - - - +
468B VAL* 1.3 63.1 + - - +
470B GLU* 3.5 3.7 + - - +
471B VAL* 2.9 25.5 + - - +
492B TYR* 2.7 48.0 + - + +
493B GLY* 3.8 15.8 + - - -
494B ASP 3.8 10.9 + - - +
495B ILE* 3.4 15.7 - - + +
498B LEU* 3.4 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B MET* 3.3 28.9 - - + -
406B ASP* 5.6 0.4 + - - +
409B LEU* 4.5 8.3 - - + -
414B GLY* 3.7 21.8 - - - +
418B GLU* 4.0 26.0 - - + +
421B TYR* 3.5 24.7 - - + -
464B ASN 3.1 16.3 + - - +
465B TYR* 3.3 5.8 + - - +
467B ARG* 1.3 76.1 - - - +
469B VAL* 1.3 63.2 + - - +
471B VAL* 3.3 7.3 - - - +
472B TRP* 3.0 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B MET* 4.1 14.4 - - - -
465B TYR 3.0 21.8 + - - +
466B VAL* 3.8 3.6 - - + +
468B VAL* 1.3 74.6 - - - +
470B GLU* 1.3 69.7 + - + +
473B TRP* 2.8 55.6 + - + +
474B ASP 4.1 1.7 + - - -
477B LYS* 3.6 33.3 - - + +
480B PHE* 3.7 34.1 - - + -
481B TYR* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B VAL* 2.9 19.2 + - + +
467B ARG* 4.1 3.8 - - - +
469B VAL* 1.3 79.0 - - - +
471B VAL* 1.3 62.0 + - - +
474B ASP* 4.8 5.7 + - - +
477B LYS* 2.7 48.4 + - - +
481B TYR* 2.5 35.7 + - + +
492B TYR* 3.8 35.0 + - + +
495B ILE* 5.3 7.0 - - + -
499B LYS* 4.4 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASP* 6.1 0.2 - - - +
418B GLU* 5.8 2.0 - - + +
467B ARG 2.9 20.6 - - - +
468B VAL* 3.3 9.6 - - - +
470B GLU* 1.3 82.1 - - - +
472B TRP* 1.3 88.4 + - + +
474B ASP* 4.3 2.1 - - - +
495B ILE* 4.1 20.6 - - + -
498B LEU* 4.0 29.8 - - + +
499B LYS* 4.3 17.8 - - + +
502B ARG* 3.4 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU* 4.1 17.1 + - + +
421B TYR* 4.0 29.2 - - + -
422B LYS* 3.2 36.7 - - + +
425B GLN* 3.7 31.2 - - + +
426B CYS* 3.8 25.8 - - - -
468B VAL* 3.0 23.9 + - + +
471B VAL* 1.3 111.0 - - + +
473B TRP* 1.3 65.8 + - + +
474B ASP 3.3 2.9 - - - -
498B LEU* 5.2 1.7 - - + +
501B PHE* 4.3 9.0 - + - -
502B ARG* 3.1 55.7 + - + -
510B PHE* 3.2 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B TRP* 4.0 16.6 - + - -
357B ASP 4.6 1.1 - - - -
358B TRP* 3.4 39.3 - + - -
360B MET* 4.4 16.4 - - + +
421B TYR* 3.3 41.1 + + - -
469B VAL* 2.8 46.3 + - + +
472B TRP* 1.3 71.0 - - + +
474B ASP* 1.3 69.4 - - - +
475B GLU 3.3 1.7 + - - -
476B TYR* 3.3 27.8 + - + -
477B LYS 4.2 4.7 - - - +
480B PHE* 3.5 35.9 - + + -
510B PHE* 3.4 41.4 - + - +
----------------------------------------------------------
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