Contacts of the helix formed by residues 461 - 476 (chain D) in PDB entry 1IAS
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 CYS 461 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D VAL* 4.3 7.6 - - - -
417D ILE* 3.5 17.3 - - + -
460D SER* 1.3 78.7 - - - +
462D GLU* 1.3 68.1 + - - +
463D ALA* 4.1 8.5 - - - +
464D LEU* 3.3 41.9 + - - +
465D ARG* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D CYS* 1.3 73.6 - - - +
463D ALA* 1.3 66.2 + - - +
465D ARG* 2.9 41.1 + - - +
466D VAL* 2.8 34.9 + - + +
495D LEU* 4.0 19.7 - - + -
498D GLN* 4.6 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D VAL* 3.5 32.5 - - + -
302D MET* 3.9 14.6 - - + -
303D ILE* 4.6 2.0 - - + -
461D CYS* 4.1 5.8 - - - +
462D GLU* 1.3 81.1 - - - +
464D LEU* 1.3 63.9 + - - +
466D VAL* 3.1 3.1 + - - +
467D MET* 3.0 23.2 + - - +
495D LEU* 3.7 26.8 - - + +
499D GLU* 5.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D VAL* 4.5 0.4 - - + -
302D MET* 4.3 8.1 - - + -
412D ALA* 4.2 20.2 - - + +
415D CYS* 3.8 19.5 - - + +
417D ILE* 3.5 18.8 - - + -
457D ARG* 5.2 3.8 - - - +
458D TRP* 3.1 66.2 - - + +
460D SER* 5.4 0.4 - - - -
461D CYS* 3.3 28.1 + - - +
462D GLU 3.4 0.6 - - - -
463D ALA* 1.3 78.3 - - - +
465D ARG* 1.3 56.2 + - - +
467D MET* 3.7 5.8 - - - +
468D ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D TRP 3.8 3.8 - - - +
459D GLN* 2.8 50.2 + - - +
460D SER 3.4 20.6 + - - -
461D CYS* 3.2 17.5 + - - +
462D GLU* 2.9 40.8 + - - +
464D LEU* 1.3 75.0 - - - +
466D VAL* 1.3 65.8 + - - +
468D ALA* 3.0 6.9 + - - +
469D LYS* 2.7 24.8 + - - +
472D ARG* 5.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D GLU* 2.8 44.8 + - + +
463D ALA 3.4 4.7 - - - +
465D ARG* 1.3 71.0 - - - +
467D MET* 1.3 62.7 + - - +
469D LYS* 3.0 23.5 - - + +
470D ILE* 3.0 27.0 + - + +
491D THR* 4.3 14.1 - - - +
492D LEU* 4.5 4.5 - - + -
495D LEU* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D MET* 3.9 37.7 - - + +
303D ILE* 6.1 1.6 - - + -
306D ALA* 4.0 20.4 - - + -
408D PHE* 3.6 56.1 - - + +
411D ILE* 4.8 1.8 - - + -
412D ALA* 4.4 8.1 - - + +
458D TRP* 6.2 0.4 - - + -
463D ALA 3.0 15.0 + - - +
464D LEU* 3.7 6.3 - - - +
466D VAL* 1.3 81.6 - - + +
468D ALA* 1.3 62.8 + - - +
470D ILE* 3.1 7.9 + - - +
471D MET* 2.9 32.8 + - - +
492D LEU* 4.2 16.4 - - + -
495D LEU* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D ILE* 3.9 27.0 - - + +
458D TRP* 4.4 8.3 - - + +
459D GLN* 5.2 2.9 - - - +
464D LEU 3.0 19.4 + - - +
465D ARG* 3.5 7.2 - - - +
467D MET* 1.3 76.5 - - - +
469D LYS* 1.3 63.9 + - - +
471D MET* 3.4 13.7 + - - +
472D ARG* 3.1 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465D ARG 2.7 12.8 + - - +
466D VAL* 3.0 16.2 - - + +
468D ALA* 1.3 76.2 - - - +
470D ILE* 1.3 65.4 + - + +
472D ARG* 3.1 22.8 + - + +
473D GLU* 3.1 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D PHE* 4.2 15.7 - - + -
466D VAL* 3.0 18.8 + - + +
467D MET* 3.4 8.7 - - - +
469D LYS* 1.3 78.3 - - + +
471D MET* 1.3 64.7 + - - +
473D GLU* 2.8 16.0 + - - +
474D CYS* 2.9 20.7 + - - -
483D LEU* 3.9 15.3 - - + -
488D ILE* 3.7 44.0 - - + -
491D THR* 4.1 15.5 - - + +
492D LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D GLY* 4.3 4.0 - - - +
408D PHE* 4.2 21.5 - - + +
409D TRP* 3.1 55.0 - - + -
412D ALA* 5.0 1.1 - - - -
454D ILE* 4.6 3.8 - - + -
458D TRP* 3.7 21.1 - - + -
467D MET* 2.9 21.0 + - - +
468D ALA* 3.6 13.2 - - - +
470D ILE* 1.3 75.3 - - + +
472D ARG* 1.3 61.7 + - - +
474D CYS* 3.2 8.6 + - - +
475D TRP* 3.0 63.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D ILE* 3.6 27.5 - - + +
459D GLN* 3.6 21.6 + - - -
465D ARG 5.1 0.2 + - - -
468D ALA* 3.1 29.2 - - - +
469D LYS* 3.1 34.9 + - + +
471D MET* 1.3 72.0 - - - +
473D GLU* 1.3 61.6 + - + +
474D CYS 2.9 10.2 + - - -
475D TRP* 3.0 18.2 + - + +
476D TYR* 3.4 22.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D LYS* 3.1 55.6 + - + +
470D ILE* 2.8 5.2 + - - +
472D ARG* 1.3 75.4 - - + +
474D CYS* 1.3 55.5 + - - +
476D TYR* 3.7 31.9 + - + +
482D ARG* 3.2 7.1 - - - -
483D LEU* 2.9 65.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D ILE* 3.5 37.0 - - - +
402D TYR* 3.5 11.8 - - - +
404D MET* 5.3 0.9 - - - -
405D GLY* 4.1 17.5 - - - -
408D PHE* 5.9 0.2 - - - -
470D ILE* 2.9 22.2 + - - -
471D MET 3.4 10.5 - - - +
472D ARG 2.9 0.6 - - - -
473D GLU* 1.3 79.1 - - - +
475D TRP* 1.3 63.7 + - + +
476D TYR 3.4 2.0 - - - -
482D ARG* 3.2 28.3 + - - -
483D LEU* 4.7 1.3 - - - -
488D ILE* 3.7 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D TYR* 3.8 24.0 - + - -
405D GLY 3.5 12.2 - - - -
406D LEU* 3.3 31.0 - - + +
409D TRP* 3.8 7.6 - + + -
451D ARG* 2.8 56.2 + - + +
452D PRO* 3.5 44.0 - - + -
454D ILE* 3.8 19.3 - - + -
471D MET* 3.0 54.1 + - + +
472D ARG* 3.0 10.2 + - + +
474D CYS* 1.3 81.8 - - + +
476D TYR* 1.3 67.3 + - - +
477D ALA 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D ARG* 4.0 0.2 + - - -
472D ARG* 3.4 18.6 - - + +
473D GLU* 3.7 35.4 + - + +
474D CYS 3.4 2.2 - - - -
475D TRP* 1.3 78.4 - - - +
477D ALA* 1.3 61.2 + - - +
478D ASN* 3.5 15.3 - - + +
481D ALA* 3.2 43.5 - - + -
482D ARG* 3.0 35.2 + - + -
----------------------------------------------------------
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