Contacts of the helix formed by residues 452 - 463 (chain D) in PDB entry 1IR1
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 SER 452 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D VAL* 4.8 0.2 - - - +
422D VAL* 4.1 16.2 - - - +
448D ALA 3.1 16.2 + - - -
449D THR* 3.6 5.1 - - - +
450D LYS 3.7 0.4 - - - -
451D TRP* 1.3 96.8 - - - +
453D PRO* 1.4 65.8 - - - +
454D GLU* 3.8 10.3 + - - +
455D LEU* 3.3 24.6 + - - +
456D ALA* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D TRP* 3.6 23.8 - - + -
449D THR 5.1 0.4 - - - +
451D TRP 3.4 11.9 - - - +
452D SER* 1.4 83.3 - - - +
454D GLU* 1.3 68.3 + - - +
456D ALA* 3.4 8.1 + - + +
457D ALA* 3.0 30.5 + - - +
2V LYS* 3.3 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D HIS* 2.9 25.1 + - - -
411D TRP* 3.8 23.9 - - + -
415D PRO* 3.7 31.4 - - + +
418D VAL* 4.0 22.9 - - + +
419D ALA* 3.7 4.2 - - - +
452D SER* 3.8 6.8 + - - +
453D PRO* 1.3 94.2 - - - +
455D LEU* 1.3 62.2 + - - +
458D ALA 3.3 6.6 + - - -
2V LYS* 4.3 15.8 - - - +
3V VAL 6.2 0.2 - - - -
4V TRP* 4.0 27.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 3.8 26.5 - - + -
419D ALA* 3.5 30.2 - - - +
422D VAL* 4.1 12.3 - - + -
423D ALA* 4.0 12.8 - - + -
445D ILE* 4.0 12.1 - - + +
448D ALA* 3.4 38.4 - - + -
449D THR* 4.0 8.3 - - + -
452D SER* 3.2 18.9 + - - +
454D GLU* 1.3 75.1 - - - +
456D ALA* 1.3 67.9 + - - +
458D ALA* 3.0 3.5 + - - +
459D CYS* 2.9 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 456 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D THR* 3.8 29.6 - - - +
452D SER 3.0 13.2 + - - +
453D PRO* 3.6 13.5 - - + +
455D LEU* 1.3 78.0 - - - +
457D ALA* 1.3 62.1 + - - +
459D CYS* 3.4 2.4 + - - +
460D GLU* 3.2 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D HIS* 3.8 18.4 - - + -
410D PRO* 4.2 8.0 - - + +
411D TRP* 3.9 21.1 - - + +
453D PRO 3.0 17.4 + - - +
454D GLU 3.7 5.4 - - - +
455D LEU 3.2 0.2 - - - -
456D ALA* 1.3 77.4 - - - +
458D ALA* 1.3 61.6 + - - +
460D GLU* 3.5 13.3 + - - +
461D VAL* 3.3 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 458 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 4.2 12.1 - - + +
409D HIS* 3.7 24.8 + - + -
410D PRO* 5.1 0.7 - - - -
419D ALA* 3.9 13.0 - - + -
454D GLU 3.3 4.9 + - - +
455D LEU 3.0 8.6 + - - +
457D ALA* 1.3 77.5 - - - +
459D CYS* 1.3 64.8 + - - +
461D VAL* 3.2 12.9 + - - +
462D TRP* 3.3 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 459 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 4.0 7.9 - - - -
385D TRP* 2.9 44.0 + - + +
445D ILE* 3.5 31.4 - - - -
449D THR* 3.8 17.3 - - + -
455D LEU* 2.9 29.1 + - - +
456D ALA* 3.8 4.5 - - - +
458D ALA* 1.3 75.8 - - - +
460D GLU* 1.3 58.1 + - - +
463D LYS* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 460 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D ALA 3.2 9.7 + - - +
457D ALA* 3.5 19.5 - - - +
459D CYS* 1.3 80.2 - - - +
461D VAL* 1.3 62.3 + - + +
463D LYS* 4.1 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 461 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D GLY 5.0 4.5 - - - +
410D PRO* 3.9 26.5 - - + -
457D ALA 3.3 15.5 - - - +
458D ALA 3.2 7.5 + - - +
460D GLU* 1.3 81.4 - - + +
462D TRP* 1.3 87.9 + - + +
463D LYS 3.6 0.4 + - - -
464D GLU 5.4 0.2 + - - -
465D ILE* 4.6 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D HIS* 3.4 54.5 - + + +
384D VAL* 4.6 5.8 - - + -
385D TRP* 3.6 6.2 - - + -
404D GLY 3.7 13.7 - - - -
405D GLY* 3.6 31.4 - - - -
408D GLY* 3.6 33.0 - - - -
409D HIS* 3.9 7.6 - + - -
458D ALA* 3.3 43.1 + - + +
461D VAL* 1.3 95.8 - - + +
463D LYS* 1.3 64.5 + - - +
464D GLU 3.3 2.9 - - - -
465D ILE* 3.2 28.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D HIS* 5.6 0.3 - - - -
385D TRP* 3.4 41.9 - - + +
446D ARG* 4.7 14.1 - - - +
459D CYS 3.0 16.4 + - - +
460D GLU* 4.3 10.5 - - - +
461D VAL 3.6 2.8 + - - -
462D TRP* 1.3 77.1 - - - +
464D GLU* 1.3 73.9 + - + +
465D ILE 3.7 1.2 + - - +
466D LYS* 5.4 4.5 - - - +
----------------------------------------------------------
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