Contacts of the helix formed by residues 452 - 463 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL* 4.9 0.2 - - - +
419B ALA* 5.4 0.2 - - - -
422B VAL* 4.0 16.6 - - - +
448B ALA 3.1 15.5 + - - -
449B THR 3.6 8.5 - - - +
450B LYS 3.6 0.2 - - - -
451B TRP* 1.3 97.9 - - - +
453B PRO* 1.3 65.5 - - - +
454B GLU* 3.8 10.7 + - - +
455B LEU* 3.4 23.8 + - - +
456B ALA 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TRP* 3.6 19.1 - - + -
449B THR 5.0 0.9 - - - +
451B TRP 3.5 11.4 - - - +
452B SER* 1.3 82.7 - - - +
454B GLU* 1.3 77.8 + - - +
456B ALA* 3.6 8.5 - - + +
457B ALA* 3.0 25.3 + - - +
2T LYS* 4.0 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B HIS* 2.9 25.7 + - - -
411B TRP* 3.9 19.6 - - + -
415B PRO* 3.7 36.1 - - + +
418B VAL* 4.0 21.3 - - + +
419B ALA* 3.6 5.4 - - - +
452B SER* 3.2 7.7 + - - +
453B PRO* 1.3 97.2 - - - +
455B LEU* 1.3 61.2 + - - +
458B ALA 3.3 6.8 + - - -
2T LYS* 4.1 13.9 - - - +
3T VAL 6.1 0.3 - - - -
4T TRP* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.8 21.5 - - + -
419B ALA* 3.5 29.1 - - - +
422B VAL* 4.1 11.9 - - + -
423B ALA* 4.0 12.3 - - + -
445B ILE* 3.9 16.2 - - + +
448B ALA* 3.5 32.8 - - + -
449B THR* 3.9 11.4 - - + +
452B SER* 3.2 18.1 + - - +
454B GLU* 1.3 77.2 - - - +
456B ALA* 1.3 61.0 + - - +
458B ALA* 3.1 1.6 + - - +
459B CYS* 2.9 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B THR* 3.9 29.8 - - - +
452B SER 3.0 13.0 + - - +
453B PRO* 3.6 12.1 - - + +
455B LEU* 1.3 78.3 - - - +
457B ALA* 1.3 62.2 + - - +
459B CYS* 3.4 2.8 + - - +
460B GLU* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B HIS* 3.8 18.6 - - + +
410B PRO* 4.2 8.6 - - + +
411B TRP* 3.9 20.4 - - + +
453B PRO 3.0 16.8 + - - +
454B GLU 3.7 5.4 - - - +
455B LEU 3.2 0.2 - - - -
456B ALA* 1.3 77.3 - - - +
458B ALA* 1.3 62.6 + - - +
460B GLU* 3.5 11.7 + - - +
461B VAL* 3.4 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 4.2 14.1 - - + +
409B HIS* 3.8 24.4 + - + -
410B PRO* 5.1 0.4 - - - -
419B ALA* 3.9 12.3 - - + -
454B GLU 3.3 6.0 + - - +
455B LEU 3.1 7.9 + - - +
457B ALA* 1.3 77.9 - - - +
459B CYS* 1.3 66.0 + - - +
461B VAL* 3.2 13.2 + - - +
462B TRP* 3.3 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 4.0 6.7 - - - -
385B TRP* 3.0 43.3 + - + +
445B ILE* 3.5 31.4 - - - -
449B THR* 3.7 17.3 - - + -
455B LEU* 2.9 29.9 + - - +
456B ALA* 3.8 4.5 - - - +
458B ALA* 1.3 75.6 - - - +
460B GLU* 1.3 63.1 + - - +
463B LYS* 3.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ALA 3.2 11.7 + - - +
457B ALA* 3.6 15.0 - - - +
458B ALA 3.2 0.2 - - - -
459B CYS* 1.3 80.8 - - - +
461B VAL* 1.3 62.8 + - + +
463B LYS* 4.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLY 4.9 4.3 - - - +
410B PRO* 4.0 26.0 - - + -
457B ALA 3.4 15.0 + - - +
458B ALA* 3.2 7.5 + - - +
460B GLU* 1.3 83.2 - - + +
462B TRP* 1.3 90.4 + - + +
463B LYS 3.5 0.7 + - - -
464B GLU 5.3 0.7 + - - -
465B ILE* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B HIS* 3.6 52.8 - + + +
384B VAL* 4.6 6.1 - - + -
385B TRP* 3.9 5.6 - - + -
404B GLY 3.7 10.5 - - - -
405B GLY* 3.6 32.3 - - - -
408B GLY* 3.6 35.7 - - - -
409B HIS* 3.9 7.2 - + + -
458B ALA* 3.3 42.0 + - + +
461B VAL* 1.3 95.9 - - + +
463B LYS* 1.3 64.7 + - - +
464B GLU 3.3 3.1 - - - -
465B ILE* 3.1 30.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
383B HIS* 5.7 0.3 - - - -
385B TRP* 3.4 31.7 + - + +
459B CYS 3.1 18.1 + - - +
460B GLU* 4.0 23.3 + - - +
461B VAL 3.5 2.2 + - - -
462B TRP* 1.3 76.5 - - - +
464B GLU* 1.3 79.9 + - + +
465B ILE 5.1 0.9 - - - +
466B LYS* 5.8 1.0 - - - +
----------------------------------------------------------
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