Contacts of the helix formed by residues 436 - 450 (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 ASP 436 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLU* 5.7 1.2 - - - +
434B GLY 3.9 1.0 + - - -
435B ARG* 1.3 69.8 - - - +
437B LEU* 1.3 55.7 + - - +
438B ALA* 3.1 20.9 + - - +
439B ARG* 3.7 24.0 - - + +
440B GLU* 2.7 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PRO* 3.8 34.4 - - + +
389B ALA* 5.3 0.3 + - - -
391B THR* 3.7 31.6 - - + -
392B GLU* 4.1 18.4 - - + +
427B CYS* 3.8 22.2 - - + +
431B ARG* 3.9 30.7 - - + +
435B ARG 3.4 4.9 + - - +
436B ASP* 1.3 73.5 + - - +
438B ALA* 1.3 58.7 + - - +
441B GLY* 2.9 30.6 + - - +
444B ILE* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA* 6.4 1.6 - - - +
392B GLU* 4.5 22.4 - - + +
436B ASP* 3.1 12.6 + - - +
437B LEU* 1.3 80.8 - - - +
439B ARG* 1.3 60.2 + - - +
441B GLY* 4.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ASP* 3.3 24.1 + - + +
438B ALA* 1.3 81.4 - - + +
440B GLU* 1.3 65.3 + - + +
441B GLY 3.5 0.4 - - - -
442B ASN* 5.3 0.9 + - - +
443B THR* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ARG* 3.0 37.2 + - - +
436B ASP* 2.7 43.3 + - + +
439B ARG* 1.3 81.3 - - + +
441B GLY* 1.3 63.8 + - - +
442B ASN 3.4 2.5 - - - -
443B THR* 2.7 33.0 + - - +
444B ILE* 3.0 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PRO* 3.6 29.4 - - - +
437B LEU 2.9 23.3 + - - -
438B ALA 4.4 1.5 + - - -
439B ARG 3.5 2.4 - - - -
440B GLU* 1.3 78.4 - - - +
442B ASN* 1.3 63.6 + - - +
444B ILE* 3.2 14.7 + - - +
445B ILE* 3.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TRP* 3.5 34.2 - - - +
439B ARG 5.3 0.6 + - - -
440B GLU 3.4 0.6 - - - -
441B GLY* 1.3 74.0 - - - +
443B THR* 1.3 64.0 + - + +
445B ILE* 3.4 4.5 + - - +
446B ARG* 3.0 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ARG* 3.8 11.0 + - - -
439B ARG 5.5 2.0 - - - +
440B GLU* 2.7 33.9 + - - +
442B ASN* 1.3 74.6 - - + +
444B ILE* 1.3 59.9 + - - +
446B ARG* 3.3 21.5 + - - +
447B GLU* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA* 3.9 31.9 - - + +
427B CYS* 4.4 13.0 - - - +
430B ALA* 3.5 22.0 - - + -
435B ARG* 3.8 26.5 - - + +
437B LEU* 3.9 21.1 - - + -
440B GLU* 3.0 27.9 + - + +
441B GLY* 3.4 9.9 - - - +
443B THR* 1.3 82.8 + - - +
445B ILE* 1.3 63.5 + - + +
447B GLU* 3.5 12.5 + - - +
448B ALA* 3.4 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL 3.9 20.0 - - - +
385B TRP* 3.8 23.1 - - + -
388B PRO* 3.9 22.9 - - + -
423B ALA* 4.1 23.8 - - + +
426B ALA* 5.6 1.6 - - + -
427B CYS* 4.3 11.0 - - - -
441B GLY 3.2 12.9 + - - +
442B ASN 3.7 6.7 - - - +
443B THR 3.3 0.2 - - - -
444B ILE* 1.3 76.4 - - + +
446B ARG* 1.3 65.7 + - - +
448B ALA* 3.1 15.0 + - - +
449B THR* 3.2 12.5 + - + +
455B LEU* 3.9 6.7 - - + +
459B CYS* 3.5 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TRP* 4.2 17.0 - - + -
442B ASN* 3.0 61.2 + - - +
443B THR* 3.6 22.3 - - - +
445B ILE* 1.3 76.3 - - - +
447B GLU* 1.3 63.1 + - + +
449B THR* 2.6 30.1 + - - +
450B LYS* 3.6 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ARG* 2.9 41.2 + - - -
443B THR* 2.9 29.8 + - - +
444B ILE* 3.6 8.8 - - - +
445B ILE 3.3 0.2 - - - -
446B ARG* 1.3 76.7 - - + +
448B ALA* 1.3 61.4 + - - +
450B LYS* 3.4 24.8 + - - +
451B TRP* 3.7 8.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B VAL* 4.5 1.1 - - + -
426B ALA* 4.2 20.9 - - + -
444B ILE 3.4 9.2 + - - +
445B ILE* 3.1 6.5 + - - +
447B GLU* 1.3 76.8 - - - +
449B THR* 1.3 59.9 + - - +
450B LYS 3.0 6.1 + - - -
451B TRP* 3.3 26.9 + - + +
452B SER* 3.1 23.4 + - - -
455B LEU* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TRP* 5.8 0.9 - - + -
445B ILE 3.2 16.3 + - - +
446B ARG* 2.6 22.4 + - - +
448B ALA* 1.3 76.4 - - - +
450B LYS* 1.3 75.7 + - - +
451B TRP 3.3 0.6 + - - -
452B SER 3.6 19.5 + - - +
453B PRO* 5.0 0.2 - - - +
455B LEU* 3.9 9.2 - - + -
456B ALA* 3.9 25.1 - - - +
459B CYS* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ARG* 3.8 19.1 - - - +
447B GLU* 3.4 19.5 - - - +
448B ALA 3.0 0.8 - - - -
449B THR* 1.3 90.0 + - - +
451B TRP* 1.3 60.2 + - + +
----------------------------------------------------------
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