Contacts of the helix formed by residues 436 - 450 (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 ASP 436 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392D GLU* 5.8 0.5 - - - +
434D GLY 3.9 1.0 + - - -
435D ARG* 1.3 68.9 - - - +
437D LEU* 1.3 55.8 + - - +
438D ALA* 3.1 20.4 + - - +
439D ARG* 3.2 33.0 + - + +
440D GLU* 2.7 51.9 + - - +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D PRO* 3.8 34.6 - - + +
391D THR* 3.7 31.2 - - + -
392D GLU* 4.0 17.3 - - + +
427D CYS* 3.8 20.0 - - + +
430D ALA* 4.4 0.2 - - + -
431D ARG* 4.0 32.3 - - + +
435D ARG 3.4 4.5 + - - +
436D ASP* 1.3 72.0 + - - +
438D ALA* 1.3 57.0 + - - +
441D GLY* 2.9 30.5 + - - +
444D ILE* 3.8 22.4 - - + -
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Residues in contact with ALA 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ALA* 6.4 1.3 - - - +
392D GLU* 4.4 24.1 - - + +
436D ASP* 3.1 11.0 + - - +
437D LEU* 1.3 79.6 - - - +
439D ARG* 1.3 61.4 + - + +
441D GLY* 4.4 1.9 + - - -
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Residues in contact with ARG 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D ASP* 3.2 30.2 + - - +
438D ALA* 1.3 81.2 - - - +
440D GLU* 1.3 101.1 + - - +
441D GLY 3.5 1.0 + - - -
442D ASN* 5.2 1.2 + - - +
443D THR* 5.5 0.2 + - - -
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Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D ARG* 3.1 39.6 + - - +
436D ASP 2.7 37.5 + - - +
439D ARG* 1.3 110.6 + - - +
441D GLY* 1.3 63.4 + - - +
442D ASN 3.4 2.5 - - - -
443D THR* 3.0 15.5 + - - +
444D ILE* 2.9 34.0 + - + +
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Residues in contact with GLY 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D PRO* 3.6 22.0 - - - +
437D LEU 2.9 22.0 + - - -
438D ALA 4.4 1.7 + - - -
439D ARG 3.5 2.8 + - - -
440D GLU* 1.3 77.5 - - - +
442D ASN* 1.3 64.2 + - - +
444D ILE* 3.3 8.0 + - - +
445D ILE* 3.2 24.9 + - - +
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Residues in contact with ASN 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D TRP* 3.7 30.9 + - - -
439D ARG 5.2 1.0 + - - +
440D GLU 3.4 0.8 - - - -
441D GLY* 1.3 75.3 - - - +
443D THR* 1.3 57.7 + - - +
445D ILE* 3.5 2.9 + - - +
446D ARG* 3.0 65.3 + - - +
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Residues in contact with THR 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D ARG* 4.6 4.7 - - - +
439D ARG 5.5 0.3 + - - -
440D GLU* 3.0 19.3 + - - -
442D ASN* 1.3 75.3 - - - +
444D ILE* 1.3 61.3 + - - +
446D ARG* 3.3 13.1 + - + +
447D GLU* 2.9 56.0 + - + +
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Residues in contact with ILE 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D PRO* 5.7 0.2 - - + -
426D ALA* 3.7 33.0 - - + +
427D CYS* 4.4 11.7 - - - +
430D ALA* 3.6 22.0 - - + -
435D ARG* 3.8 27.1 - - + +
437D LEU* 3.8 22.2 - - + -
440D GLU* 2.9 32.3 + - + +
441D GLY* 3.3 9.6 + - - +
443D THR* 1.3 78.4 - - - +
445D ILE* 1.3 61.5 + - + +
447D GLU* 3.4 11.3 + - - +
448D ALA* 3.3 20.3 + - - +
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Residues in contact with ILE 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D VAL 3.9 20.2 - - - +
385D TRP* 3.8 22.9 - - + +
388D PRO* 3.9 22.7 - - + -
423D ALA* 4.0 25.1 - - + +
426D ALA* 5.6 1.6 - - + -
427D CYS* 4.3 10.3 - - - -
441D GLY 3.2 13.9 + - - +
442D ASN 3.8 5.8 - - - +
444D ILE* 1.3 76.1 - - + +
446D ARG* 1.3 65.9 + - - +
448D ALA* 3.2 14.7 + - - +
449D THR* 3.2 13.0 + - + +
455D LEU* 4.0 5.1 - - + +
459D CYS* 3.5 30.3 - - - -
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Residues in contact with ARG 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D TRP* 4.0 17.9 - - + -
442D ASN* 3.0 65.9 + - - +
443D THR* 3.7 13.0 + - + +
445D ILE* 1.3 75.9 - - - +
447D GLU* 1.3 61.1 + - - +
449D THR* 2.6 29.3 + - - +
450D LYS* 3.2 21.0 - - - +
463D LYS* 4.7 14.3 - - - +
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Residues in contact with GLU 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D ARG* 2.6 45.0 + - - -
443D THR* 2.9 39.1 + - + +
444D ILE* 3.5 6.2 - - - +
446D ARG* 1.3 76.3 - - - +
448D ALA* 1.3 61.0 + - - +
450D LYS* 3.3 24.8 + - - +
451D TRP* 3.7 8.7 - - - -
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Residues in contact with ALA 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D VAL* 4.4 1.6 - - + -
426D ALA* 4.2 16.2 - - + -
444D ILE 3.3 8.6 + - - +
445D ILE* 3.2 6.5 + - - +
447D GLU* 1.3 75.8 - - - +
449D THR* 1.3 63.4 + - - +
450D LYS 3.1 2.9 + - - -
451D TRP* 3.4 30.0 + - + +
452D SER* 3.1 24.9 + - - -
455D LEU* 3.4 23.8 - - + -
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Residues in contact with THR 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D TRP* 5.9 1.1 - - + -
445D ILE 3.2 16.2 - - - +
446D ARG* 2.6 23.0 + - - +
448D ALA* 1.3 77.3 - - - +
450D LYS* 1.3 74.1 + - - +
451D TRP 3.3 0.8 + - - -
452D SER 3.6 18.6 + - - +
453D PRO* 4.8 0.3 - - - +
455D LEU* 4.0 9.6 - - + -
456D ALA* 3.8 25.3 - - - +
459D CYS* 3.8 28.7 - - + -
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Residues in contact with LYS 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D ARG* 3.2 29.3 + - - +
447D GLU* 3.3 13.2 - - - +
448D ALA 3.1 0.6 - - - -
449D THR* 1.3 86.7 + - - +
451D TRP* 1.3 61.2 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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