Contacts of the helix formed by residues 475 - 486 (chain D) in PDB entry 5IWM
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 ASN 475 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D ILE* 6.1 0.3 - - - +
462D LEU* 3.5 32.6 + - + +
471D ARG 3.2 11.9 + - - +
472D ILE 3.3 13.8 + - - +
474D ASN* 1.3 76.2 - - - +
476D ASN* 1.3 64.5 + - - +
477D GLU* 3.0 26.4 + - - +
478D ILE* 3.2 23.5 + - + +
479D ARG* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D ASN 3.3 4.4 + - - -
475D ASN* 1.3 73.4 + - - +
477D GLU* 1.3 74.9 + - - +
479D ARG* 3.6 25.5 + - - +
480D GLN* 3.2 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D LEU* 4.3 21.4 - - + +
458D ARG* 3.5 43.4 - - - +
461D ILE* 4.9 15.7 - - + -
475D ASN* 3.0 13.2 + - - +
476D ASN* 1.3 90.4 + - - +
478D ILE* 1.3 65.8 + - + +
480D GLN* 3.4 14.5 + - - +
481D MET* 3.2 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D ILE* 4.5 14.4 - - + -
462D LEU* 4.8 9.4 - - + +
464D VAL* 4.7 7.4 - - + -
472D ILE* 3.4 32.5 - - + +
473D LEU* 5.1 2.9 - - + -
475D ASN* 3.2 26.5 + - + +
477D GLU* 1.3 76.7 - - + +
479D ARG* 1.3 63.5 + - + +
481D MET* 3.4 20.0 + - + +
482D ILE* 3.2 37.7 + - + +
489D ILE* 5.9 0.4 - - + -
523D PHE* 3.6 42.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D LEU* 3.4 26.2 + - - +
474D ASN* 3.5 32.9 + - - +
475D ASN 3.1 13.3 + - - +
476D ASN* 3.9 27.7 - - - +
478D ILE* 1.3 78.0 - - + +
480D GLN* 1.3 54.1 - - + +
482D ILE* 3.3 10.2 + - + +
483D THR* 2.7 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 480 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D LYS* 3.3 30.5 - - - +
418D LEU* 5.5 0.7 - - - +
455D LEU* 3.6 22.2 - - + +
456D PRO 4.5 4.3 - - - +
457D LEU* 5.3 2.5 - - + +
476D ASN* 3.2 41.4 + - - +
477D GLU* 3.7 17.2 + - - +
478D ILE 3.3 0.2 - - - -
479D ARG* 1.3 77.5 - - + +
481D MET* 1.3 57.6 + - - +
483D THR* 3.6 6.1 + - - -
484D ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 481 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D LEU* 4.4 11.9 - - + -
455D LEU* 3.9 21.1 - - + -
457D LEU* 4.3 13.9 - - + -
461D ILE* 4.6 4.3 - - + -
477D GLU* 3.2 20.8 + - + +
478D ILE* 3.8 20.9 - - + +
479D ARG 3.3 0.2 - - - -
480D GLN* 1.3 75.2 - - - +
482D ILE* 1.3 60.4 + - - +
484D ALA* 3.2 1.6 + - - +
485D PHE* 2.9 49.5 + - + -
520D LEU* 3.7 29.8 - - + -
523D PHE* 3.8 30.5 - - + -
524D PHE* 4.4 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 482 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D LEU* 5.5 2.7 - - + -
478D ILE* 3.2 32.6 + - + +
479D ARG* 3.8 10.1 - - + +
481D MET* 1.3 75.4 - - - +
483D THR* 1.3 55.2 + - - +
485D PHE* 3.7 0.3 - - - +
486D GLY* 2.8 33.4 + - - -
487D THR 4.1 0.9 + - - -
488D GLY* 4.1 29.2 - - - +
489D ILE* 3.8 31.9 - - + -
523D PHE* 4.1 5.6 - - + -
528D MET* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 483 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D LEU* 5.5 1.1 - - + +
479D ARG* 2.7 25.8 + - - +
480D GLN* 3.8 6.3 - - - -
482D ILE* 1.3 77.1 - - - +
484D ALA* 1.3 63.3 + - - +
486D GLY* 3.6 8.9 + - - -
499D ARG* 5.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D LEU* 3.9 23.0 - - + +
431D ILE* 3.9 25.6 - - + -
455D LEU* 4.0 8.7 - - + -
480D GLN 2.9 19.1 + - - +
481D MET* 3.4 6.5 - - - +
482D ILE 3.2 0.2 - - - -
483D THR* 1.3 78.6 - - - +
485D PHE* 1.3 64.8 + - + +
499D ARG* 3.5 12.5 + - - +
500D TYR* 3.4 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 485 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D ILE* 3.8 23.8 - - + -
433D LEU* 4.2 9.9 - - + -
481D MET* 2.9 41.4 + - + +
482D ILE 4.2 1.8 - - - +
484D ALA* 1.3 75.5 - - + +
486D GLY* 1.3 63.3 + - - +
487D THR* 3.4 19.6 + - + +
498D ALA* 3.7 0.6 - - + -
499D ARG* 3.1 30.6 + - - +
500D TYR* 4.7 3.1 - + - +
503D ILE* 3.4 48.5 - - + -
523D PHE* 5.0 0.2 - + - -
524D PHE* 3.5 28.3 - + - -
528D MET* 3.6 25.8 - - + -
531D LEU* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 486 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ILE 2.8 19.7 + - - -
483D THR* 4.1 7.6 - - - -
484D ALA 3.4 2.6 - - - -
485D PHE* 1.3 72.2 - - - +
487D THR* 1.3 57.6 + - - +
488D GLY 3.7 0.9 - - - -
497D LYS* 3.2 30.7 - - - +
499D ARG* 4.3 8.7 - - - -
----------------------------------------------------------
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