Contacts of the helix formed by residues 528 - 534 (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 MET 528 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ILE* 3.6 25.8 - - + -
485D PHE* 3.6 36.8 - - + -
487D THR* 4.3 7.2 - - - +
488D GLY 4.2 5.8 - - - +
489D ILE* 3.6 24.0 - - + -
493D PHE* 3.8 22.0 - - + -
523D PHE* 4.3 9.0 - - + -
524D PHE* 2.8 28.2 + - - +
527D PHE* 1.3 84.4 - - + +
529D ARG* 1.3 58.9 + - - +
530D PRO* 3.2 5.8 - - - -
531D LEU* 2.9 40.0 + - + +
532D ILE* 3.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 529 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D PHE 3.0 8.7 + - - -
525D TYR* 3.3 46.8 + - + +
526D ARG 5.6 1.1 - - - -
527D PHE 3.7 1.4 - - - -
528D MET* 1.3 75.6 - - - +
530D PRO* 1.4 65.0 - - + +
532D ILE* 3.0 23.6 + - + +
533D GLU* 3.2 35.4 + - - +
608D LEU* 4.2 8.6 - - + +
611D ALA* 3.4 30.1 - - - +
615D ASP* 4.9 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 530 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D GLY 6.0 0.4 - - - +
493D PHE* 3.5 35.9 - - + -
495D LEU* 4.5 5.7 - - + +
527D PHE 5.3 0.4 - - - +
528D MET* 3.2 7.9 - - - -
529D ARG* 1.4 92.6 - - + +
531D LEU* 1.3 55.5 + - - +
532D ILE 3.2 0.2 - - - -
533D GLU* 3.7 19.9 - - + +
534D ALA* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D PHE* 4.6 9.6 - - + -
487D THR* 5.0 4.0 - - + -
493D PHE* 4.0 20.5 - - + -
495D LEU* 4.2 7.2 - - + -
498D ALA* 4.9 7.2 - - + -
503D ILE* 4.2 22.4 - - + -
524D PHE* 4.8 7.6 - - + -
528D MET* 2.9 39.7 + - + +
530D PRO* 1.3 79.1 - - - +
532D ILE* 1.3 60.1 + - + +
534D ALA 3.9 0.3 + - - -
535D GLY 3.8 1.4 + - - -
536D TYR* 3.1 65.5 + - + +
537D VAL* 3.8 14.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 532 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.9 22.7 - - + -
521D LEU* 4.5 4.5 - - + +
524D PHE* 3.7 16.2 - - + +
525D TYR* 3.7 38.6 - - + +
528D MET 4.4 0.7 - - - +
529D ARG 3.0 9.3 + - - +
531D LEU* 1.3 76.9 - - - +
533D GLU* 1.3 63.3 + - + +
534D ALA 3.3 0.2 - - - -
535D GLY* 3.3 9.4 + - - -
537D VAL* 3.9 23.8 - - + +
606D VAL* 3.6 42.3 - - + +
607D LYS* 5.0 0.3 - - - -
608D LEU* 4.5 20.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 533 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D ARG* 3.2 41.8 + - - +
530D PRO* 3.7 22.4 - - + +
531D LEU 3.4 0.2 - - - -
532D ILE* 1.3 76.4 - - - +
534D ALA* 1.3 57.8 + - - +
535D GLY 3.2 1.2 + - - -
608D LEU* 3.8 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D LEU* 3.7 24.7 - - + -
530D PRO 3.1 16.3 + - - +
531D LEU 4.3 1.6 - - - +
532D ILE 3.3 0.6 - - - -
533D GLU* 1.3 76.4 - - - +
535D GLY* 1.3 60.8 + - - +
536D TYR* 3.5 27.0 - - + -
605D GLN* 5.1 0.3 + - - -
----------------------------------------------------------
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