Contacts of the helix formed by residues 432 - 437 (chain A) in PDB entry 1U9J
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 THR 432 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 1.3 79.4 + - - +
433A SER* 1.3 68.0 + - - +
434A GLU* 3.2 19.0 + - + +
435A VAL* 3.2 29.3 + - + +
463A TYR* 3.7 31.7 + - + -
464A SER* 5.0 1.8 - - - -
467A LYS* 3.6 31.2 - - + -
489A ARG* 3.7 10.3 - - - +
490A PRO* 4.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A THR* 1.3 75.4 + - - +
434A GLU* 1.3 60.9 + - - +
435A VAL 3.1 1.3 - - - -
436A TYR* 3.2 30.3 + - - +
437A GLY 4.5 0.5 + - - -
444A PHE* 4.9 0.2 - - - -
489A ARG* 4.3 1.7 - - - +
490A PRO 3.6 22.2 + - - -
491A PHE* 3.6 37.0 - - - -
492A ASN 5.6 0.3 + - - -
619A ARG* 3.7 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PRO* 5.1 2.3 - - - +
398A TYR* 2.9 24.4 + - - -
432A THR* 3.1 16.7 + - + +
433A SER* 1.3 75.3 + - - +
435A VAL* 1.3 63.4 + - - +
436A TYR 3.1 3.1 - - - -
437A GLY* 2.9 15.2 + - - +
460A ARG* 2.8 39.8 + - - +
461A TRP* 4.8 0.7 - - - -
463A TYR* 3.7 17.5 - - + -
464A SER* 2.7 29.9 + - - -
619A ARG* 3.6 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 4.7 0.9 - - - +
432A THR* 3.2 18.4 + - + +
433A SER 3.1 0.8 - - - -
434A GLU* 1.3 79.3 - - - +
436A TYR* 1.3 70.7 + - + +
437A GLY* 3.2 1.0 + - - -
451A LEU* 3.6 28.9 - - + +
452A ILE 4.7 0.5 + - - -
453A VAL* 5.0 2.4 - - - +
464A SER* 3.6 15.2 + - - +
467A LYS 4.5 0.9 - - - -
468A GLN* 3.2 51.7 - - + +
471A ASP* 4.1 9.0 - - - +
489A ARG* 3.5 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A SER* 3.2 22.7 - - - +
434A GLU 3.1 0.6 - - - -
435A VAL* 1.3 77.5 - - + +
437A GLY* 1.3 63.8 + - - +
439A CYS* 3.1 19.9 + - + +
444A PHE* 3.5 54.3 - + + -
445A ASP 3.9 17.5 - - - -
446A GLU* 3.3 8.1 - - - +
449A SER* 4.2 10.1 - - - -
451A LEU* 3.8 19.4 - - + -
452A ILE 3.2 15.1 + - - -
489A ARG* 3.1 38.2 + - - -
491A PHE* 4.0 9.4 - + - -
564A ASN* 2.5 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A SER 4.5 0.4 + - - -
434A GLU* 2.9 19.8 + - - +
435A VAL 3.1 1.7 - - - -
436A TYR* 1.3 78.6 - - - +
438A MET* 1.3 62.0 + - - -
439A CYS 3.3 3.8 + - - -
444A PHE* 4.3 12.0 - - - -
452A ILE 3.1 9.4 - - - -
453A VAL* 4.8 1.6 - - - -
460A ARG* 5.9 0.2 - - - -
461A TRP* 3.8 17.3 - - - -
616A VAL* 4.4 14.7 - - - +
618A HIS 5.2 0.2 - - - +
619A ARG* 6.0 0.5 - - - -
----------------------------------------------------------
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