Contacts of the helix formed by residues 432 - 444 (chain A) in PDB entry 2D2O
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 432 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 4.1 1.3 - - - +
429A CYS* 3.0 24.3 + - - +
430A GLY 3.2 2.1 + - - +
431A GLY* 1.3 76.4 - - - +
433A GLU* 1.3 60.3 + - - +
434A ALA* 3.0 24.7 + - - +
435A LYS* 3.0 40.9 + - + +
436A PHE* 3.1 20.4 + - - +
576A TYR* 5.1 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 4.3 7.6 - - + -
431A GLY 3.2 7.8 + - - +
432A ASN* 1.3 70.5 + - - +
434A ALA* 1.3 61.3 + - - +
436A PHE* 3.4 9.8 - - + +
437A ARG* 2.8 73.9 + - + +
480A ASN* 3.2 27.4 + - - -
483A LEU* 4.3 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ASN* 3.0 10.4 + - - +
433A GLU* 1.3 78.2 - - - +
435A LYS* 1.3 62.0 + - - +
437A ARG* 3.6 6.7 + - - +
438A LEU* 3.3 22.2 + - - +
575A PRO 5.5 0.9 - - - +
576A TYR* 3.8 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PHE* 3.5 30.2 - - - +
385A ALA 4.4 12.4 + - - +
386A THR 6.1 1.2 - - - -
429A CYS* 4.1 14.0 + - + +
432A ASN* 3.0 40.3 + - + +
434A ALA* 1.3 73.2 - - - +
436A PHE* 1.3 66.7 + - - +
438A LEU* 3.3 5.2 + - - +
439A ALA* 3.2 21.7 + - - +
534A ASN* 5.3 1.3 - - - +
576A TYR* 3.5 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 4.6 2.5 - - + -
425A PHE* 3.6 30.3 - + + -
426A LEU* 3.7 39.7 - - + -
429A CYS* 3.9 8.9 - - - -
432A ASN 3.1 12.4 + - - +
433A GLU* 3.4 14.6 - - + +
434A ALA 3.3 0.2 - - - -
435A LYS* 1.3 78.8 - - - +
437A ARG* 1.3 66.6 + - + +
439A ALA* 3.1 6.6 + - - +
440A VAL* 3.0 38.8 + - + +
456A ASP* 3.8 23.8 - - + -
459A GLY* 6.3 0.2 - - - -
460A MET 5.9 0.2 - - - -
483A LEU* 3.7 31.9 - - + -
487A TYR* 3.6 18.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLU* 2.8 55.7 + - + +
434A ALA* 3.9 5.6 - - - +
436A PHE* 1.3 76.8 - - + +
438A LEU* 1.3 58.2 + - - +
440A VAL* 3.2 2.5 + - - +
441A LEU* 2.8 29.3 + - - +
480A ASN* 4.2 1.2 + - - -
482A GLY* 3.4 33.0 + - - -
483A LEU* 3.4 14.8 - - + +
486A PHE* 3.4 49.9 - - + +
576A TYR 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PHE* 3.6 16.8 - - + -
434A ALA 3.3 11.5 + - - +
435A LYS* 3.7 9.2 - - - +
436A PHE 3.2 0.6 - - - -
437A ARG* 1.3 77.6 - - - +
439A ALA* 1.3 57.5 + - - +
441A LEU* 3.2 9.1 + - + +
442A PHE* 2.9 27.2 + - - +
532A LEU* 3.8 25.2 - - + +
533A ASN 3.8 9.0 - - - +
534A ASN* 3.6 42.8 - - + +
576A TYR* 3.7 23.3 + - + +
577A GLN 3.9 14.4 - - - +
578A GLY* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL* 4.1 4.3 - - + -
384A PHE* 3.9 25.0 - - + -
417A LEU* 4.4 5.9 - - + +
425A PHE* 3.3 39.7 - - + -
435A LYS 3.2 8.4 + - - +
436A PHE 3.1 5.7 + - - +
438A LEU* 1.3 77.6 - - - +
440A VAL* 1.3 57.0 + - - +
442A PHE* 3.1 5.9 + - - +
443A GLN* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 4.0 11.4 - - + -
436A PHE* 3.0 37.6 + - + +
437A ARG* 3.5 9.4 - - - +
439A ALA* 1.3 73.1 - - - +
441A LEU* 1.3 67.1 + - - +
443A GLN* 3.2 10.3 + - - +
444A MET* 2.9 30.2 + - + +
483A LEU* 5.4 0.4 - - + -
486A PHE* 4.5 3.4 - - + -
487A TYR* 3.5 47.8 - - + +
490A LEU* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG 2.8 13.8 + - - +
438A LEU* 3.4 14.4 - - + +
440A VAL* 1.3 77.6 - - - +
442A PHE* 1.3 60.9 + - - +
444A MET* 3.5 1.2 + - - +
445A THR* 3.0 27.2 + - - +
486A PHE* 4.2 15.3 - - + -
490A LEU* 3.7 22.2 - - + +
530A VAL* 4.0 13.9 - - + -
532A LEU* 3.7 22.0 - - + -
557A LEU* 3.8 20.4 - - + -
578A GLY* 3.7 29.2 - - - +
580A ILE* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 3.4 25.6 - + - -
380A VAL* 3.7 18.4 - - + -
384A PHE* 3.7 24.0 - + + -
394A PHE* 3.7 23.6 - + - -
398A LEU* 3.8 13.2 - - + -
438A LEU 2.9 12.8 + - - +
439A ALA 3.1 8.3 + - - +
441A LEU* 1.3 74.5 - - - +
443A GLN* 1.3 67.3 - - - +
445A THR* 3.0 6.9 + - - -
446A TYR* 2.9 64.3 + + - +
517A TYR* 4.2 1.8 - + - -
519A PHE* 3.7 22.4 - + - -
532A LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 4.1 19.4 - - + -
415A ASN* 2.8 32.7 + - + +
416A LEU* 4.0 0.3 - - - -
417A LEU* 3.7 38.4 - - + +
439A ALA 2.8 16.5 + - - +
440A VAL* 3.5 19.6 + - - +
442A PHE* 1.3 75.3 - - - +
444A MET* 1.3 66.0 + - - +
445A THR 3.3 0.9 + - - -
446A TYR* 3.8 8.3 + - - +
448A GLY 5.6 0.2 - - - +
450A PRO* 3.7 25.1 - - + +
451A LEU 2.9 20.0 + - - +
452A ILE* 5.0 4.2 - - - +
487A TYR* 4.8 7.1 + - - -
494A ARG* 4.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.3 11.2 - - + -
440A VAL* 2.9 26.2 + - + +
441A LEU 4.0 3.8 - - - +
442A PHE 3.2 0.2 - - - -
443A GLN* 1.3 80.7 - - + +
445A THR* 1.3 58.9 + - + +
450A PRO* 3.8 19.5 - - + -
452A ILE* 5.0 7.2 - - - -
487A TYR* 5.3 3.4 - - + -
490A LEU* 3.8 32.8 - - + +
491A ILE* 3.2 44.9 - - + -
494A ARG* 2.6 56.0 + - - +
500A LEU* 4.5 1.6 - - - +
----------------------------------------------------------
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