Contacts of the helix formed by residues 439 - 453 (chain A) in PDB entry 3RAW
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 SER 439 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 3.5 6.7 + - - +
438A ASP* 1.3 81.7 - - - +
440A LEU* 1.3 66.7 + - - +
441A GLU* 3.8 9.5 - - - +
442A HIS* 3.1 29.8 + - - +
443A VAL* 3.0 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A SER* 1.3 72.9 - - - +
441A GLU* 1.3 57.7 + - - +
443A VAL* 2.9 16.8 + - + +
444A GLN* 2.8 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.2 32.4 - - + +
258A PRO* 5.0 7.3 - - - +
261A ARG* 3.3 24.1 + - - +
439A SER* 3.8 7.5 + - - +
440A LEU* 1.3 77.3 - - - +
442A HIS* 1.3 73.9 + - + +
444A GLN* 3.4 12.3 + - - +
445A LEU* 3.1 22.7 + - - +
471A PHE* 3.6 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 4.3 19.5 - - + +
368A TYR* 2.6 41.5 + + - +
435A MET* 3.8 3.6 - - + -
436A LEU* 4.8 2.9 - - + -
437A GLN* 3.1 60.4 + - + +
439A SER* 3.1 29.5 + - - +
441A GLU* 1.3 92.1 + - + +
443A VAL* 1.3 64.7 + - - +
444A GLN 3.2 0.2 + - - -
445A LEU* 3.3 2.3 + - - +
446A PHE* 3.1 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A MET* 3.3 24.9 - - + -
438A ASP* 3.8 10.8 - - - +
439A SER 3.0 14.6 + - - +
440A LEU* 2.9 21.5 + - + +
442A HIS* 1.3 76.1 - - - +
444A GLN* 1.3 59.8 + - + +
446A PHE* 3.4 3.5 + - - +
447A ASP* 3.0 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 2.8 51.7 + - + +
441A GLU* 3.8 14.2 + - - +
443A VAL* 1.3 76.5 - - + +
445A LEU* 1.3 64.8 + - - +
447A ASP* 3.2 6.4 + - - -
448A LEU* 2.9 19.9 + - - +
469A HIS* 3.3 12.8 - - + -
470A PRO* 3.3 30.4 + - + +
471A PHE* 3.7 31.1 - - - +
473A ALA* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.8 9.0 - - + -
260A VAL* 4.3 12.8 - - + -
364A LEU* 4.4 12.1 - - + -
368A TYR* 3.4 46.0 - - + -
441A GLU 3.1 9.6 + - - +
442A HIS 3.6 6.7 - - - +
444A GLN* 1.3 76.1 - - - +
446A PHE* 1.3 65.9 + - + +
448A LEU* 3.2 4.2 + - + +
449A MET* 2.8 45.8 + - + +
471A PHE* 3.5 40.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 5.0 2.7 - + - -
368A TYR* 3.4 36.3 - + - -
431A LEU* 3.3 51.8 - - + +
432A LYS* 4.3 10.5 - - + -
434A TYR* 4.0 6.7 - - + -
435A MET* 3.7 39.5 - - + -
442A HIS 3.1 16.2 + - - +
443A VAL 3.8 7.2 - - - +
445A LEU* 1.3 86.6 - - + +
447A ASP* 1.3 59.3 + - - +
449A MET* 3.8 13.7 - - - +
450A ARG* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A VAL* 3.0 17.0 + - + +
444A GLN* 3.2 11.0 + - + +
446A PHE* 1.3 73.4 - - - +
448A LEU* 1.3 63.9 + - - +
450A ARG* 3.5 4.8 + - - +
451A ARG* 3.1 45.9 + - - +
469A HIS* 2.8 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 4.8 8.5 - - + -
444A GLN 2.9 12.9 + - - +
445A LEU* 3.5 8.5 - - + +
447A ASP* 1.3 75.5 - - - +
449A MET* 1.3 63.2 + - - +
451A ARG* 3.0 4.1 + - - -
452A MET* 2.9 46.4 + - + +
461A ILE* 4.2 10.1 - - + -
466A ALA* 4.0 22.4 - - + -
469A HIS* 3.7 27.5 + - + +
471A PHE* 3.9 28.3 - - + -
472A PHE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLY* 3.9 14.6 - - - +
364A LEU* 3.5 20.4 - - + +
365A PHE* 3.3 50.5 - - + +
368A TYR* 5.1 1.3 - - + -
431A LEU* 4.4 11.4 - - + -
445A LEU* 2.8 39.2 + - + +
446A PHE* 3.8 19.5 - - + +
448A LEU* 1.3 72.5 - - - +
450A ARG* 1.3 58.5 + - - +
452A MET* 3.1 12.1 + - - +
453A LEU* 2.9 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE 4.7 4.4 + - - -
390A LEU* 4.6 21.0 + - + +
431A LEU* 4.0 29.8 - - + +
432A LYS* 3.8 34.6 - - - +
446A PHE* 3.0 22.3 + - - +
447A ASP* 3.9 5.6 - - - +
448A LEU 3.2 0.2 - - - -
449A MET* 1.3 76.2 - - - +
451A ARG* 1.3 64.4 + - + +
453A LEU* 3.3 12.3 + - - +
454A GLU* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ASP* 3.1 34.8 + - - +
448A LEU* 3.0 5.4 + - - +
450A ARG* 1.3 77.3 - - + +
452A MET* 1.3 62.0 + - - +
453A LEU 3.5 0.3 + - - -
454A GLU* 3.6 16.2 + - - +
459A GLN 5.9 0.8 + - - -
460A ARG* 3.7 2.1 - - - +
461A ILE* 3.3 67.1 + - + +
465A GLU* 4.8 9.5 + - - +
469A HIS* 4.2 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A CYS* 3.6 31.2 - - - -
357A VAL* 3.7 21.8 - - + +
358A TRP* 3.6 11.4 + - - -
360A ILE* 3.8 15.7 - - + -
361A GLY* 3.8 26.5 - - - -
364A LEU* 4.1 12.8 - - + -
448A LEU* 2.9 39.8 + - + +
449A MET* 3.1 9.4 + - - +
451A ARG* 1.3 77.7 - - - +
453A LEU* 1.3 56.9 + - - +
454A GLU 3.3 1.3 - - - -
460A ARG* 3.2 22.8 - - - -
461A ILE* 3.8 12.1 - - + -
463A LEU* 4.3 7.4 - - + -
466A ALA* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TRP* 3.2 58.8 - - + +
361A GLY* 4.2 5.6 - - - -
362A CYS* 3.9 16.2 - - - +
373A LEU* 3.7 25.4 - - + -
390A LEU* 3.8 38.8 - - + +
431A LEU* 4.3 6.3 - - + -
449A MET* 2.9 34.6 + - + +
450A ARG* 3.3 7.5 + - - +
452A MET* 1.3 75.6 - - - +
454A GLU* 1.3 65.3 + - - +
455A PHE* 3.4 3.3 + - - -
----------------------------------------------------------
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