Contacts of the helix formed by residues 418 - 428 (chain B) 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 418 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ALA* 6.0 0.2 - - - -
414B TRP* 4.3 4.2 - - - -
415B ASP* 2.9 32.3 + - - +
417B ASN* 1.3 82.2 - - - +
419B SER* 1.3 58.7 + - - +
420B ASP* 3.6 7.8 + - - +
421B GLY 2.8 19.8 + - - -
422B ARG* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU 4.2 3.5 - - - +
352A ALA* 6.5 0.2 - - - -
354A PRO* 6.6 0.2 - - - -
400A ARG* 5.2 0.9 - - - -
456A ASP* 5.5 0.4 - - - -
457A PRO* 4.6 14.4 - - - -
458A ALA* 3.3 38.0 - - - +
418B SER* 1.3 75.8 - - - +
420B ASP* 1.3 65.4 + - - +
422B ARG* 3.4 6.8 + - - +
423B TYR* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG* 3.2 17.4 + - - +
377B HIS* 3.1 26.2 + - - -
378B GLU* 4.6 5.0 - - - +
381B GLU* 3.3 19.8 - - - +
414B TRP* 3.4 23.3 - - + -
418B SER* 3.6 4.7 + - - +
419B SER* 1.3 81.1 + - - +
421B GLY* 1.3 65.3 + - - +
423B TYR* 3.3 1.4 + - - +
424B VAL* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B TRP* 3.3 26.6 + - - -
415B ASP 3.6 1.8 - - - -
416B GLU* 3.2 16.7 - - - +
418B SER* 2.8 19.3 + - - -
420B ASP* 1.3 76.6 - - - +
422B ARG* 1.3 60.8 + - - +
424B VAL* 3.4 1.4 + - - +
425B LYS* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP* 2.8 28.5 + - - +
329A GLU 5.1 0.6 + - - -
331A HIS* 3.5 31.8 + - - +
349A LEU 3.8 2.2 - - - -
350A GLY* 3.7 4.5 - - - -
351A TRP 3.2 40.2 + - - +
352A ALA* 4.1 2.0 - - + -
416B GLU* 3.3 22.6 + - - +
417B ASN* 2.9 41.7 + - - +
418B SER 2.8 21.9 + - - +
419B SER* 3.8 6.5 - - - +
421B GLY* 1.3 70.2 - - - +
423B TYR* 1.3 67.3 + - - +
425B LYS* 3.7 20.0 - - - +
426B GLU* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.1 39.4 + - + +
400A ARG* 2.7 69.7 + - + +
402A ARG* 3.8 10.6 + - - -
375B GLN* 3.5 21.1 - - + +
385B MET* 3.6 29.2 - - + -
419B SER 2.9 17.5 + - - +
420B ASP 3.6 4.0 - - - +
421B GLY 3.3 0.2 - - - -
422B ARG* 1.3 75.5 - - - +
424B VAL* 1.3 60.9 + - + +
427B ASN* 2.9 65.3 + - + +
428B CYS* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 3.8 18.2 - - + +
384B VAL* 4.0 14.6 - - + -
385B MET* 3.7 31.4 - - + -
388B LYS* 3.9 29.2 - - + -
414B TRP* 4.3 8.1 - - + +
420B ASP 3.0 22.0 + - - +
421B GLY* 3.9 5.2 - - - +
423B TYR* 1.3 77.5 - - + +
425B LYS* 1.3 60.3 + - - +
428B CYS* 2.8 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A HIS* 5.5 6.9 + - - -
331A HIS* 6.5 0.7 - - + -
388B LYS* 3.4 25.5 - - + +
416B GLU* 3.7 21.1 - - + +
421B GLY 3.0 18.3 + - - +
422B ARG* 3.7 21.8 - - - +
424B VAL* 1.3 80.6 - - - +
426B GLU* 1.3 61.8 + - - +
427B ASN 3.6 0.2 + - - -
428B CYS 4.5 1.4 - - - +
429B LYS* 3.5 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A HIS* 4.4 9.5 - - - +
332A THR 4.9 0.3 - - - +
333A THR* 2.7 49.0 + - - +
348A GLU* 3.6 31.6 - - + +
350A GLY* 4.0 13.2 - - - +
351A TRP* 5.9 1.2 + - - -
422B ARG 2.9 20.5 + - - +
425B LYS* 1.3 74.1 - - - +
427B ASN* 1.3 67.3 + - - +
429B LYS* 3.4 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLU* 3.0 29.3 + - - +
402A ARG* 3.4 41.1 + - - +
423B TYR* 2.9 63.4 + - + +
426B GLU* 1.3 83.2 - - - +
428B CYS* 1.3 56.7 + - - +
429B LYS* 3.7 5.1 + - - +
434B TYR* 2.8 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG* 5.7 3.1 - - - -
373B LEU 5.2 3.6 - - - -
385B MET* 3.9 42.0 - - - -
388B LYS* 3.8 21.2 - - + +
389B ILE* 4.0 21.1 - - + -
423B TYR* 5.1 0.9 - - - -
424B VAL* 2.8 38.4 + - + +
425B LYS 4.5 2.3 - - - +
426B GLU 3.9 0.2 - - - -
427B ASN* 1.3 77.6 - - - +
429B LYS* 1.3 66.2 + - - +
434B TYR* 3.4 4.0 - - - -
----------------------------------------------------------
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