Contacts of the helix formed by residues 419 - 426 (chain B) in PDB entry 2V4M
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 ALA 419 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A GLU* 5.2 0.2 + - - -
390B ILE* 3.8 24.9 - - + -
391B ALA 3.0 10.7 + - - +
392B CYS* 3.6 25.8 - - - +
417B GLU 3.6 1.2 + - - -
418B LEU* 1.3 71.0 - - - +
420B SER* 1.3 62.9 + - - +
422B PHE* 3.4 2.6 - - - +
423B LEU* 3.1 28.4 + - - +
446B ASP* 3.7 7.2 - - - +
447B THR* 3.6 23.1 - - - +
450B GLY* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ARG* 3.5 18.8 + - - +
589A LEU* 3.5 20.3 - - - +
591A GLY* 3.9 21.4 - - - -
592A GLU* 4.2 6.6 + - - +
392B CYS* 4.8 2.5 - - - -
418B LEU 4.5 1.0 + - - -
419B ALA* 1.3 77.2 - - - +
421B ASP* 1.3 60.8 + - - +
423B LEU* 3.4 3.9 + - - +
424B ASP* 3.1 34.4 + - - +
446B ASP* 3.5 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ARG* 4.3 4.3 + - - -
564A GLY* 4.4 20.4 + - - +
567A TYR* 4.7 14.8 - - - -
589A LEU* 4.1 25.7 - - + +
418B LEU* 3.0 13.3 + - + +
420B SER* 1.3 78.0 + - - +
422B PHE* 1.3 67.1 + - - +
424B ASP* 3.2 6.0 + - - +
425B ARG* 3.0 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 4.4 7.2 - - + -
390B ILE* 3.3 35.9 - - + -
417B GLU* 3.8 21.8 - - + -
418B LEU 2.8 13.0 + - - +
419B ALA* 3.4 13.7 - - - +
421B ASP* 1.3 76.9 - - - +
423B LEU* 1.3 73.8 + - + +
425B ARG* 4.0 5.9 - - - +
426B ASN* 3.4 11.4 + - - -
427B THR* 3.2 49.1 + - + -
429B VAL* 3.7 17.7 - - + -
450B GLY* 4.3 9.4 - - - -
453B TYR* 3.6 26.4 - + - -
454B CYS* 3.6 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A HIS* 5.2 0.9 - - - -
619A LYS* 4.5 14.2 + - - +
419B ALA 3.1 14.6 + - - +
420B SER* 3.9 4.0 - - - +
422B PHE* 1.3 81.1 - - + +
424B ASP* 1.3 67.5 + - - +
425B ARG 3.3 0.3 + - - -
426B ASN* 3.4 18.0 + - - +
446B ASP* 3.5 37.9 - - + +
449B MET* 3.7 41.1 - - + +
450B GLY* 3.9 10.1 - - - +
453B TYR* 4.3 16.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 3.1 10.6 + - - -
563A ARG* 2.7 34.8 + - - +
564A GLY* 4.0 14.5 + - - -
589A LEU* 5.9 0.5 - - - +
615A HIS* 3.1 29.8 - - + +
616A THR* 3.8 14.9 - - + +
619A LYS* 2.7 39.0 + - - +
420B SER 3.1 20.1 + - - +
421B ASP* 3.2 9.7 + - - +
423B LEU* 1.3 76.6 - - - +
425B ARG* 1.3 59.7 + - + +
426B ASN* 3.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ARG* 2.9 35.1 - - - +
404A GLN* 3.8 40.0 + - + +
407A GLU* 2.7 49.5 + - - +
408A GLU* 5.7 2.4 + - - +
564A GLY* 5.8 1.6 - - - -
417B GLU* 2.4 30.7 + - - -
421B ASP* 3.0 44.7 + - - +
422B PHE 4.0 11.1 - - - +
423B LEU 3.2 0.2 - - - -
424B ASP* 1.3 77.6 - - + +
426B ASN* 1.3 71.6 + - - +
427B THR* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 5.4 2.2 - - - +
407A GLU* 5.4 0.5 - - - +
615A HIS* 5.3 5.1 + - - -
422B PHE 3.4 5.3 + - - -
423B LEU 3.4 10.8 + - - +
424B ASP 4.2 7.9 + - - -
425B ARG* 1.3 81.3 + - - +
427B THR* 1.3 64.1 + - - +
428B PRO* 3.3 6.5 - - - +
453B TYR* 2.9 35.7 + - - +
457B ARG* 4.7 5.9 + - - +
----------------------------------------------------------
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