Contacts of the helix formed by residues 415 - 420 (chain A) in PDB entry 2PFP
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 CYS 415 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A VAL* 3.6 17.9 - - - -
414A ALA* 1.3 74.6 - - - +
416A GLY* 1.3 73.7 + - - +
418A TYR* 3.2 10.6 + - - +
419A ARG* 3.1 19.4 + - - -
429A ASP* 2.6 16.8 + - - +
431A LEU* 3.8 20.4 - - - -
503A LEU* 3.8 25.8 - - - -
506A PHE* 3.3 34.3 - - + +
507A THR* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A CYS* 1.3 87.1 - - - +
417A SER* 1.3 61.8 + - - -
419A ARG* 3.2 7.1 + - - +
420A ARG* 3.3 20.2 + - - +
429A ASP* 3.4 8.8 + - - -
506A PHE 2.8 18.2 + - - -
507A THR* 3.5 3.9 - - - +
755A DCP 3.4 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 4.2 2.7 - - - -
416A GLY* 1.3 71.0 - - - -
418A TYR* 1.3 63.8 + - - +
420A ARG* 3.3 22.2 + - - +
421A GLY 3.3 4.3 + - - -
422A LYS* 3.0 43.9 + - - +
425A CYS* 3.7 18.7 - - - +
427A ASP 5.0 0.9 + - - -
429A ASP* 4.5 0.2 + - - -
750A MG 4.4 0.2 - - - -
755A DCP 2.5 41.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 3.0 62.5 + - + +
392A ALA* 3.8 19.5 - - + -
393A THR* 2.8 41.6 + - - +
396A GLU* 5.9 1.1 - - + -
414A ALA* 3.4 33.7 - - + -
415A CYS 3.2 9.4 + - - +
416A GLY 3.1 0.4 - - - -
417A SER* 1.3 80.5 + - - +
419A ARG* 1.3 61.5 + - - +
421A GLY* 2.9 16.5 + - - -
425A CYS* 3.8 16.4 - - - -
427A ASP 5.9 1.3 - - - +
428A VAL* 6.4 2.5 - - + -
429A ASP 6.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A VAL* 4.7 7.1 - - - +
414A ALA 3.5 20.9 - - - +
415A CYS* 3.1 12.1 + - - +
416A GLY 3.9 3.1 - - - +
418A TYR* 1.3 78.7 - - - +
420A ARG* 1.3 59.1 + - - +
421A GLY* 3.0 7.2 + - - -
503A LEU* 3.6 26.9 - - - +
507A THR* 2.8 38.5 + - + +
556A GLU* 2.6 40.4 + - - -
567A TYR* 4.6 2.8 + - - -
570A PRO* 3.2 30.9 - - + +
573A ARG* 3.4 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A GLY 3.5 1.6 - - - +
417A SER* 3.3 29.7 + - - +
418A TYR 3.1 1.4 - - - -
419A ARG* 1.3 77.2 - - - +
421A GLY* 1.3 60.4 + - - +
422A LYS* 3.5 5.5 - - + +
507A THR* 2.9 39.6 + - + +
508A GLY 3.9 2.2 - - - -
509A SER* 3.7 28.9 - - - +
570A PRO 3.6 25.4 - - - +
571A ALA* 3.2 24.6 - - - +
573A ARG 3.7 8.3 - - - -
574A ASP* 2.9 40.6 + - - +
755A DCP 3.0 31.7 + - - -
----------------------------------------------------------
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