Contacts of the helix formed by residues 424 - 429 (chain A) in PDB entry 3PM0
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 GLN 424 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 4.7 4.0 - - - -
393A SER* 6.0 0.4 - - - -
395A VAL* 2.9 27.7 + - - +
396A PRO 2.9 10.1 + - - +
398A THR* 3.7 25.3 - - + +
422A VAL* 3.4 6.5 + - + +
423A ASN* 1.3 69.5 - - - +
425A TRP* 1.3 57.0 + - - +
426A SER 2.9 2.2 - - - -
427A VAL* 2.7 29.5 + - - +
428A ASN* 3.1 14.7 + - - +
461A MET* 3.1 36.0 - - + +
462A ILE* 3.0 23.3 + - - +
464A SER* 2.9 26.0 + - - -
900A HEM 3.7 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 3.1 50.5 + + + +
72A LEU* 3.4 22.2 - - + -
75A ALA* 3.4 25.4 - - + -
391A PHE 5.1 0.6 + - - -
392A SER 4.8 2.9 + - - -
393A SER* 3.5 26.7 + - - -
396A PRO* 3.1 17.0 + - + +
423A ASN* 3.4 7.6 - - - +
424A GLN* 1.3 77.6 - - - +
426A SER* 1.3 64.8 + - - +
429A HIS* 3.0 72.5 + + + +
438A GLU* 4.3 13.5 - - - -
511A ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.1 24.0 - - - +
98A ASN* 3.1 30.4 + - - +
99A GLY* 5.2 1.7 - - - -
423A ASN* 2.9 38.2 + - - -
424A GLN 2.9 0.8 + - - -
425A TRP* 1.3 83.3 - - - +
427A VAL* 1.3 57.3 + - - +
429A HIS* 4.1 2.0 - - - +
430A ASP* 3.7 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN 3.6 8.7 - - - +
99A GLY* 5.5 0.2 - - - -
100A GLU* 3.5 44.6 - - + +
103A ILE* 3.5 31.9 - - + -
423A ASN 4.0 1.3 - - - +
424A GLN 2.7 15.4 + - - +
426A SER* 1.3 73.2 - - - +
428A ASN* 1.3 58.9 + - - +
429A HIS 3.3 0.8 + - - -
430A ASP* 3.9 3.4 + - - -
433A LYS* 3.4 18.3 + - - +
434A TRP* 3.3 18.7 + - - -
459A ARG 4.4 5.6 - - - +
461A MET* 4.3 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A MET 3.9 4.2 + - - -
390A ARG* 2.9 65.1 + - + +
393A SER* 2.7 26.8 + - - +
424A GLN* 3.1 7.9 + - - +
425A TRP 3.4 2.0 + - - +
427A VAL* 1.3 81.5 - - - +
429A HIS* 1.3 58.0 + - + +
430A ASP 3.6 0.4 - - - -
434A TRP* 3.3 10.2 + - - +
459A ARG 4.7 0.3 - - - +
460A VAL* 3.8 7.1 - - - +
461A MET* 3.0 47.2 + - - +
462A ILE* 5.0 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 3.4 18.8 + - - +
391A PHE* 3.0 32.8 + + - -
393A SER* 3.9 1.3 + - - -
425A TRP* 3.0 70.4 + + + +
426A SER* 4.4 2.2 - - - -
428A ASN* 1.3 81.8 - - - +
430A ASP* 1.3 63.4 + - - +
431A PRO* 3.2 9.2 - - - +
434A TRP* 5.2 0.2 - - - -
437A PRO* 3.0 41.5 + - - +
438A GLU* 3.8 18.4 + - - +
----------------------------------------------------------
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