Contacts of the helix formed by residues 425 - 430 (chain A) in PDB entry 3DLX
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 GLY 425 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLN* 3.7 19.6 - - - +
344A GLU* 3.8 19.3 + - - -
386A PHE* 3.9 9.8 - - - -
423A MET 3.4 0.2 + - - -
424A GLY* 1.3 69.9 - - - -
426A ALA* 1.3 56.1 + - - +
427A MET 3.5 2.2 - - - -
428A ASP* 3.4 8.7 + - - +
429A LEU* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 4.5 7.7 - - + +
412A ASN* 3.8 17.9 - - - +
413A TRP* 5.5 1.1 - - + -
423A MET* 3.0 19.5 + - + +
424A GLY 3.3 0.2 - - - -
425A GLY* 1.3 76.2 - - - +
427A MET* 1.3 63.1 + - - +
429A LEU* 3.2 18.2 + - - +
430A VAL* 3.4 20.8 + - - +
461A THR* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GOL 3.1 33.7 + - - +
137A PRO* 4.0 10.1 - - + -
159A THR* 3.8 12.6 - - + -
160A GLY* 4.2 5.6 - - - -
163A THR* 3.5 28.0 - - - +
165A VAL* 3.9 14.1 - - + -
413A TRP* 3.4 40.8 - - + +
423A MET* 3.8 29.0 + - + +
424A GLY 4.8 0.6 + - - -
425A GLY 3.5 0.4 - - - -
426A ALA* 1.3 75.4 - - - +
428A ASP* 1.3 61.2 + - - +
430A VAL* 3.3 7.7 - - - +
431A SER 3.4 1.4 + - - -
460A LEU 3.7 7.6 - - - +
461A THR* 3.4 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 3.8 1.7 - - - +
138A GLN 3.7 8.5 + - - -
139A GLY* 3.0 42.7 + - - -
140A THR* 4.0 0.3 + - - -
159A THR* 2.8 36.5 + - - +
386A PHE* 3.6 22.1 - - + -
389A ILE* 3.4 13.6 - - + +
390A ARG* 4.3 10.9 + - - +
425A GLY* 3.4 7.1 + - - +
426A ALA 3.3 0.4 - - - -
427A MET* 1.3 75.8 - - - +
429A LEU* 1.3 63.9 + - - +
431A SER* 2.7 21.2 + - - +
432A SER* 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASN* 3.6 37.9 - - + +
322A GLY* 5.9 1.3 - - - -
344A GLU* 4.0 17.7 - - - +
389A ILE* 3.8 27.8 - - + +
394A VAL* 5.9 0.7 - - + -
397A THR* 3.5 43.8 + - + +
399A LEU* 4.5 16.6 - - + -
425A GLY 3.0 23.0 + - - +
426A ALA* 3.2 12.5 + - - +
428A ASP* 1.3 76.4 - - - +
430A VAL* 1.3 58.5 + - - +
431A SER 3.4 0.2 - - - -
432A SER* 4.9 2.6 + - - -
435A THR* 4.6 7.1 - - - +
437A VAL* 4.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GOL 4.1 7.2 + - - -
399A LEU* 3.4 33.2 - - + -
410A LEU* 4.1 12.8 - - + -
426A ALA 3.6 8.5 - - - +
427A MET 3.3 14.1 - - - +
429A LEU* 1.3 77.0 - - - +
431A SER* 1.3 61.7 + - - +
432A SER 3.5 5.4 + - - +
437A VAL* 4.1 20.3 - - + +
461A THR* 3.9 20.4 - - + +
462A GLY* 4.1 3.6 - - - -
465A CYS* 3.6 36.7 - - + +
----------------------------------------------------------
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