Contacts of the helix formed by residues 425 - 430 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D GLN* 3.6 11.7 - - - +
344D GLU* 3.7 13.0 + - - -
386D PHE* 3.8 24.4 - - - -
423D MET 3.3 0.2 + - - -
424D GLY* 1.3 69.2 - - - -
426D ALA* 1.3 57.7 + - - +
427D MET 3.3 2.7 - - - -
428D ASP* 3.1 10.6 + - - +
429D LEU* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399D LEU* 4.7 11.7 - - + -
412D ASN* 4.0 19.1 - - - +
423D MET 3.0 15.8 + - - +
425D GLY* 1.3 77.4 - - - +
427D MET* 1.3 62.4 + - - +
429D LEU* 3.3 10.3 + - - +
430D VAL* 3.2 29.8 + - - +
461D THR* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D PRO* 3.9 26.2 - - + -
159D THR* 3.5 18.4 - - + +
160D GLY* 4.1 9.2 + - - +
163D THR* 3.5 27.1 - - - +
165D VAL* 4.0 5.6 - - + -
413D TRP* 3.7 23.1 - - + +
423D MET* 3.9 22.3 + - + -
424D GLY 4.8 0.8 + - - -
425D GLY 3.3 0.8 - - - -
426D ALA* 1.3 76.9 - - - +
428D ASP* 1.3 60.7 + - - +
430D VAL* 3.5 6.9 - - - +
431D SER* 3.5 19.8 + - - -
460D LEU 3.6 20.4 - - - +
461D THR* 3.2 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D PRO* 3.9 1.7 - - - +
138D GLN 3.8 8.5 + - - -
139D GLY* 2.9 41.4 + - - -
140D THR 3.9 0.6 + - - -
159D THR* 2.9 35.5 + - - +
386D PHE* 3.6 18.1 - - + -
389D ILE* 3.5 15.0 - - + +
390D ARG* 4.3 13.9 + - + +
425D GLY* 3.1 11.4 + - - +
427D MET* 1.3 75.7 - - - +
429D LEU* 1.3 63.4 + - - +
431D SER* 2.9 20.3 + - - +
432D SER 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ASN* 3.2 47.8 - - + +
322D GLY* 5.3 1.3 - - - -
344D GLU* 4.0 17.5 - - + +
389D ILE* 3.8 29.5 - - + +
394D VAL* 5.6 2.9 - - + -
397D THR* 3.5 32.8 - - + +
399D LEU* 3.9 21.8 - - + -
425D GLY* 2.9 22.7 + - - +
426D ALA* 3.3 6.5 + - - +
428D ASP* 1.3 75.3 - - - +
430D VAL* 1.3 60.5 + - - +
431D SER 3.7 0.5 + - - -
432D SER* 4.8 2.4 + - - +
435D THR* 4.1 12.6 - - - +
437D VAL* 4.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399D LEU* 3.5 26.2 - - + -
410D LEU* 3.9 15.3 - - + -
426D ALA 3.3 14.6 - - - +
427D MET 3.5 13.7 - - - +
428D ASP 3.2 0.8 - - - -
429D LEU* 1.3 78.9 - - - +
431D SER* 1.3 58.5 + - - +
432D SER 3.6 4.5 - - - +
437D VAL* 4.1 18.0 - - + +
461D THR* 3.9 19.7 - - + +
462D GLY* 4.0 4.5 - - - -
465D CYS* 3.6 39.9 - - + +
----------------------------------------------------------
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