Contacts of the helix formed by residues 324 - 329 (chain D) in PDB entry 1DGB
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 ASN 324 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 4.7 4.2 - - - +
389A ASP* 5.3 0.4 + - - -
396A ASP 3.7 14.1 - - - +
397A ASN* 3.1 41.1 + - - +
399A GLY* 3.0 22.5 + - - +
172B PRO* 3.6 12.7 + - - +
322D PRO* 4.5 0.4 - - - -
323D VAL* 1.3 79.3 - - + +
325D TYR* 1.3 60.4 + - - +
326D PHE* 3.4 6.3 + - - +
327D ALA* 2.9 29.6 + - + -
328D GLU* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 3.0 16.5 + - - +
173B GLN 3.9 13.7 + - - +
174B THR 5.0 1.1 - - - -
175B HIS* 3.2 66.0 + + + +
76D ALA 5.2 0.5 + - - -
77D LYS* 5.8 0.3 - - - +
78D GLY 2.7 34.8 + - - -
79D ALA* 4.5 6.1 - - - -
80D GLY 4.8 0.9 - - - -
112D ARG* 4.4 2.4 + - - -
262D ILE* 4.6 6.1 - - + -
322D PRO* 4.6 4.2 - - + +
324D ASN* 1.3 70.5 - - - +
326D PHE* 1.3 61.8 + - + +
329D VAL* 2.5 63.8 + - + +
330D GLU* 3.0 35.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASP* 3.1 55.4 - - + +
390A GLY 3.6 28.7 - - - -
393A CYS* 3.9 4.0 - - + -
397A ASN* 3.8 4.3 - - - -
172B PRO 4.6 1.0 + - - -
67D GLU 4.1 8.5 - - - -
68D ARG* 5.6 0.4 - - - -
69D ILE* 4.2 23.3 - - + -
324D ASN* 3.3 6.8 + - - +
325D TYR* 1.3 84.4 - + + +
327D ALA* 1.3 69.0 + - - +
330D GLU* 3.3 29.6 + - + -
331D GLN* 3.1 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A CYS* 4.7 1.8 - - - -
395A GLN 4.0 15.0 - - - +
396A ASP* 4.4 2.7 - - - +
397A ASN* 3.8 19.3 - - + -
324D ASN* 2.9 21.2 + - + +
326D PHE* 1.3 80.4 - - - +
328D GLU* 1.3 64.6 + - + +
331D GLN* 3.5 27.3 + - - +
373D ILE* 4.6 1.2 - - - +
375D VAL* 3.6 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP 5.5 0.5 - - - +
82D PHE* 3.3 38.7 - - + -
320D ARG* 5.3 3.6 + - - -
321D ASN 4.5 0.9 - - - +
322D PRO* 3.5 5.7 - - + +
323D VAL* 2.8 42.3 + - - +
324D ASN* 2.9 24.7 + - - +
327D ALA* 1.3 81.9 - - + +
329D VAL* 1.3 63.7 + - - +
332D ILE* 3.8 7.3 - - - +
375D VAL* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ARG* 2.9 18.2 + - - -
79D ALA 4.3 0.7 - - - -
80D GLY* 3.8 25.6 - - - +
82D PHE* 5.3 2.0 - - + -
112D ARG* 3.9 19.7 - - + +
322D PRO* 3.7 31.4 - - + -
325D TYR* 2.5 52.9 + - + +
328D GLU* 1.3 79.2 - - + +
330D GLU* 1.3 67.5 + - - +
331D GLN 3.1 1.1 - - - -
332D ILE* 3.0 13.0 + - + +
----------------------------------------------------------
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