Contacts of the helix formed by residues 139 - 147 (chain D) in PDB entry 5D0A
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 SER 139 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.7 29.1 - - - +
57D ARG* 3.5 17.0 + - - +
137D GLU 3.8 0.6 + - - -
138D LEU* 1.3 72.8 - - - +
140D ASP* 1.3 62.5 + - - +
142D ALA* 3.0 27.8 + - - +
143D VAL* 3.2 17.5 + - - +
503D B12 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D MET* 4.7 2.3 - - - +
133D VAL* 5.1 1.1 - - - -
134D ASP* 2.8 32.3 + - - -
136D GLY 5.8 0.5 + - - -
138D LEU 3.5 8.7 - - - +
139D SER* 1.3 71.8 - - - +
141D ARG* 1.3 57.0 + - - +
143D VAL* 3.6 2.4 + - - +
144D ALA* 2.9 29.3 + - - +
169D LEU* 3.8 11.3 - - + +
171D GLU* 2.7 39.9 - - - +
503D B12 2.8 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D SER* 3.2 1.5 + - - +
140D ASP* 1.3 77.0 - - - +
142D ALA* 1.3 55.0 + - - +
144D ALA 3.2 0.2 + - - -
145D GLU* 2.8 36.4 + - - +
156D CYS* 2.8 29.3 + - - +
157D MET* 3.4 23.4 - - - -
158D ILE* 3.5 23.6 - - + +
169D LEU* 4.0 1.3 - - + -
503D B12 2.9 150.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.5 25.0 - - + -
33D LEU* 4.1 16.6 - - + -
139D SER* 3.0 27.4 + - - +
141D ARG* 1.3 75.5 - - - +
143D VAL* 1.3 63.6 + - - +
145D GLU* 3.5 6.4 + - - +
146D ARG* 3.1 24.1 + - - +
503D B12 3.7 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D THR* 4.5 4.3 - - + +
30D PHE* 3.7 24.7 - - + -
70D ILE* 3.7 29.8 - - + -
72D ALA* 4.0 11.4 - - + -
138D LEU* 4.0 27.8 - - + -
139D SER 3.2 12.3 + - - +
140D ASP 3.7 6.7 - - - +
142D ALA* 1.3 77.3 - - - +
144D ALA* 1.3 62.5 + - - +
146D ARG* 3.3 4.0 + - - +
147D ALA* 3.0 22.0 + - - +
171D GLU* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA* 4.3 6.5 - - + -
140D ASP 2.9 18.9 + - - +
141D ARG 3.7 3.1 - - - +
143D VAL* 1.3 78.9 - - - +
145D GLU* 1.3 62.9 + - - +
147D ALA 3.3 0.9 + - - -
148D GLY 3.2 3.8 + - - -
149D ILE* 3.0 51.7 + - + +
150D GLY 4.6 0.9 - - - -
158D ILE* 4.2 6.5 - - + -
169D LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG 2.8 21.3 + - - +
142D ALA* 3.8 5.8 - - - +
144D ALA* 1.3 72.3 - - - +
146D ARG* 1.3 64.8 + - - +
148D GLY* 3.3 12.0 + - - -
150D GLY 3.6 17.8 - - - +
151D PHE* 5.0 1.6 - - - -
152D SER* 3.3 28.8 + - - +
158D ILE* 3.9 9.5 - - + +
183D PRO* 3.9 18.8 - - + +
503D B12 4.1 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D THR* 3.0 27.4 + - - +
26D THR* 3.1 31.5 + - - -
27D ALA 4.1 0.6 - - - -
28D ASP* 2.6 37.2 + - - +
29D THR 3.1 16.2 + - - -
30D PHE* 3.4 39.7 - - + +
142D ALA 3.1 14.9 + - - +
143D VAL 3.9 2.5 - - - +
144D ALA 3.3 0.2 - - - -
145D GLU* 1.3 83.4 - - - +
147D ALA* 1.3 58.1 + - - +
148D GLY 3.3 0.6 + - - -
181D ASP 4.0 13.9 - - - +
183D PRO* 4.3 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLY* 3.5 17.0 - - - -
24D PHE 3.4 34.5 - - - +
25D THR* 3.9 6.1 - - + +
72D ALA* 3.9 16.2 - - + +
143D VAL 3.0 16.5 + - - +
144D ALA 4.0 2.2 - - - +
145D GLU 3.2 0.4 - - - -
146D ARG* 1.3 76.2 - - - +
148D GLY* 1.3 63.4 + - - +
149D ILE* 3.3 1.3 - - + -
181D ASP* 3.5 18.9 - - - +
182D VAL 4.9 0.2 - - - -
----------------------------------------------------------
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