Contacts of the helix formed by residues 140 - 149 (chain F) in PDB entry 6DVD
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 140 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ARG* 5.6 0.4 - - - +
69D ARG* 3.3 31.5 + - - +
134F SER* 6.0 0.2 - - - -
139F TRP* 1.3 80.0 - - - +
141F THR* 1.3 75.0 + - - +
142F ALA* 3.4 8.2 + - - +
143F GLN* 3.5 21.8 - - - -
144F ILE* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F SER* 1.3 81.5 + - - +
142F ALA* 1.3 59.3 + - - -
144F ILE* 3.6 4.9 + - - +
145F ALA* 3.4 19.8 + - - +
152F GLU* 3.2 24.1 - - - +
155F VAL* 4.2 16.0 - - + +
156F LYS* 3.8 32.4 - - + +
159F LEU* 5.6 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F SER* 3.9 5.3 + - - +
141F THR* 1.3 77.0 - - - +
143F GLN* 1.3 64.6 + - + +
144F ILE 3.4 0.2 - - - -
145F ALA* 3.4 3.4 + - - +
146F THR* 2.8 31.3 + - - +
152F GLU* 3.4 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ARG* 3.3 38.6 - - - +
70D PHE* 5.8 0.4 - - - -
139F TRP* 3.5 35.4 - - + +
140F SER* 3.5 24.3 + - - +
141F THR 3.3 0.8 - - - -
142F ALA* 1.3 76.9 - - + +
144F ILE* 1.3 64.9 + - - +
146F THR* 3.4 6.7 + - - -
147F ASP* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 4.1 9.4 - - + +
133F ARG* 3.5 51.4 - - + +
134F SER* 3.6 19.5 - - - +
139F TRP* 3.9 11.7 - - + +
140F SER 3.2 18.3 + - - +
141F THR* 3.6 0.9 + - - +
142F ALA 3.4 0.4 - - - -
143F GLN* 1.3 73.7 - - - +
145F ALA* 1.3 64.9 + - - +
147F ASP* 3.3 1.9 + - - +
148F LEU* 3.0 45.8 + - + +
155F VAL* 4.0 27.4 - - + -
159F LEU* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F THR 3.4 9.4 + - - +
142F ALA* 3.8 11.0 - - - +
143F GLN 3.3 0.4 - - - -
144F ILE* 1.3 79.9 - - - +
146F THR* 1.3 60.8 + - - +
149F GLY* 3.2 18.0 + - - -
150F ILE* 3.2 21.2 + - - +
151F ALA 3.6 26.0 - - - +
152F GLU* 4.2 8.1 - - - +
155F VAL* 3.7 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F ALA* 2.8 19.3 + - - +
143F GLN* 3.7 7.3 - - - -
144F ILE 3.3 0.2 - - - -
145F ALA* 1.3 78.0 - - - +
147F ASP* 1.3 63.0 + - - +
149F GLY* 3.7 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ARG* 3.1 30.9 + - - +
139F TRP* 3.3 23.7 - - + -
143F GLN 3.2 15.7 + - - +
144F ILE* 3.3 3.8 + - - +
146F THR* 1.3 80.8 - - - +
148F LEU* 1.3 66.0 + - + +
149F GLY* 3.2 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F GLU 5.3 0.2 - - - +
129F ALA* 4.1 10.3 - - + +
130F VAL* 3.6 31.2 - - + -
133F ARG* 3.7 33.9 - - - +
144F ILE* 3.0 29.5 + - + +
147F ASP* 1.3 76.9 - - + +
149F GLY* 1.3 61.8 + - - +
150F ILE* 3.5 30.8 + - + +
158F ARG* 4.3 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F ALA 3.2 8.2 + - - -
146F THR 3.7 5.6 + - - -
147F ASP 3.2 6.4 + - - -
148F LEU* 1.3 79.5 - - - +
150F ILE* 1.3 62.1 + - - +
----------------------------------------------------------
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