Contacts of the helix formed by residues 140 - 155 (chain D) in PDB entry 5DIR
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 140 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASP* 4.0 3.1 - - - +
27D LYS* 3.3 10.4 - - - +
112D ASN* 3.2 20.4 + - - -
122D VAL* 3.6 4.8 - - - +
123D VAL 2.9 26.7 + - - +
124D ASP* 3.5 7.3 + - - -
125D PHE* 3.7 17.3 - - + -
126D ILE* 3.9 12.8 - - - -
139D PHE* 1.3 78.2 - - - +
141D LEU* 1.3 63.0 + - - +
142D ALA* 3.0 6.3 + - - +
143D ASP* 2.6 39.1 + - - -
144D SER* 2.8 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 4.9 4.6 - - + +
22D LEU* 3.6 23.1 - - + +
23D ASP* 3.5 15.0 + - + +
26D SER* 3.5 17.9 - - - +
125D PHE* 3.4 26.2 - - + -
126D ILE* 4.5 6.1 - - + -
140D ASN* 1.3 74.1 - - - +
142D ALA* 1.3 60.8 + - - +
144D SER* 3.1 7.7 + - - -
145D ALA* 2.8 32.1 + - - +
202D OLC 3.5 55.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
19D VAL* 5.1 1.1 - - - -
23D ASP* 2.7 31.3 + - - +
108D GLY* 3.2 33.9 - - - +
111D GLY* 4.4 0.2 - - - -
112D ASN* 3.3 23.3 - - - +
140D ASN* 3.0 1.5 + - - +
141D LEU* 1.3 73.8 - - - +
143D ASP* 1.3 62.9 + - - +
145D ALA* 3.4 0.6 + - - -
146D ILE* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ASN* 2.9 24.8 + - - -
139D PHE* 3.3 18.7 - - + +
140D ASN* 2.6 27.5 + - - +
142D ALA* 1.3 71.9 - - - +
144D SER* 1.3 58.2 + - - +
146D ILE* 3.3 2.4 + - - +
147D THR* 2.9 33.1 + - - -
201D OLC 3.3 25.0 - - - -
202G IIL 3.4 11.2 - - - +
203G SER* 2.2 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ILE* 4.4 3.3 - - - +
139D PHE* 3.5 19.9 - - - -
140D ASN 2.8 17.5 + - - -
141D LEU* 3.1 12.7 + - - -
143D ASP* 1.3 79.0 - - - +
145D ALA* 1.3 57.2 + - - +
147D THR* 3.3 1.4 + - - -
148D VAL* 3.0 36.4 + - - +
201D OLC 3.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 3.6 25.8 - - + -
104D LEU* 3.4 38.9 - - + +
108D GLY* 4.5 0.2 - - - -
141D LEU 2.8 18.4 + - - +
142D ALA 3.8 2.9 - - - +
144D SER* 1.3 72.0 - - - +
146D ILE* 1.3 58.6 + - - +
148D VAL* 3.5 4.5 + - - +
149D GLY* 2.9 25.1 + - - -
201D OLC 5.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 3.8 31.0 - - + +
108D GLY* 3.5 28.7 - - - +
109D ALA* 3.6 2.5 - - - +
112D ASN* 4.3 1.1 - - - +
142D ALA 3.0 20.6 + - - +
143D ASP 3.6 3.8 - - - +
145D ALA* 1.3 76.3 - - - +
147D THR* 1.3 58.8 + - - +
149D GLY* 3.4 0.9 + - - -
150D ALA* 2.8 31.0 + - + +
201G MLE 3.7 36.3 - - + +
202G IIL 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ASP 2.9 15.0 + - - -
144D SER 3.7 4.0 - - - -
146D ILE* 1.3 77.9 - - - +
148D VAL* 1.3 58.3 + - + +
150D ALA* 3.1 8.0 + - + +
151D VAL* 2.8 38.6 + - + +
201D OLC 3.1 50.1 + - + +
202G IIL 4.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.7 20.0 - - + -
144D SER 3.0 20.3 + - - +
145D ALA* 3.9 3.6 - - - +
147D THR* 1.3 71.7 - - + +
149D GLY* 1.3 61.5 + - - +
151D VAL* 3.2 9.1 + - + +
152D MET* 2.8 40.4 + - + +
201D OLC 3.6 55.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ALA* 3.5 30.5 - - - +
104D LEU* 4.1 5.1 - - - +
105D VAL* 3.8 8.7 - - - -
145D ALA 2.9 17.4 + - - -
146D ILE 3.7 1.6 - - - -
148D VAL* 1.3 77.0 - - - +
150D ALA* 1.3 51.3 + - - +
152D MET* 3.2 2.1 + - - +
153D LEU* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 4.0 4.0 - - + +
146D ILE* 2.8 21.7 + - + +
147D THR* 3.3 9.0 - - - +
149D GLY* 1.3 74.9 - - - +
151D VAL* 1.3 64.5 + - + +
153D LEU* 3.3 8.1 + - - +
154D ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D THR* 2.8 29.5 + - + +
148D VAL* 3.2 9.8 + - + +
150D ALA* 1.3 78.0 - - + +
152D MET* 1.3 64.7 + - + +
154D ALA* 3.5 5.0 + - - +
155D LEU* 3.2 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D TRP* 2.9 86.7 - - + +
100D ILE* 3.8 20.6 - - + -
101D ALA* 3.5 10.1 - - + +
104D LEU* 3.9 26.9 - - - -
148D VAL* 2.8 25.3 + - + +
149D GLY 3.5 4.5 - - - +
151D VAL* 1.3 77.4 - - + +
153D LEU* 1.3 65.6 + - - +
155D LEU 3.2 0.7 + - - -
156D ASP* 3.1 9.7 + - - +
201D OLC 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 5.6 3.1 - - + -
87D TRP* 3.6 35.9 - - + -
98D LEU* 4.9 5.3 - - + +
101D ALA* 3.9 8.0 - - + +
102D LEU* 4.0 14.4 - - + -
105D VAL* 5.9 5.8 - - + -
149D GLY 2.7 20.9 + - - +
150D ALA* 3.7 7.9 - - - +
152D MET* 1.3 73.5 - - - +
154D ALA* 1.3 66.3 + - + +
156D ASP* 3.3 17.4 + - - +
157D MET* 3.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ALA 3.0 17.7 + - - +
151D VAL* 3.8 6.3 - - - +
152D MET 3.3 0.2 - - - -
153D LEU* 1.3 82.2 - - + +
155D LEU* 1.3 65.7 + - + +
156D ASP 3.6 0.5 + - - -
157D MET* 4.3 8.9 + - - +
158D PHE* 3.7 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D TRP* 3.9 21.5 - - + -
151D VAL* 3.2 34.7 + - + +
152D MET 3.2 3.3 + - - -
154D ALA* 1.3 82.5 - - + +
156D ASP* 1.3 59.7 + - - +
157D MET 3.6 0.2 - - - -
158D PHE* 3.8 15.6 + - + +
159D ARG* 3.2 29.9 - - + +
----------------------------------------------------------
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