Contacts of the helix formed by residues 144 - 160 (chain D) in PDB entry 1OVM
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 144 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B THR* 4.2 1.8 - - - -
139D VAL 3.3 16.7 - - - +
140D LEU* 3.5 4.2 - - - +
141D THR* 2.6 45.2 + - - +
143D GLN* 1.3 77.3 - - - +
145D ALA* 1.3 91.6 + - - +
146D CYS 3.2 2.6 + - - -
147D TYR* 3.2 33.7 + - + +
148D GLU* 3.0 39.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
320B THR* 4.1 10.5 - - + +
7D VAL* 3.9 35.2 - - + -
140D LEU* 4.3 8.7 - - + +
141D THR 2.9 11.4 + - - +
142D GLU* 4.8 2.5 - - - +
143D GLN 3.8 0.6 - - - -
144D ASN* 1.3 89.4 - - - +
146D CYS* 1.3 60.8 + - - +
148D GLU* 3.8 1.7 - - - +
149D ILE* 2.9 34.4 + - - +
171D VAL* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B CYS* 6.1 1.1 - - - -
320B THR* 2.6 39.3 + - - +
321B GLY* 5.0 1.8 - - - -
7D VAL* 5.4 1.8 - - - -
10D TYR* 3.8 44.9 - - + +
144D ASN 3.2 1.0 + - - -
145D ALA* 1.3 84.3 - - - +
147D TYR* 1.3 58.6 + - - +
149D ILE* 3.4 2.9 + - - +
150D ASP* 3.0 34.1 + - - -
175D ALA 5.9 0.2 - - - -
176D ALA* 4.4 17.3 - - - -
177D THR 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 3.4 60.0 - + + +
311B ALA* 4.5 0.4 - - + +
320B THR* 4.4 0.4 - - - -
321B GLY* 3.8 17.7 - - - -
143D GLN 3.5 10.7 + - - -
144D ASN* 3.2 39.1 + - + +
146D CYS* 1.3 76.3 - - - +
148D GLU* 1.3 79.0 + - + +
150D ASP* 3.9 8.3 - - - +
151D ARG* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ALA* 3.5 12.3 - - + +
140D LEU* 3.9 17.5 - - + -
144D ASN* 3.0 43.4 + - + +
145D ALA 3.8 2.2 - - - +
147D TYR* 1.3 91.1 - - + +
149D ILE* 1.3 67.1 + - - +
151D ARG* 2.8 47.9 + - - +
152D VAL* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.2 17.9 - - + -
10D TYR* 4.1 17.7 - - + -
11D LEU* 3.9 38.4 - - + -
14D ARG* 4.2 14.6 - - + -
140D LEU* 3.9 23.3 - - + -
145D ALA 2.9 28.4 + - - +
146D CYS* 3.5 5.6 - - - +
148D GLU* 1.3 78.1 - - - +
150D ASP* 1.3 63.3 + - - +
152D VAL* 3.6 1.7 - - - +
153D LEU* 3.3 34.5 + - + +
165D LEU* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 2.7 25.2 + - - -
14D ARG* 2.7 34.0 + - - +
146D CYS* 3.0 17.7 + - - +
147D TYR* 3.9 7.5 - - - +
149D ILE* 1.3 75.9 - - - +
151D ARG* 1.3 57.3 + - - +
153D LEU* 3.9 0.7 - - - +
154D THR* 2.7 38.3 + - - +
183D LEU* 3.5 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ARG* 4.5 18.8 - - - +
136D ALA* 4.1 23.0 - - - +
137D GLN 3.0 24.2 + - - +
138D ALA* 3.8 3.8 - - - +
147D TYR* 3.0 19.1 + - + +
148D GLU* 2.8 43.7 + - - +
150D ASP* 1.3 75.1 - - - +
152D VAL* 1.3 69.8 + - - +
154D THR* 3.2 6.0 + - - -
155D THR* 2.9 33.9 + - - +
158D ARG* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 4.6 0.4 - - + -
136D ALA* 3.8 21.8 - - + +
137D GLN* 4.0 17.0 - - - +
138D ALA* 4.0 15.0 - - + -
148D GLU 3.0 12.7 + - - +
149D ILE 3.6 10.3 - - - +
151D ARG* 1.3 81.1 - - - +
153D LEU* 1.3 57.2 + - + +
155D THR* 3.1 3.8 + - - -
156D MET* 2.8 56.1 + - + +
164D TYR 4.8 1.3 - - - +
165D LEU* 3.7 36.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
11D LEU* 5.1 3.8 - - + -
14D ARG* 3.3 40.4 - - + +
15D LEU* 4.8 2.7 - - + +
18D CYS* 4.1 5.2 - - - -
68D PHE* 3.5 26.0 - - + -
97D LEU* 3.9 13.2 - - + -
149D ILE* 3.3 25.7 + - + +
151D ARG 3.3 0.2 - - - -
152D VAL* 1.3 83.1 - - + +
154D THR* 1.3 62.5 + - - +
156D MET* 3.2 27.1 + - + +
157D LEU* 3.0 29.2 + - - +
165D LEU* 5.6 0.7 - - + -
183D LEU* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ASP* 2.7 23.9 + - - +
151D ARG* 3.6 5.6 - - - -
153D LEU* 1.3 78.4 - - - +
155D THR* 1.3 61.4 + - - +
157D LEU* 3.3 9.1 + - - +
158D ARG* 3.1 34.1 + - + +
183D LEU* 3.9 19.2 - - - +
184D THR 4.9 10.8 + - - +
185D HIS* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D VAL* 3.7 33.0 - - + +
136D ALA* 3.8 13.0 - - + +
151D ARG* 2.9 25.0 + - - +
152D VAL 3.5 6.7 - - - -
154D THR* 1.3 76.1 - - - +
156D MET* 1.3 64.5 + - - +
158D ARG* 3.1 35.0 + - - +
159D GLU* 2.9 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D PHE* 4.1 12.3 - - + -
95D PRO* 4.6 3.8 - - + +
96D VAL 4.2 3.4 - - - +
97D LEU* 3.1 46.9 - - + -
135D VAL* 4.4 5.4 - - + -
136D ALA* 5.6 0.2 - - + -
152D VAL* 2.8 23.1 + - + +
153D LEU* 3.3 31.0 - - + +
155D THR* 1.3 75.4 - - - +
157D LEU* 1.3 61.5 + - + +
160D ARG* 2.6 37.4 + - - -
161D ARG 3.3 21.9 + - - +
162D PRO 4.0 1.8 - - - +
163D GLY* 3.5 28.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D CYS* 3.7 26.2 - - + +
68D PHE* 3.4 38.8 - - + -
95D PRO* 5.1 1.1 - - + -
153D LEU 3.0 15.2 + - - +
154D THR* 3.8 7.2 - - - +
155D THR 3.3 0.2 - - - -
156D MET* 1.3 81.6 - - - +
158D ARG* 1.3 61.2 + - - +
160D ARG* 3.0 46.7 + - - +
183D LEU* 4.9 6.3 - - + +
184D THR 5.5 2.7 - - - +
185D HIS* 3.5 40.6 - - + +
187D GLN* 4.2 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 4.6 19.2 - - - +
151D ARG 5.3 0.2 + - - -
154D THR* 3.1 24.1 + - + +
155D THR* 3.1 44.7 + - - +
157D LEU* 1.3 80.2 - - - +
159D GLU* 1.3 81.5 + - - +
160D ARG 3.7 0.2 + - - -
187D GLN* 4.0 22.1 + - + +
223D HIS* 3.9 15.6 + - - -
310D HIS* 4.3 14.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D HIS* 3.6 17.0 - - - -
135D VAL* 4.1 29.2 - - + -
155D THR* 2.9 26.0 + - + +
158D ARG* 1.3 106.6 + - - +
160D ARG* 1.3 73.0 + - - +
161D ARG* 3.9 3.5 - - + +
223D HIS* 4.6 3.4 - - - -
309D PRO* 5.7 0.2 - - - +
310D HIS* 3.1 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLY* 3.3 27.5 + - - -
93D HIS* 2.8 39.0 - - + +
95D PRO* 4.0 18.7 - - + +
156D MET 2.6 18.2 + - - -
157D LEU* 3.0 43.6 + - - +
159D GLU* 1.3 77.9 - - - +
161D ARG* 1.3 56.0 + - - +
185D HIS* 5.6 8.7 + - - +
187D GLN* 5.5 3.6 - - - +
222D ARG* 3.3 28.0 + - + +
223D HIS* 3.7 34.6 - - + +
----------------------------------------------------------
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