Contacts of the helix formed by residues 143 - 158 (chain O) in PDB entry 5OOM
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 THR 143 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307 PHE 3.5 20.6 - - - +
1317 LYS* 4.4 10.1 - - + -
1327 ASP 4.4 0.4 - - - +
1357 PRO* 4.1 11.7 - - + -
1397 ASN* 3.9 2.0 - - - +
3067 LEU* 4.0 14.9 - - + +
52E HIS 4.4 1.9 + - - -
139O ASP* 5.1 4.9 - - + +
140O SER* 3.6 23.6 - - - +
141O HIS 3.3 1.0 - - - -
142O LEU* 1.3 82.2 - - - +
144O LEU* 1.3 60.9 + - - +
145O LEU* 4.2 1.4 + - - +
146O ASN* 2.7 32.3 + - - +
147O GLN* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307 PHE* 5.0 6.5 + - + -
1397 ASN* 3.3 42.1 + - + +
1427 TYR* 4.3 21.3 - - + -
1437 TRP* 4.4 8.3 - - + -
1747 VAL* 3.6 22.4 - - + +
3017 SER 3.9 12.8 - - - +
3027 LEU* 3.6 23.8 - - + -
3037 PRO* 4.7 4.3 - - + -
3067 LEU* 3.6 14.8 - - + +
143O THR* 1.3 75.2 - - - +
145O LEU* 1.3 59.6 + - - +
147O GLN* 3.3 2.9 + - - +
148O LEU* 3.0 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3027 LEU* 4.2 13.9 - - + -
3067 LEU* 3.5 37.4 - - + +
3077 ARG 3.7 15.3 - - - +
3087 ALA* 3.8 20.4 - - + -
3127 ILE* 5.5 1.1 - - + -
3167 LEU* 5.2 4.0 - - + -
52E HIS* 4.2 18.4 - - + +
53E LEU* 3.7 30.1 - - + -
143O THR* 3.4 1.5 - - - +
144O LEU* 1.3 79.9 - - - +
146O ASN* 1.3 60.3 + - - +
148O LEU* 3.3 4.5 + - - +
149O LEU* 2.9 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E HIS 3.0 18.5 + - - +
53E LEU* 3.4 7.8 - - - -
54E SER* 2.9 28.1 + - - +
57E ASN* 3.0 21.3 - - - +
139O ASP* 4.1 3.2 + - - +
140O SER 2.6 23.9 + - - -
141O HIS* 3.3 21.4 - - - +
143O THR* 2.7 17.9 + - - +
144O LEU 3.3 0.6 - - - -
145O LEU* 1.3 79.9 - - - +
147O GLN* 1.3 58.7 + - - +
149O LEU* 4.5 1.6 - - - +
150O GLN* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397 ASN* 4.7 4.9 - - - +
1747 VAL* 4.1 18.6 - - + -
1757 ILE* 3.3 46.2 - - + +
141O HIS* 2.8 30.7 + - - +
142O LEU* 3.9 27.4 - - + +
143O THR 2.9 21.4 + - - +
144O LEU 3.8 3.8 - - - +
145O LEU 3.2 0.2 - - - -
146O ASN* 1.3 77.9 - - - +
148O LEU* 1.3 59.4 + - - +
150O GLN* 3.7 8.2 - - - +
151O GLY* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 TRP* 4.1 13.5 - - + -
1747 VAL* 3.5 22.9 - - + +
1757 ILE* 5.5 0.4 - - - +
1777 GLY* 4.0 24.0 - - - +
3007 VAL* 4.2 16.6 - - + -
3017 SER 4.7 1.1 - - - +
3027 LEU* 3.9 28.7 - - + -
3167 LEU* 3.8 31.0 - - + +
3197 ARG* 4.6 5.1 + - - +
144O LEU* 3.0 25.1 + - + +
145O LEU* 3.7 4.9 - - - +
147O GLN* 1.3 76.0 - - - +
149O LEU* 1.3 56.8 + - - +
151O GLY* 3.3 2.8 + - - -
152O LEU* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3127 ILE* 3.8 24.5 - - + -
3157 LYS* 6.2 0.7 - - + -
3167 LEU* 3.9 18.8 - - + -
53E LEU* 4.1 20.0 - - + -
57E ASN* 4.1 19.7 + - + +
60E PHE* 3.9 7.9 - - + -
61E ILE* 4.1 25.6 - - + -
145O LEU* 2.9 42.2 + - + +
146O ASN* 4.1 1.8 - - - +
148O LEU* 1.3 72.2 - - - +
150O GLN* 1.3 61.2 + - - +
152O LEU* 3.3 14.0 + - + +
153O ARG* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1757 ILE* 4.8 1.1 - - + -
56E GLU* 3.5 23.0 + - - +
57E ASN* 4.2 3.8 - - - +
141O HIS* 3.0 31.6 + - + +
146O ASN 2.9 20.7 + - - +
147O GLN* 3.7 18.2 - - - +
148O LEU 3.3 0.2 - - - -
149O LEU* 1.3 77.0 - - - +
151O GLY* 1.3 57.9 + - - +
153O ARG* 3.2 12.3 + - - +
154O GLN* 3.0 46.2 + - - +
157O ARG* 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1757 ILE* 3.7 31.2 - - - +
3197 ARG* 3.3 18.8 + - - -
147O GLN 3.0 12.3 + - - -
148O LEU 3.7 3.4 - - - -
150O GLN* 1.3 77.5 - - - +
152O LEU* 1.3 57.6 + - - +
154O GLN* 3.2 7.3 + - - +
155O ASP* 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 LYS* 3.4 42.2 - - + +
3167 LEU* 3.7 17.5 - - + -
3197 ARG* 3.7 22.8 - - + +
60E PHE* 3.8 7.2 - - + -
64E LEU* 3.7 30.3 - - + -
148O LEU 2.9 15.0 + - - +
149O LEU* 3.7 11.4 - - + +
150O GLN 3.2 0.2 - - - -
151O GLY* 1.3 72.8 - - - +
153O ARG* 1.3 59.9 + - - +
155O ASP* 3.2 2.9 + - + +
156O LEU* 3.0 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLU* 2.4 57.3 + - - +
59E PRO* 5.7 1.2 - - - +
60E PHE* 3.5 50.9 - - + +
63E GLN* 5.6 3.4 + - - -
149O LEU 3.0 14.5 + - - +
150O GLN* 3.5 16.4 - - - +
152O LEU* 1.3 77.0 - - - +
154O GLN* 1.3 56.4 + - - +
156O LEU* 3.8 1.1 - - - +
157O ARG* 2.9 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1757 ILE* 3.9 20.0 - - - +
3197 ARG* 5.0 3.4 + - - +
150O GLN* 3.0 43.1 + - - +
151O GLY* 3.2 11.8 + - - +
153O ARG* 1.3 77.3 - - - +
155O ASP* 1.3 59.9 + - - +
157O ARG* 3.6 11.7 + - - +
158O GLN* 3.1 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3197 ARG* 3.1 45.8 + - + +
3227 LYS* 4.0 24.4 - - - +
151O GLY 3.0 13.9 + - - +
152O LEU* 3.2 6.9 + - + +
154O GLN* 1.3 77.0 - - - +
156O LEU* 1.3 64.0 + - + +
158O GLN* 3.0 43.9 + - - +
159O SER* 3.3 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E PHE* 4.2 9.6 - - + -
64E LEU* 4.0 24.9 - - + -
152O LEU* 3.0 41.3 + - + +
153O ARG* 4.2 4.0 - - - +
155O ASP* 1.3 78.4 - - + +
157O ARG* 1.3 57.2 + - - +
159O SER* 3.6 17.8 - - - +
160O GLN* 2.9 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150O GLN* 5.9 1.0 + - - -
153O ARG* 2.9 52.2 + - + +
154O GLN* 3.8 11.6 - - - +
155O ASP 3.2 0.2 - - - -
156O LEU* 1.3 73.4 - - - +
158O GLN* 1.3 59.9 + - - +
159O SER 3.1 5.9 + - - -
160O GLN* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154O GLN* 3.1 24.6 + - - +
155O ASP* 3.0 31.3 + - - +
157O ARG* 1.3 72.6 - - + +
159O SER* 1.3 57.1 + - - +
160O GLN 3.1 11.4 + - - +
----------------------------------------------------------
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