Contacts of the helix formed by residues 143 - 152 (chain A) in PDB entry 3ARE
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 LEU 143 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 5.4 3.1 - - + -
125A VAL* 3.7 32.5 - - + +
126A VAL* 4.7 9.9 - - + -
135A THR* 4.4 11.4 - - + -
139A ALA* 4.7 3.4 - - + -
140A PRO* 3.4 36.5 + - + +
141A SER 3.0 0.6 - - - -
142A TRP* 1.3 108.9 - - + +
144A ASP* 1.3 62.0 + - - +
145A LEU 3.4 0.2 - - - -
146A PRO* 3.3 8.4 - - + +
147A ILE* 3.1 27.9 + - + +
601A 4GH 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.9 21.3 + - - +
140A PRO 4.9 1.7 - - - +
141A SER* 3.2 27.7 + - - +
143A LEU* 1.3 76.7 - - - +
145A LEU* 1.3 52.5 + - - +
147A ILE* 3.2 8.2 + - - +
148A LYS* 2.7 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 3.9 23.6 - - + +
88A MET* 3.8 23.6 - - + -
141A SER 4.7 0.2 + - - -
142A TRP 3.9 5.9 + - - +
144A ASP* 1.3 79.5 - - - +
146A PRO* 1.4 66.6 - - + +
148A LYS* 3.3 11.3 + - + +
149A VAL* 3.1 31.4 + - + +
30D ASN* 5.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.7 33.7 - - + -
87A MET* 4.1 2.9 - - + -
88A MET* 4.1 22.4 - - + -
142A TRP* 3.2 22.0 - - + +
143A LEU* 3.3 14.1 - - + +
145A LEU* 1.4 89.2 - - + +
147A ILE* 1.3 61.7 + - + +
149A VAL* 3.1 1.9 + - - +
150A LEU* 2.8 36.9 + - + +
601A 4GH 4.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 3.8 28.7 - - + -
133A TRP* 3.7 36.1 - - + +
134A GLN* 4.8 2.2 - - - +
135A THR* 3.8 22.7 - - + -
143A LEU* 3.1 19.6 + - + +
144A ASP* 3.2 7.6 + - - +
146A PRO* 1.3 75.2 - - + +
148A LYS* 1.3 65.4 + - - +
150A LEU* 3.4 6.6 + - + +
151A ASN* 3.1 41.5 + - - +
601A 4GH 4.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP 2.7 20.8 + - - +
145A LEU* 3.5 13.5 - - + +
147A ILE* 1.3 74.5 - - - +
149A VAL* 1.3 62.4 + - + +
151A ASN* 3.9 7.3 + - - +
152A ALA* 3.7 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.6 1.3 - - + -
87A MET* 3.8 21.3 - - + -
145A LEU* 3.1 20.6 + - + +
146A PRO* 3.1 10.1 + - + +
148A LYS* 1.3 77.1 - - + +
150A LEU* 1.3 64.1 + - - +
151A ASN 3.2 0.2 - - - -
152A ALA* 3.2 20.1 + - - +
153A ASP 4.1 1.9 + - - -
97C SER* 4.2 7.3 - - - -
98C ALA* 4.2 23.8 - - + +
99C LEU* 3.8 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 4.9 6.5 - - + +
84A LEU* 3.8 31.4 - - + -
133A TRP* 3.9 30.2 + - + +
146A PRO* 2.8 31.8 + - + +
147A ILE* 3.9 7.9 - - + +
149A VAL* 1.3 72.6 - - - +
151A ASN* 1.3 61.5 + - - +
153A ASP* 3.4 27.9 + - + +
156A THR* 5.6 2.9 - - + -
157A SER* 5.4 0.9 - - - -
601A 4GH 3.9 55.2 - - + -
99C LEU* 4.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.3 17.8 + - - -
133A TRP* 3.1 48.0 + - - +
147A ILE* 3.1 25.4 + - - +
148A LYS* 4.1 8.6 - - - +
149A VAL 3.2 0.2 - - - -
150A LEU* 1.3 72.8 - - - +
152A ALA* 1.3 57.4 + - - +
153A ASP 2.9 16.7 + - - +
154A GLN* 4.3 5.7 + - - +
157A SER* 5.2 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS 3.7 10.5 + - - +
149A VAL* 3.2 15.2 + - - +
151A ASN* 1.3 75.5 - - - +
153A ASP* 1.3 56.2 + - - +
154A GLN* 3.7 6.8 + - - +
96C GLY 3.0 14.0 - - - +
97C SER* 4.4 6.6 - - - -
98C ALA 5.7 2.0 - - - +
----------------------------------------------------------
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