Contacts of the helix formed by residues 131 - 137 (chain A) in PDB entry 2INU
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 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE* 3.5 10.2 - - - -
130A PHE* 1.3 81.0 - - - +
132A ARG* 1.3 63.0 + - - +
134A ILE* 3.2 39.5 + - - +
135A LEU* 3.3 13.7 + - - +
143A TRP* 5.3 1.0 - - - -
244A GLU* 2.8 26.2 + - - -
174C ARG* 5.3 4.0 - - - -
211C ASP* 4.7 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.1 26.6 + - + +
131A SER* 1.3 70.9 - - - +
133A SER* 1.3 59.6 + - - +
135A LEU* 3.2 11.2 + - + +
136A ASP* 2.8 35.4 + - - +
146A LEU 4.0 12.1 + - - -
147A GLN* 3.3 29.9 + - - +
148A PRO* 3.8 8.1 - - + +
154A ARG* 4.2 6.1 - - - +
186A ASP* 2.8 43.2 + - - -
188A VAL* 3.3 33.2 + - - +
221A VAL* 4.8 2.2 - - + -
222A TYR* 3.5 35.4 - - + -
244A GLU* 3.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 4.1 0.7 - - - -
132A ARG* 1.3 79.6 - - - +
134A ILE* 1.3 64.8 + - - +
136A ASP* 3.3 0.9 + - - +
137A ASN* 3.0 32.4 + - - +
195A ASN* 4.9 0.2 + - - -
197A TYR* 5.1 2.1 + - - -
222A TYR* 3.2 18.3 + - - -
244A GLU* 2.9 30.3 + - - -
292A ARG* 4.8 4.5 + - - -
343A TYR* 4.3 5.9 - - - -
346A PHE* 4.0 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.2 28.4 + - - +
133A SER* 1.3 77.0 - - - +
135A LEU* 1.3 61.8 + - - +
137A ASN 3.2 1.2 + - - -
138A SER* 2.7 41.5 + - - +
143A TRP* 4.1 14.8 - - + -
343A TYR* 3.5 24.9 - - + +
174C ARG* 4.2 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 4.0 7.4 - - + -
131A SER 3.3 11.6 + - - +
132A ARG* 3.2 20.1 + - + +
134A ILE* 1.3 79.7 - - - +
136A ASP* 1.3 66.9 + - - +
138A SER* 3.1 20.3 + - - +
140A PRO* 3.3 33.3 - - + +
143A TRP* 3.6 36.5 - - + -
146A LEU* 3.3 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 2.8 17.0 + - - +
133A SER 3.7 4.7 - - - +
135A LEU* 1.3 78.2 - - - +
137A ASN* 1.3 62.8 + - - +
138A SER 3.5 1.9 + - - +
189A GLY* 5.4 1.2 - - - -
190A PHE 5.5 0.2 + - - -
194A LYS* 2.9 52.8 + - + +
195A ASN* 4.7 0.4 - - - +
222A TYR* 2.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 3.0 28.6 + - - +
135A LEU 3.1 0.6 - - - -
136A ASP* 1.3 78.9 - - - +
138A SER* 1.3 61.3 + - - +
194A LYS* 3.7 11.8 - - - +
195A ASN* 2.8 41.8 + - - -
343A TYR* 3.4 22.3 + - - +
345A PRO* 3.4 29.5 - - + +
346A PHE* 4.5 0.8 - - - -
----------------------------------------------------------
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