Contacts of the helix formed by residues 149 - 163 (chain A) in PDB entry 2IAI
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 GLU 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 1.3 75.4 - - - +
150A VAL* 1.3 63.3 + - - +
151A ARG* 3.3 2.1 + - + +
152A LEU* 3.1 21.9 + - + +
153A ALA* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 3.4 30.1 - - + +
135A LEU* 3.8 26.3 - - + +
136A LYS* 3.8 27.4 - - + +
139A ALA* 4.6 11.7 - - + -
145A ARG 6.2 0.2 - - - +
148A VAL 3.3 4.8 + - - +
149A GLU* 1.3 76.5 + - - +
151A ARG* 1.3 63.0 + - + +
153A ALA* 3.4 2.0 + - - +
154A THR* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 4.9 6.1 + - - +
129A HIS* 3.1 38.3 + - - +
132A ALA* 4.0 25.8 - - + +
149A GLU* 3.3 2.4 + - + +
150A VAL* 1.3 80.8 - - + +
152A LEU* 1.3 60.7 + - - +
154A THR* 3.8 6.1 - - - -
155A ARG* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 4.6 11.4 - - + -
149A GLU* 3.1 21.8 + - + +
151A ARG* 1.3 77.1 - - - +
153A ALA* 1.3 65.3 + - - +
155A ARG* 3.2 9.5 + - + +
156A LEU* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.2 18.2 - - + -
144A VAL* 6.3 0.2 - - + -
148A VAL* 4.0 19.2 - - + +
149A GLU 2.8 16.3 + - - +
150A VAL* 3.7 4.9 - - - +
152A LEU* 1.3 78.7 - - - +
154A THR* 1.3 62.4 + - - +
156A LEU* 3.3 6.7 + - - +
157A VAL* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 3.6 21.5 - - - +
131A VAL* 4.5 4.3 - - + -
132A ALA* 3.6 33.2 - - + +
135A LEU* 3.5 18.7 - - + +
150A VAL 2.8 22.1 + - - -
151A ARG* 3.8 7.0 - - - -
153A ALA* 1.3 76.9 - - - +
155A ARG* 1.3 57.6 + - - +
157A VAL* 3.3 3.8 + - - -
158A PHE* 2.9 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 5.9 3.2 - - - +
128A ASP* 3.4 38.8 + - - +
151A ARG 3.0 19.7 + - - +
152A LEU* 3.2 13.7 + - + +
154A THR* 1.3 77.3 - - - +
156A LEU* 1.3 59.1 + - + +
158A PHE* 3.4 13.5 + - - +
159A GLY* 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 5.5 4.0 - - + -
152A LEU* 2.9 45.7 + - + +
153A ALA* 3.8 7.2 - - - +
155A ARG* 1.3 77.6 - - + +
157A VAL* 1.3 66.5 + - + +
159A GLY* 3.1 3.4 + - - +
160A MSE 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 4.4 9.4 - - + -
135A LEU* 5.4 6.3 - - + -
153A ALA* 2.9 26.4 + - + +
154A THR* 3.8 5.6 - - - +
156A LEU* 1.3 74.8 - - + +
158A PHE* 1.3 70.3 + - + +
160A MSE 3.2 7.8 + - - +
161A ILE* 3.0 39.8 + - + +
201A VAL* 4.0 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 6.4 0.4 - - + -
93A MSE 3.8 23.8 - - + -
124A ARG* 5.8 4.3 - - - -
127A PHE* 3.8 25.4 - + - -
128A ASP* 4.0 24.9 - - + -
131A VAL* 3.6 46.9 - - + -
154A THR* 2.9 27.4 + - + +
155A ARG* 3.7 15.5 - - - +
157A VAL* 1.3 82.9 - - + +
159A GLY* 1.3 54.8 + - - +
161A ILE* 4.4 5.4 - - + +
162A ASN* 2.7 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG 2.9 16.8 + - - -
156A LEU* 3.1 6.0 + - - -
158A PHE* 1.3 76.4 - - - +
160A MSE 1.3 61.8 + - - +
162A ASN* 4.0 4.7 - - - +
163A SER* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU 3.0 11.6 + - - +
157A VAL* 3.5 10.1 - - - +
159A GLY* 1.3 75.7 - - - +
161A ILE* 1.3 61.5 + - + +
163A SER* 2.7 26.1 + - - +
164A ILE* 3.8 6.1 - - - +
197A VAL* 4.7 16.6 - - + -
200A LEU* 4.3 35.9 - - + +
201A VAL* 3.9 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 4.1 22.0 - - + +
93A MSE 4.1 47.3 - - + +
94A VAL* 4.2 15.3 - - + +
97A LEU* 3.1 20.5 - - + +
157A VAL* 3.0 38.4 + - + +
158A PHE* 3.9 4.9 - - + +
160A MSE 1.3 77.6 - - + +
162A ASN* 1.3 65.9 + - - +
164A ILE* 3.1 26.4 + - + +
197A VAL* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MSE 4.8 7.8 - - - +
97A LEU* 3.8 8.7 - - - +
104A VAL* 5.4 1.9 - - - +
108A LEU* 3.8 36.8 - - + +
124A ARG* 3.9 11.1 - - - +
158A PHE* 2.7 39.1 + - - +
159A GLY* 4.2 4.6 - - - +
161A ILE* 1.3 79.5 - - - +
163A SER* 1.3 61.0 + - - +
164A ILE 3.0 1.8 + - - -
165A VAL* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 3.1 17.3 + - - -
160A MSE 2.7 19.8 + - - +
162A ASN* 1.3 75.7 - - - +
164A ILE* 1.3 57.0 + - - +
165A VAL 3.1 0.4 - - - -
166A GLU* 2.9 31.2 + - - +
167A TRP* 3.3 23.4 + - - -
----------------------------------------------------------
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