Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 2I2X
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 LYS 142 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 4.6 9.1 + - - +
129A ILE* 3.8 33.9 + - + +
130A ARG* 4.5 11.4 - - + -
131A GLU 3.1 30.7 + - - +
132A ASN* 4.5 4.8 - - - +
137A GLN* 4.1 21.5 - - + +
140A GLY* 3.1 1.4 - - - -
141A ASP* 1.3 85.3 - - + +
143A TYR* 1.3 63.5 + - - +
144A SER 3.2 0.2 - - - -
145A VAL* 3.0 15.4 + - + +
146A PHE* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 3.7 14.5 - - - +
138A LEU 3.2 20.9 - - - +
139A ARG* 4.4 10.3 - - - +
140A GLY* 3.1 17.9 + - - +
142A LYS* 1.3 77.1 - - - +
144A SER* 1.3 60.3 + - - +
146A PHE* 3.0 27.2 - + - +
147A LEU* 3.1 30.7 + - + +
198A LEU* 3.5 35.1 - - + +
199A ILE* 3.7 26.1 - - + -
202A ASP* 2.5 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 4.7 0.2 + - - -
141A ASP 3.7 12.8 + - - -
142A LYS 3.2 0.2 - - - -
143A TYR* 1.3 79.1 - - - +
145A VAL* 1.3 67.4 + - - +
147A LEU* 3.5 10.3 + - - +
148A GLU* 3.0 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 3.9 5.8 - - - +
93A ASN* 3.7 24.0 - - - +
95A PRO* 4.0 10.4 - - + +
129A ILE* 3.7 17.5 - - + -
141A ASP 4.2 11.2 - - - +
142A LYS* 3.0 17.9 + - + +
144A SER* 1.3 78.2 + - - +
146A PHE* 1.3 64.9 + - - +
148A GLU* 3.0 16.5 + - - +
149A ALA* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 3.7 6.3 - - + -
127A GLY 3.6 25.6 - - - -
128A ASP* 4.0 12.1 - - - -
129A ILE* 3.8 19.4 - - + +
130A ARG* 3.9 23.6 - - + -
142A LYS 2.9 11.3 + - - +
143A TYR* 3.0 22.2 - + - +
145A VAL* 1.3 73.8 - - - +
147A LEU* 1.3 70.3 + - + +
149A ALA* 3.2 17.3 + - - +
150A PHE* 3.3 46.1 - + - -
163A VAL* 4.1 16.8 - - + -
199A ILE* 4.0 29.2 - - + -
203A ILE* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.1 41.6 + - + +
144A SER* 3.7 10.1 - - - +
146A PHE* 1.3 86.8 - - + +
148A GLU* 1.3 60.9 + - - +
150A PHE* 3.1 13.7 + - + +
151A GLU* 3.0 27.8 + - - +
199A ILE 5.3 0.7 - - - +
202A ASP* 3.8 32.8 - - + +
203A ILE* 5.0 3.8 - - + +
206A ILE* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.7 22.0 - - + +
144A SER* 3.0 29.4 + - - +
145A VAL* 3.0 18.9 + - - +
147A LEU* 1.3 73.1 - - - +
149A ALA* 1.3 60.1 + - - +
151A GLU* 4.5 10.8 - - - +
152A GLN* 2.9 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.9 3.8 - - + -
92A SER* 3.8 28.9 - - - +
95A PRO* 4.0 12.5 - - + +
126A ILE* 3.8 24.2 - - + -
145A VAL 2.9 6.9 + - - +
146A PHE* 3.4 11.7 - - - +
147A LEU 3.1 0.2 - - - -
148A GLU* 1.3 77.6 - - - +
150A PHE* 1.3 62.0 + - - +
152A GLN* 4.2 0.4 - - - +
153A CYS* 3.1 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 3.7 23.6 - - + -
146A PHE* 3.3 53.5 + + - -
147A LEU* 3.1 12.1 + - + +
149A ALA* 1.3 78.1 - - - +
151A GLU* 1.3 64.1 + - - +
153A CYS* 4.0 1.6 - - - +
154A ALA* 3.0 24.6 + - - +
161A LEU* 4.1 22.6 - - + +
162A SER 3.3 26.9 - - - -
163A VAL* 3.7 21.1 - - + -
203A ILE* 3.5 40.4 - - + -
206A ILE* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.0 15.9 + - - +
148A GLU* 4.4 12.4 - - - +
150A PHE* 1.3 79.5 - - - +
152A GLN* 1.3 65.4 + - - +
154A ALA* 3.3 2.5 + - - +
155A GLU* 3.0 49.7 + - - +
206A ILE* 3.4 32.6 - - + +
209A LYS* 3.3 31.9 + - - +
210A THR* 4.4 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 4.0 22.7 - - + +
96A SER* 5.1 6.5 - - - +
99A ALA* 3.9 17.1 - - + +
148A GLU* 2.9 29.2 + - + +
149A ALA 4.2 1.1 - - - +
151A GLU* 1.3 83.2 - - + +
153A CYS* 1.3 62.7 + - - +
155A GLU* 3.2 24.9 + - - +
156A ASN* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 3.4 36.3 - - - -
95A PRO 4.8 2.0 - - - -
98A GLY* 3.5 16.8 - - - -
99A ALA* 3.8 7.9 - - - +
102A ALA* 4.1 2.3 - - + +
124A HIS* 3.5 20.6 - - + -
126A ILE* 4.3 5.6 - - + -
149A ALA* 3.1 22.2 + - - +
150A PHE 4.0 2.2 - - - +
152A GLN* 1.3 75.9 - - - +
154A ALA* 1.3 61.1 + - - +
156A ASN 3.2 7.6 + - - -
157A GLY 3.4 1.2 + - - -
158A ALA* 3.0 31.5 + - + -
161A LEU* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE 3.0 19.3 + - - +
151A GLU* 3.6 6.3 - - - +
152A GLN 3.2 0.2 - - - -
153A CYS* 1.3 77.5 - - - +
155A GLU* 1.3 60.2 + - - +
156A ASN 3.2 0.7 + - - -
157A GLY 4.4 1.7 + - - -
158A ALA* 4.0 11.8 - - - +
161A LEU* 4.0 12.6 - - + -
206A ILE* 4.7 0.4 - - + -
210A THR* 3.6 29.0 - - + +
212A THR* 3.5 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 3.0 36.7 + - - +
152A GLN* 3.2 25.6 + - - +
153A CYS 3.2 0.4 - - - -
154A ALA* 1.3 76.9 - - - +
156A ASN* 1.3 67.9 + - - +
157A GLY 3.7 1.3 - - - -
209A LYS* 5.0 6.2 + - - -
210A THR* 4.0 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 3.4 31.8 + - + +
100A GLU* 6.3 1.0 - - - +
102A ALA* 3.3 1.3 - - - -
103A HIS* 3.1 52.6 + - + +
106A LYS* 4.8 0.2 - - - +
152A GLN* 2.8 29.7 - - - +
153A CYS 3.2 5.4 + - - +
155A GLU* 1.3 89.0 + - - +
157A GLY* 1.3 56.9 + - - +
158A ALA 3.8 0.2 - - - -
----------------------------------------------------------
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