Contacts of the helix formed by residues 142 - 156 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ASN* 4.4 9.6 + - - +
129C ILE* 3.5 35.2 + - + +
130C ARG* 4.2 11.7 - - - -
131C GLU 3.0 26.9 + - - -
132C ASN* 4.4 5.3 - - - +
137C GLN* 3.4 25.2 + - - +
140C GLY 3.3 0.6 - - - -
141C ASP* 1.3 85.9 - - + +
143C TYR* 1.3 65.3 + - - +
144C SER 3.3 0.2 - - - -
145C VAL* 3.0 14.7 + - + +
146C PHE* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 3.7 13.0 - - - +
137C GLN 5.3 0.2 + - - -
138C LEU 3.3 20.4 - - - +
139C ARG* 4.5 10.8 - - - +
140C GLY 3.3 17.0 + - - +
141C ASP 3.2 0.8 - - - -
142C LYS* 1.3 77.5 - - - +
144C SER* 1.3 66.3 + - - +
146C PHE* 3.1 24.7 - + - +
147C LEU* 3.1 30.0 + - + +
198C LEU* 3.4 40.6 + - + +
199C ILE* 3.8 20.6 - - + -
202C ASP* 2.4 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLY 4.5 0.6 + - - -
141C ASP 3.8 11.9 + - - -
142C LYS 3.3 0.2 - - - -
143C TYR* 1.3 83.7 - - - +
145C VAL* 1.3 62.3 + - - +
147C LEU* 3.6 9.1 + - - +
148C GLU* 3.1 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C SER 3.7 19.3 - - - +
93C ASN* 3.7 17.5 - - - +
95C PRO* 4.0 9.5 - - + +
129C ILE* 3.7 11.0 - - + -
141C ASP 4.4 8.5 - - - +
142C LYS* 3.0 15.8 + - + +
144C SER* 1.3 80.2 - - - +
146C PHE* 1.3 59.4 + - - +
148C GLU* 3.1 16.4 + - - +
149C ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 4.0 3.4 - - + -
127C GLY 3.7 25.4 - - - -
128C ASP* 3.9 15.9 - - - -
129C ILE* 3.7 17.4 - - + +
130C ARG* 4.0 16.6 - - + -
142C LYS 2.9 11.9 + - - +
143C TYR* 3.1 23.1 - + - +
145C VAL* 1.3 73.6 - - - +
147C LEU* 1.3 69.0 + - + +
149C ALA* 3.2 16.1 + - - +
150C PHE* 3.2 41.8 - + - -
163C VAL* 3.9 28.0 - - + -
199C ILE* 3.8 31.0 - - + -
203C ILE* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 3.1 40.5 + - + +
144C SER* 3.9 10.1 - - - +
145C VAL 3.3 0.2 - - - -
146C PHE* 1.3 91.6 - - + +
148C GLU* 1.3 62.5 + - - +
150C PHE* 3.2 11.2 + - + -
151C GLU* 3.1 21.8 + - - +
199C ILE 5.1 0.4 - - - +
202C ASP* 3.5 35.9 - - + +
203C ILE* 4.8 3.6 - - + +
206C ILE* 3.4 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 3.5 23.6 - - + +
144C SER* 3.1 28.6 + - - +
145C VAL* 3.1 17.8 + - - +
147C LEU* 1.3 72.3 - - - +
149C ALA* 1.3 66.3 + - - +
151C GLU* 4.5 12.1 - - + +
152C GLN* 3.0 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 5.1 2.0 - - + -
91C MET 5.0 1.3 - - - +
92C SER* 3.9 24.9 - - - +
95C PRO* 4.1 12.7 - - + +
126C ILE* 3.9 23.8 - - + -
145C VAL 2.9 12.0 + - - +
146C PHE* 3.4 11.0 - - - +
147C LEU 3.2 0.2 - - - -
148C GLU* 1.3 77.1 - - - +
150C PHE* 1.3 62.1 + - - +
152C GLN* 4.0 0.2 - - - +
153C CYS* 3.2 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 3.7 29.6 - - + -
146C PHE* 3.2 51.3 + + - -
147C LEU* 3.2 12.2 + - + +
149C ALA* 1.3 78.6 - - - +
151C GLU* 1.3 58.1 + - - +
153C CYS* 3.9 1.9 - - - +
154C ALA* 2.9 29.6 + - - +
161C LEU* 4.0 22.3 - - + +
162C SER 3.5 21.8 - - - -
163C VAL* 3.9 14.6 - - + -
203C ILE* 3.6 42.4 - - + -
206C ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU* 3.1 12.6 + - - +
148C GLU* 4.5 13.4 - - + +
150C PHE* 1.3 79.9 - - - +
152C GLN* 1.3 64.3 + - - +
154C ALA* 3.5 3.1 + - - +
155C GLU* 2.9 49.3 + - - +
206C ILE* 3.6 31.1 - - + +
209C LYS* 3.3 35.0 + - - +
210C THR* 4.2 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 3.9 22.2 - - + +
96C SER* 4.6 8.5 - - - -
99C ALA* 3.9 21.9 - - + +
148C GLU* 3.0 30.9 + - + +
149C ALA 4.0 1.3 - - - +
151C GLU* 1.3 79.4 - - - +
153C CYS* 1.3 64.3 + - - +
155C GLU* 3.1 23.8 + - - -
156C ASN* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 3.5 35.0 - - - -
95C PRO 4.9 2.0 - - - -
98C GLY 3.6 20.2 - - - -
99C ALA* 3.8 8.0 - - - +
102C ALA* 4.1 2.9 - - - +
124C HIS* 3.7 11.0 - - + -
126C ILE* 4.5 6.1 - - + -
149C ALA* 3.2 20.3 + - - +
150C PHE 3.9 2.5 - - - +
152C GLN* 1.3 77.9 - - - +
154C ALA* 1.3 60.8 + - - +
156C ASN 3.2 8.0 + - - -
157C GLY 3.3 0.9 + - - -
158C ALA* 3.0 38.6 + - + +
161C LEU* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C PHE 2.9 19.1 + - - +
151C GLU* 3.7 5.4 - - - +
153C CYS* 1.3 76.4 - - - +
155C GLU* 1.3 61.3 + - - +
156C ASN 3.5 0.3 + - - -
157C GLY 4.2 2.4 + - - -
158C ALA* 4.1 12.6 - - - +
161C LEU* 4.0 13.4 - - + +
206C ILE* 4.7 0.9 - - + -
210C THR* 3.3 29.8 - - + +
212C THR* 3.6 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 2.9 36.5 + - - +
152C GLN* 3.1 25.1 + - - +
154C ALA* 1.3 77.1 - - - +
156C ASN* 1.3 67.9 + - - +
157C GLY 3.7 0.9 - - - -
209C LYS* 4.9 6.1 - - - -
210C THR* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA* 3.4 28.0 + - - +
100C GLU* 6.0 2.0 - - - +
102C ALA* 3.4 1.5 - - - -
103C HIS* 3.1 53.6 + - + +
106C LYS* 4.8 0.3 - - - +
152C GLN* 3.0 29.8 + - - +
153C CYS 3.2 5.1 + - - +
155C GLU* 1.3 89.5 + - - +
157C GLY* 1.3 57.0 + - - +
----------------------------------------------------------
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