Contacts of the helix formed by residues 142 - 155 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93M ASN* 4.4 9.0 - - - +
129M ILE* 3.7 34.1 + - + +
130M ARG* 4.3 11.2 - - + +
131M GLU 3.1 28.7 + - - +
132M ASN* 4.7 3.6 - - - +
137M GLN* 3.3 30.0 + - - +
140M GLY 3.3 0.6 - - - -
141M ASP* 1.3 84.3 - - + +
143M TYR* 1.3 62.1 + - - +
144M SER 3.3 0.7 - - - -
145M VAL* 3.2 15.3 + - + +
146M PHE* 3.1 22.4 + - - +
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Residues in contact with TYR 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M ARG* 3.7 21.4 - - + +
137M GLN 5.5 0.4 + - - -
138M LEU 3.3 20.9 - - - +
139M ARG* 4.3 13.0 - - - +
140M GLY 3.2 15.7 + - - +
141M ASP 3.1 2.6 - - - -
142M LYS* 1.3 78.5 - - - +
144M SER* 1.3 62.2 + - - +
146M PHE* 3.3 19.8 - + - +
147M LEU* 3.4 32.5 + - + +
198M LEU* 3.5 35.7 - - + +
199M ILE* 3.8 17.3 - - + -
202M ASP* 2.7 32.6 + - - +
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Residues in contact with SER 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M GLY 4.7 0.6 + - - -
141M ASP 3.6 12.8 + - - -
143M TYR* 1.3 78.8 - - - +
145M VAL* 1.3 64.2 + - - +
147M LEU* 3.4 10.3 + - - +
148M GLU* 3.0 40.1 + - - +
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Residues in contact with VAL 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M SER 3.8 11.0 - - - +
93M ASN* 3.7 24.2 - - - +
95M PRO* 3.8 10.3 - - + +
129M ILE* 3.9 10.1 - - + -
141M ASP 4.3 8.3 - - - +
142M LYS* 3.2 18.8 + - + +
144M SER* 1.3 83.7 - - - +
146M PHE* 1.3 59.2 + - - +
148M GLU* 3.3 14.1 + - - +
149M ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M ILE* 4.1 2.0 - - + -
127M GLY 3.5 15.7 - - - -
128M ASP* 3.5 26.7 - - - -
129M ILE* 4.0 17.0 - - + +
130M ARG* 3.8 30.5 - - + -
142M LYS 3.1 12.5 + - - +
143M TYR* 3.3 19.3 - + - +
145M VAL* 1.3 75.4 - - - +
147M LEU* 1.3 70.7 + - + +
149M ALA* 3.3 14.1 - - - +
150M PHE* 3.0 46.7 - + - -
163M VAL* 3.9 21.1 - - + -
199M ILE* 4.0 22.4 - - + -
203M ILE* 4.8 1.3 - - + -
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Residues in contact with LEU 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M TYR* 3.4 39.6 + - + +
144M SER* 3.7 10.3 - - - +
145M VAL 3.2 0.4 - - - -
146M PHE* 1.3 88.1 - - + +
148M GLU* 1.3 65.9 + - + +
149M ALA 3.1 1.1 - - - -
150M PHE* 2.9 19.8 + - + +
151M GLU* 3.0 15.0 + - - +
199M ILE* 5.4 0.7 - - - +
202M ASP* 3.8 32.5 - - + +
203M ILE* 4.9 2.9 - - + +
206M ILE* 3.7 24.5 - - + +
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Residues in contact with GLU 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M PRO* 3.8 22.1 - - + +
144M SER* 3.0 32.8 + - - +
145M VAL* 3.3 16.6 + - - +
147M LEU* 1.3 73.6 - - - +
149M ALA* 1.3 54.9 + - - +
151M GLU* 3.3 10.8 + - - +
152M GLN* 2.8 43.7 + - + +
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Residues in contact with ALA 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M HIS* 5.1 2.0 - - + -
91M MET 5.6 0.2 - - - -
92M SER* 4.1 21.5 - - - +
95M PRO* 3.9 13.0 - - + +
126M ILE* 3.9 25.9 - - + +
145M VAL 2.9 12.8 + - - +
146M PHE* 3.3 14.1 - - - +
148M GLU* 1.3 78.1 - - - +
150M PHE* 1.3 63.1 + - - +
152M GLN* 4.3 0.4 - - - +
153M CYS* 3.4 27.0 + - - -
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Residues in contact with PHE 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M ILE* 3.6 27.1 - - + -
146M PHE* 3.0 51.7 + + - -
147M LEU* 2.9 12.1 + - + +
149M ALA* 1.3 79.4 - - - +
151M GLU* 1.3 59.6 + - - +
153M CYS* 3.2 2.8 + - - +
154M ALA* 2.8 27.6 + - - +
161M LEU* 4.0 18.9 - - + +
162M SER 3.5 24.0 - - - -
163M VAL* 3.8 19.3 - - + -
203M ILE* 3.4 41.7 - - + -
206M ILE* 4.1 17.9 - - + -
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Residues in contact with GLU 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M LEU* 3.0 12.6 + - - +
148M GLU* 4.3 10.7 - - - +
150M PHE* 1.3 77.5 - - - +
152M GLN* 1.3 69.3 + - - +
154M ALA* 3.6 3.5 - - - +
155M GLU* 2.9 49.6 + - - +
206M ILE* 3.4 30.5 - - + +
209M LYS* 3.0 32.1 + - - +
210M THR* 4.7 4.2 - - + +
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Residues in contact with GLN 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M PRO* 3.9 26.0 - - + +
96M SER* 4.7 6.0 - - - +
99M ALA* 3.7 18.4 - - + +
148M GLU* 2.8 28.8 + - + +
149M ALA 4.3 1.6 - - - +
151M GLU* 1.3 80.1 - - - +
153M CYS* 1.3 62.4 + - - +
155M GLU* 3.4 14.7 + - - +
156M ASN* 2.9 41.2 + - - +
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Residues in contact with CYS 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M HIS* 3.7 13.0 - - - -
95M PRO 5.0 2.0 - - - -
98M GLY* 3.7 23.6 - - - -
99M ALA* 3.7 6.3 - - - +
102M ALA* 4.4 2.4 - - + +
124M HIS* 3.6 31.9 - - + -
126M ILE* 4.6 4.0 - - + -
149M ALA 3.4 18.1 + - - +
150M PHE 3.2 3.9 + - - +
152M GLN* 1.3 79.7 - - - +
154M ALA* 1.3 61.7 + - - +
156M ASN 3.1 11.6 + - - -
157M GLY 3.3 1.2 + - - -
158M ALA* 3.1 34.1 + - + -
161M LEU* 4.9 0.9 - - + -
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Residues in contact with ALA 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150M PHE 2.8 17.3 + - - +
151M GLU* 3.6 8.1 - - - +
152M GLN 3.3 0.2 - - - -
153M CYS* 1.3 77.8 - - - +
155M GLU* 1.3 58.3 + - - +
156M ASN 3.4 0.4 + - - -
157M GLY* 4.4 2.4 + - - -
158M ALA* 4.0 12.0 - - - +
161M LEU* 4.1 13.6 - - + +
206M ILE* 4.5 1.8 - - + -
210M THR* 3.2 32.3 + - + +
212M THR* 3.3 26.6 - - - +
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Residues in contact with GLU 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M GLU* 2.9 41.5 + - - +
152M GLN* 3.4 16.7 + - - +
153M CYS 3.2 0.2 - - - -
154M ALA* 1.3 75.3 - - - +
156M ASN* 1.3 69.0 + - - +
157M GLY 3.7 1.3 - - - -
209M LYS* 4.5 6.4 + - - -
210M THR* 3.9 20.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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