Contacts of the helix formed by residues 141 - 156 (chain G) 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 ASP 141 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G GLN* 3.9 16.3 + - - +
140G GLY* 1.3 70.3 - - - -
142G LYS* 1.3 67.6 + - + +
143G TYR 3.1 6.7 + - - -
144G SER* 3.2 24.1 + - - -
145G VAL* 3.9 5.6 - - - +
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Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G ASN* 4.7 8.3 + - - +
129G ILE* 3.9 32.8 + - + +
130G ARG* 4.0 12.9 - - - +
131G GLU 3.2 30.6 + - - +
132G ASN* 4.7 4.8 - - - +
137G GLN* 4.7 21.0 + - + +
140G GLY* 3.3 1.2 - - - -
141G ASP* 1.3 87.1 - - + +
143G TYR* 1.3 58.3 + - - +
144G SER 3.4 0.7 - - - -
145G VAL* 3.9 13.9 - - + +
146G PHE* 3.1 27.7 + - - +
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Residues in contact with TYR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ARG* 3.7 21.4 - - - +
137G GLN 5.0 0.4 + - - -
138G LEU 3.1 24.5 - - - +
139G ARG* 4.1 12.3 - - - +
140G GLY* 3.2 17.7 + - - +
141G ASP 3.1 0.4 - - - -
142G LYS* 1.3 74.9 - - - +
144G SER* 1.3 65.7 + - - +
146G PHE* 3.2 21.7 - + - +
147G LEU* 3.3 36.8 + - + +
198G LEU* 3.8 34.2 + - + +
199G ILE* 3.9 11.2 - - + -
202G ASP* 2.6 26.9 + - - +
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Residues in contact with SER 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G GLY 4.4 0.8 + - - -
141G ASP 3.2 14.7 + - - -
143G TYR* 1.3 83.8 - - - +
145G VAL* 1.3 63.4 + - - +
147G LEU* 3.2 10.5 + - - +
148G GLU* 3.0 35.7 + - - +
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Residues in contact with VAL 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G SER 3.9 11.0 - - - +
93G ASN* 4.0 9.0 - - - +
95G PRO* 3.8 25.7 - - + +
129G ILE* 4.1 10.8 - - + -
141G ASP 3.9 16.4 - - - +
142G LYS* 3.6 15.7 + - + +
143G TYR 3.3 0.2 - - - -
144G SER* 1.3 76.6 - - - +
146G PHE* 1.3 63.9 + - - +
148G GLU* 3.0 13.6 + - - +
149G ALA* 2.9 24.1 + - - +
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Residues in contact with PHE 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G ILE* 4.1 9.4 - - + +
127G GLY 3.7 23.8 - - - -
128G ASP* 3.8 20.4 - - - -
129G ILE* 4.0 11.6 - - + +
130G ARG* 4.1 24.5 - - + -
142G LYS 3.1 15.1 + - - +
143G TYR* 3.2 17.5 - + - +
145G VAL* 1.3 75.7 - - - +
147G LEU* 1.3 73.6 + - + +
149G ALA* 3.3 18.0 - - - +
150G PHE* 3.4 32.0 + + - -
163G VAL* 3.8 24.2 - - + -
199G ILE* 4.2 26.5 - - + -
203G ILE* 4.5 2.9 - - + -
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Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G TYR* 3.3 36.8 + - + +
144G SER* 3.2 12.1 + - - +
146G PHE* 1.3 92.7 - - + +
148G GLU* 1.3 65.4 + - + +
150G PHE* 3.2 6.9 + - + +
151G GLU* 2.9 32.1 + - - +
199G ILE 5.2 0.7 - - - +
202G ASP* 3.9 30.5 - - + +
203G ILE* 4.8 9.2 - - + -
206G ILE* 3.6 19.1 - - + +
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Residues in contact with GLU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G PRO* 3.8 23.8 - - + +
144G SER* 3.0 22.7 + - - +
145G VAL* 3.0 15.6 + - - +
147G LEU* 1.3 75.3 - - - +
149G ALA* 1.3 54.0 + - - +
151G GLU* 3.2 15.8 + - + +
152G GLN* 2.7 44.1 + - + +
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Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G HIS* 5.0 2.2 - - + -
91G MET 5.0 0.2 - - - +
92G SER* 4.2 22.4 - - - +
95G PRO* 4.1 14.3 - - + +
126G ILE* 3.7 24.9 - - + -
145G VAL 2.9 12.0 + - - +
146G PHE* 3.3 13.0 - - - +
147G LEU 3.2 0.2 - - - -
148G GLU* 1.3 74.7 - - - +
150G PHE* 1.3 63.4 - - - +
152G GLN* 3.9 0.8 - - - +
153G CYS* 3.0 30.4 + - - -
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Residues in contact with PHE 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G ILE* 3.9 23.8 - - + +
146G PHE* 3.4 40.0 + + - -
147G LEU* 3.2 10.6 + - + +
149G ALA* 1.3 78.8 - - - +
151G GLU* 1.3 58.5 + - - +
153G CYS* 3.8 1.6 - - - +
154G ALA* 2.9 30.5 + - - +
161G LEU* 3.8 24.7 - - + +
162G SER 3.5 28.7 - - - -
163G VAL* 3.8 11.7 - - + -
203G ILE* 3.6 55.2 - - + -
206G ILE* 4.0 17.7 - - + -
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Residues in contact with GLU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G LEU* 2.9 32.5 + - - +
148G GLU* 3.8 18.0 + - + +
150G PHE* 1.3 72.0 - - - +
152G GLN* 1.3 58.5 + - + +
154G ALA* 3.4 2.5 + - - +
155G GLU* 2.9 48.5 + - - +
206G ILE* 3.7 32.8 - - + +
209G LYS* 3.9 24.3 + - - +
210G THR* 4.4 2.4 - - + +
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Residues in contact with GLN 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G PRO* 3.9 20.9 - - + +
96G SER* 3.9 23.0 + - - -
99G ALA* 3.4 18.9 - - + +
148G GLU* 2.7 29.4 + - + +
149G ALA 3.9 2.5 - - - +
151G GLU* 1.3 74.6 - - + +
153G CYS* 1.3 59.4 + - - +
155G GLU* 3.4 17.5 + - - -
156G ASN* 3.0 33.1 + - - +
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Residues in contact with CYS 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G HIS* 3.5 23.6 - - - -
95G PRO 5.0 1.1 - - - -
98G GLY* 3.5 29.8 - - - -
99G ALA* 3.8 6.7 - - - +
102G ALA* 4.4 1.9 - - + +
124G HIS* 3.6 13.9 - - + -
126G ILE* 4.2 5.6 - - + -
149G ALA* 3.0 21.9 + - - +
150G PHE 3.9 2.0 - - - +
152G GLN* 1.3 72.9 - - - +
154G ALA* 1.3 66.3 + - - +
156G ASN 3.0 12.6 + - - -
157G GLY 3.3 1.2 + - - -
158G ALA* 3.2 33.3 + - + +
161G LEU* 5.0 1.6 - - + -
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Residues in contact with ALA 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G PHE 2.9 18.8 + - - +
151G GLU* 3.8 0.9 - - - +
153G CYS* 1.3 76.3 - - - +
155G GLU* 1.3 60.0 + - - +
156G ASN 3.5 0.2 + - - -
157G GLY 4.2 3.1 + - - -
158G ALA 4.1 11.7 - - - +
161G LEU* 4.0 16.2 - - + +
206G ILE* 4.6 0.9 - - + -
210G THR* 3.4 35.9 - - + +
212G THR* 3.7 25.8 - - - +
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Residues in contact with GLU 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G GLU* 2.9 38.4 + - - +
152G GLN* 3.7 16.3 + - - +
153G CYS 3.1 0.6 - - - -
154G ALA* 1.3 77.9 - - - +
156G ASN* 1.3 70.7 + - - +
157G GLY 3.8 0.8 + - - -
209G LYS* 5.6 3.6 + - - +
210G THR* 4.2 16.1 - - + +
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Residues in contact with ASN 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ALA* 3.6 27.7 + - + +
100G GLU* 5.9 3.0 - - - +
102G ALA* 3.4 1.5 - - - -
103G HIS* 3.1 52.7 + - + +
106G LYS* 4.7 0.2 - - - +
152G GLN* 3.0 28.3 + - - +
153G CYS 3.0 7.6 + - - +
155G GLU* 1.3 90.2 + - - +
157G GLY* 1.3 56.2 + - - +
158G ALA 3.9 0.2 - - - -
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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