Contacts of the helix formed by residues 136 - 150 (chain F) 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 HIS 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130F VAL* 3.9 16.4 - - - +
134F ASP* 2.5 31.5 + - - +
135F VAL* 1.3 72.2 - - - +
137F ASP* 1.3 65.9 + - - +
138F ILE 3.5 0.6 + - - -
139F GLY 4.3 0.2 + - - -
181F THR* 4.1 3.3 - - - +
183F LEU* 3.4 39.4 - - + +
184F MET* 3.9 13.0 - - + -
500F B13 2.7 110.7 + + + +
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Residues in contact with ASP 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E ASP* 5.7 1.5 - - + +
130F VAL* 4.7 2.9 - - - -
135F VAL* 2.9 20.1 + - - +
136F HIS* 1.3 71.3 - - - +
138F ILE* 1.3 55.9 + - + +
139F GLY 2.8 0.9 + - - -
140F LYS* 2.7 65.5 + - - +
141F ASN* 3.1 25.9 + - - +
159F ARG* 3.3 30.1 + - - +
500F B13 3.2 14.6 + - - +
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Residues in contact with ILE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ASP* 3.4 15.5 - - + +
176E VAL* 4.9 2.5 - - + -
177E LEU* 4.5 22.7 - - + -
225E THR* 3.9 6.7 - - + -
229E ILE* 3.7 33.0 - - + -
137F ASP* 1.3 78.5 - - + +
139F GLY* 1.3 62.5 + - - +
141F ASN* 3.6 9.2 - - - +
142F ILE* 3.0 35.7 + - + +
500F B13 3.1 64.3 + - + +
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Residues in contact with GLY 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F HIS 4.3 2.6 + - - -
137F ASP 2.8 5.5 + - - -
138F ILE* 1.3 72.9 - - - +
140F LYS* 1.3 65.6 + - - +
142F ILE* 3.3 2.8 + - - +
143F VAL* 3.1 23.7 + - - +
181F THR* 4.1 7.4 - - - -
500F B13 3.2 48.4 + - - +
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Residues in contact with LYS 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F CYS* 4.5 18.6 - - + +
129F HIS 5.1 2.9 - - - +
130F VAL* 3.8 26.9 - - + +
137F ASP* 2.7 40.2 + - - +
139F GLY* 1.3 70.2 - - - -
141F ASN* 1.3 75.3 + - - +
143F VAL* 2.8 10.8 + - - +
144F THR* 2.5 43.1 + - - +
156F ASP* 3.3 31.9 + - - +
158F GLY* 3.9 19.9 - - - +
159F ARG* 4.4 0.6 - - - +
181F THR* 3.6 19.7 + - - +
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Residues in contact with ASN 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E LEU* 4.9 16.9 - - + +
99F MET* 4.6 9.1 - - + +
137F ASP* 3.1 34.5 + - - +
138F ILE* 3.6 14.2 - - - +
139F GLY 3.3 0.2 - - - -
140F LYS* 1.3 101.6 + - - +
142F ILE* 1.3 57.4 + - + +
144F THR* 3.2 11.5 + - - +
145F ALA* 3.1 26.7 + - - +
156F ASP* 4.1 3.3 - - - +
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Residues in contact with ILE 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E LEU* 5.5 3.1 - - + -
229E ILE* 5.9 1.8 - - + -
237E ASN* 4.9 7.0 - - - +
88F TYR* 5.0 5.4 - - - +
95F LEU* 3.7 46.2 - - + -
99F MET* 5.2 4.3 - - - -
138F ILE* 3.0 37.3 + - + +
139F GLY 3.9 3.6 - - - +
141F ASN* 1.3 74.7 - - + +
143F VAL* 1.3 59.8 + - - +
145F ALA* 3.3 4.7 + - - +
146F LEU* 2.9 38.0 + - + +
231F ALA* 3.4 23.8 - - + -
500F B13 4.0 23.6 - - + +
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Residues in contact with VAL 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F CYS* 4.8 2.2 - - - -
139F GLY 3.1 13.8 + - - +
140F LYS* 2.8 10.0 + - - +
142F ILE* 1.3 73.2 - - - +
144F THR* 1.3 66.0 + - - +
146F LEU* 3.4 4.1 + - - -
147F LEU* 3.1 34.2 + - + +
179F THR* 4.1 23.1 - - + +
231F ALA* 3.8 21.1 - - + +
234F ALA* 3.5 22.7 - - + -
500F B13 3.7 35.2 - - + +
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F CYS* 5.0 5.2 - - - +
140F LYS* 2.5 40.3 + - - +
141F ASN* 3.2 17.8 - - - +
143F VAL* 1.3 74.4 - - - +
145F ALA* 1.3 63.9 + - + +
147F LEU* 3.5 3.2 + - - +
148F ARG* 3.2 59.6 + - - +
154F VAL* 4.0 15.4 - - + +
156F ASP* 3.5 16.5 + - - +
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Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F LEU* 6.1 0.7 - - + -
98F VAL* 5.7 5.8 - - + -
99F MET* 3.7 30.7 - - + -
102F ALA* 5.0 12.4 - - + +
141F ASN 3.1 14.3 + - - +
142F ILE* 3.7 4.3 - - - +
143F VAL 3.3 0.2 - - - -
144F THR* 1.3 80.7 - - + +
146F LEU* 1.3 63.1 + - + +
148F ARG* 3.4 7.1 + - - +
149F ALA* 2.8 32.9 + - - +
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Residues in contact with LEU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ILE* 4.4 26.5 - - + -
88F TYR* 4.4 24.5 - - + -
89F ASP* 5.5 1.3 - - - +
95F LEU* 5.4 2.7 - - + -
98F VAL* 4.9 13.9 - - + -
142F ILE* 2.9 37.8 + - + +
143F VAL 3.4 3.3 + - - +
145F ALA* 1.3 74.0 - - + +
147F LEU* 1.3 56.7 + - - +
149F ALA* 3.6 5.1 - - + +
150F ASN* 2.8 33.4 + - - +
231F ALA* 4.3 6.3 - - + +
232F ALA* 4.2 23.1 - - + +
235F PRO* 3.7 28.5 - - + +
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F VAL* 3.8 35.4 - - + -
128F CYS* 4.1 17.0 - - - -
143F VAL* 3.1 26.5 + - + +
146F LEU* 1.3 74.3 - - + +
148F ARG* 1.3 64.6 + - - +
150F ASN* 3.1 11.1 + - - -
151F GLY 3.4 0.3 + - - -
152F TYR* 3.0 35.5 + - + +
154F VAL* 3.5 14.4 - - + -
177F MET* 6.0 0.7 - - - -
179F THR* 4.7 4.5 - - + -
234F ALA* 3.5 17.5 - - + +
235F PRO* 3.4 35.4 - - + -
238F ALA* 5.3 1.3 - - + -
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Residues in contact with ARG 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F MET* 4.9 1.4 - - - +
102F ALA* 6.1 1.6 - - + -
105F MET* 3.8 21.5 - - + +
106F LEU* 3.8 39.4 - - + +
109F ILE* 5.9 0.7 - - - +
144F THR* 3.2 43.2 + - - +
145F ALA* 3.9 6.5 - - - +
147F LEU* 1.3 77.6 - - - +
149F ALA* 1.3 60.7 + - - +
151F GLY* 3.5 10.6 + - - -
152F TYR 3.6 14.6 + - - +
154F VAL* 3.6 36.8 + - + +
156F ASP* 4.2 17.0 + - - +
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Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F MET* 3.4 17.2 - - - +
81F MET* 3.6 38.5 - - + +
85F ILE* 3.1 26.9 - - + +
98F VAL* 5.3 4.3 - - + -
102F ALA* 5.0 3.4 - - + -
105F MET* 4.3 4.9 - - - +
145F ALA 2.8 19.8 + - - +
146F LEU* 3.7 6.3 - - + +
148F ARG* 1.3 77.9 - - - +
150F ASN* 1.3 55.8 + - - +
151F GLY 3.2 1.1 - - - -
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Residues in contact with ASN 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F MET* 3.8 6.8 - - - +
85F ILE* 4.1 26.6 - - - +
123F LYS* 3.8 12.6 + - - -
146F LEU* 2.8 17.6 + - - +
147F LEU 3.1 5.0 + - - +
149F ALA* 1.3 75.6 - - - +
151F GLY* 1.3 59.4 + - - +
152F TYR* 3.6 12.6 - - + -
235F PRO* 3.5 32.2 - - + +
239F ASP* 4.1 12.0 - - - +
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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