Contacts of the helix formed by residues 150 - 159 (chain A) in PDB entry 2IL1
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 GLY 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLY 3.4 1.0 - - - -
149A VAL* 1.3 79.4 - - - +
151A LYS* 1.3 58.0 + - - +
152A THR 3.3 2.2 - - - -
153A SER* 3.7 0.5 - - - -
154A LEU* 2.8 42.6 + - - +
251A ASN* 3.6 10.3 + - - -
401A GDP 3.0 33.7 + - - -
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.7 33.3 - - + +
144A ILE* 3.4 36.1 - - - +
145A GLY* 3.0 21.5 + - - +
146A SER 3.1 11.3 + - - -
147A ARG* 4.1 2.6 - - - +
149A VAL* 3.7 12.9 - - + +
150A GLY* 1.3 77.1 - - - +
152A THR* 1.3 61.9 + - - +
154A LEU* 3.5 3.3 + - - +
155A MET* 3.1 23.0 + - - +
193A ASP* 3.9 8.9 - - - +
194A THR* 3.4 26.2 - - - -
196A GLY* 4.2 6.9 - - - +
217A VAL* 4.2 5.4 - - + -
401A GDP 2.9 33.6 + - - +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LYS* 1.3 74.3 - - - +
153A SER* 1.3 60.8 + - - +
155A MET* 3.3 5.7 + - + +
156A GLU* 2.8 58.1 + - + +
193A ASP* 2.4 27.7 + - - +
401A GDP 3.3 13.3 + - - +
402A MG 2.3 30.1 - - - -
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLY 3.3 2.4 + - - -
152A THR* 1.3 79.5 - - - +
154A LEU* 1.3 56.8 + - - +
156A GLU* 3.8 6.6 - - - +
157A ARG* 2.9 32.6 + - - +
283A ALA* 3.8 8.3 - - - +
401A GDP 2.7 61.9 + - - -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 5.4 2.5 - - + -
150A GLY 2.8 23.5 + - - +
151A LYS* 3.8 4.5 - - - +
153A SER* 1.3 74.4 - - - +
155A MET* 1.3 62.9 + - - +
157A ARG* 3.5 0.8 + - - -
158A PHE* 3.2 23.6 + - - +
215A ILE* 5.7 0.2 - - + -
217A VAL* 4.0 29.4 - - + -
249A VAL* 4.3 4.5 - - + -
251A ASN* 3.8 25.4 - - + +
281A ALA* 4.4 5.4 - - + -
283A ALA* 3.7 21.3 - - + +
289A VAL* 3.7 24.8 - - + +
292A ILE* 3.8 32.3 - - + -
293A PHE* 3.9 6.6 - - + -
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Residues in contact with MET 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.6 14.8 - - + -
151A LYS 3.1 12.6 + - - +
152A THR* 3.7 2.9 - - + +
154A LEU* 1.3 77.0 - - - +
156A GLU* 1.3 67.2 + - + +
158A PHE* 3.3 2.8 + - - +
159A THR* 2.8 32.1 + - - +
174A ASP* 5.0 6.5 - - + -
175A PHE 4.6 2.7 - - - -
176A LYS* 3.7 39.0 - - + +
191A ILE* 3.7 42.0 - - + +
193A ASP* 3.6 38.4 - - + +
293A PHE* 4.1 10.7 - - - -
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 2.8 45.6 + - + +
153A SER* 4.2 5.8 - - - +
155A MET* 1.3 76.6 - - + +
157A ARG* 1.3 63.1 + - - +
158A PHE 3.4 0.3 + - - -
159A THR* 3.4 18.1 - - - +
160A ASP* 3.4 29.0 + - - +
176A LYS* 4.6 13.5 + - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER 2.9 22.9 + - - +
154A LEU 3.9 4.5 - - - +
156A GLU* 1.3 72.6 - - - +
158A PHE* 1.3 60.9 + - - +
159A THR 3.8 3.3 + - - +
283A ALA* 3.0 25.8 + - - +
284A LYS* 3.0 22.6 + - - +
285A ASP* 4.1 2.2 - - - +
286A ASN* 3.5 49.5 - - + +
289A VAL* 3.9 11.3 - - + +
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU 3.2 17.0 + - - +
155A MET 3.7 2.7 - - - +
156A GLU 3.2 0.6 - - - -
157A ARG* 1.3 77.3 - - - +
159A THR* 1.3 63.0 + - + +
178A LYS* 3.0 52.7 + - + -
180A VAL* 3.9 17.5 - - + -
189A LEU* 4.1 6.5 - - + -
191A ILE* 3.8 23.8 - - + -
289A VAL* 3.8 6.5 - - + +
290A ASP* 3.7 46.4 - - + -
293A PHE* 3.4 41.7 - + + -
294A LEU* 4.6 9.6 - - + -
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A MET* 2.8 21.6 + - + +
156A GLU 3.4 5.0 - - - +
157A ARG 4.4 2.9 - - - +
158A PHE* 1.3 82.6 - - + +
160A ASP* 1.3 81.5 + - - +
176A LYS* 3.5 34.9 - - + +
177A ILE 5.1 2.7 - - - +
178A LYS* 4.0 32.1 - - + -
191A ILE* 4.0 15.9 - - + -
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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