Contacts of the helix formed by residues 157 - 167 (chain E) in PDB entry 4IGM
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 LEU 157 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E MET* 3.7 41.5 - - + +
122E PRO* 4.5 1.6 - - + -
147E VAL* 4.4 7.2 - - + -
150E TRP* 3.9 25.8 - - + -
151E ASP 3.6 23.6 - - - +
152E LEU* 3.9 25.8 - - + -
154E ALA* 2.9 15.5 + - + +
156E GLU* 1.3 76.4 - - - +
158E PHE* 1.3 60.1 + - - +
159E PRO* 3.3 1.6 - - - -
160E VAL* 2.8 31.6 + - + +
161E TYR* 3.2 27.2 + - + +
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Residues in contact with PHE 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ASN 3.4 24.0 - - - -
154E ALA 3.2 11.9 - - - -
155E GLN* 2.8 44.5 + - - +
157E LEU* 1.3 76.0 - - - +
159E PRO* 1.4 57.3 - - + +
161E TYR* 3.2 11.0 + + - -
162E ALA* 2.9 26.3 + - - +
209E GLY 4.2 12.1 - - - -
211E VAL* 3.9 28.9 - - + -
214E LYS* 4.4 21.8 - - + -
215E PHE* 3.6 34.7 - + + -
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Residues in contact with PRO 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E PRO* 4.8 9.6 - - + +
126E VAL* 3.2 19.7 - - + +
155E GLN 3.5 6.7 - - - +
156E GLU* 2.9 29.2 - - - +
157E LEU 3.4 0.7 - - - -
158E PHE* 1.4 80.4 - - + +
160E VAL* 1.3 61.8 + - - +
162E ALA* 3.9 8.2 - - + +
163E ALA* 3.2 17.8 + - - +
166E ARG* 4.6 1.9 + - - -
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LEU* 4.2 6.3 - - + -
119E MET* 4.0 33.2 - - + -
122E PRO* 4.0 35.7 - - + +
125E ALA* 4.4 7.4 - - + -
126E VAL* 3.8 6.5 - - + -
129E MET* 3.5 21.4 - - + +
143E ILE* 5.9 0.4 - - + -
157E LEU* 2.8 24.0 + - + +
159E PRO* 1.3 73.5 - - - +
161E TYR* 1.3 64.0 + - + +
164E ALA* 3.0 27.8 + - + +
171E LEU* 5.7 4.9 - - + -
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Residues in contact with TYR 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E MET* 5.4 3.6 - - + -
143E ILE* 4.9 8.7 - - + -
152E LEU* 2.7 56.1 + - + +
157E LEU* 3.7 29.9 - - + +
158E PHE* 3.2 22.0 + + - +
160E VAL* 1.3 82.8 - - + +
162E ALA* 1.3 64.6 + - - +
164E ALA* 3.5 0.4 + - - -
165E GLU* 3.0 24.4 + - - +
171E LEU* 4.1 26.7 - - + -
206E MET* 4.6 7.2 - - + -
211E VAL* 3.8 25.4 - - + -
215E PHE* 3.7 22.0 - + + -
218E LEU* 3.7 17.2 - - + +
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Residues in contact with ALA 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E PHE 2.9 16.2 + - - +
159E PRO* 3.9 9.0 - - + +
160E VAL 3.4 0.2 - - - -
161E TYR* 1.3 73.1 - - - +
163E ALA* 1.3 66.3 + - - +
165E GLU* 3.1 6.2 + - - +
166E ARG* 2.9 38.8 + - - +
215E PHE* 3.6 18.5 - - + -
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Residues in contact with ALA 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 3.8 22.2 - - + -
129E MET* 4.3 8.7 - - + -
130E GLU* 6.6 0.2 - - - -
159E PRO 3.2 15.2 + - - +
160E VAL 3.8 2.9 - - - +
162E ALA* 1.3 77.5 - - - +
164E ALA* 1.3 55.1 + - - +
166E ARG* 3.1 31.5 - - - +
167E LEU* 2.7 45.4 + - + +
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Residues in contact with ALA 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E MET* 3.7 22.6 - - + -
160E VAL 3.0 19.5 + - - +
161E TYR* 3.9 4.0 - - - +
162E ALA 3.3 0.4 - - - -
163E ALA* 1.3 76.6 - - - +
165E GLU* 1.3 57.8 + - - +
168E LYS* 3.2 3.5 + - - -
169E CYS* 2.6 48.9 + - + +
171E LEU* 4.2 12.8 - - + -
218E LEU* 4.0 11.0 - - + -
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Residues in contact with GLU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E TYR 3.0 17.2 + - - +
162E ALA* 3.6 3.6 - - - +
164E ALA* 1.3 76.2 - - - +
166E ARG* 1.3 66.6 + - - +
168E LYS* 3.1 18.7 + - - +
214E LYS 4.6 0.9 - - - +
215E PHE* 3.6 24.7 - - + -
216E PRO* 3.6 11.5 - - - +
217E LYS* 3.0 46.1 + - + +
218E LEU* 3.6 26.4 - - + +
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Residues in contact with ARG 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 4.6 9.7 - - - +
130E GLU* 5.0 10.8 + - - -
159E PRO 4.6 2.6 + - - -
162E ALA* 2.9 30.2 + - - +
163E ALA* 3.1 42.7 - - - +
165E GLU* 1.3 72.2 - - - +
167E LEU* 1.3 65.3 + - + +
168E LYS* 3.1 13.9 + - - +
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Residues in contact with LEU 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL 5.0 0.7 - - - +
129E MET* 3.9 18.4 - - + -
130E GLU* 3.7 58.6 - - + +
133E VAL* 4.0 20.3 - - + +
134E LYS* 4.2 30.5 - - + +
163E ALA* 2.7 29.9 + - + +
166E ARG* 1.3 80.0 - - + +
168E LYS* 1.3 70.9 + - - +
169E CYS* 3.2 9.5 + - + -
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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