Contacts of the helix formed by residues 142 - 153 (chain B) in PDB entry 4IWN
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 GLU 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B ARG* 3.3 47.5 + - - +
138B LEU* 3.8 10.5 - - + +
139B GLU* 2.9 46.2 + - + +
141B SER* 1.3 82.2 - - - +
143B ARG* 1.3 63.6 + - - +
144B GLN 3.5 1.6 - - - -
145B ALA* 3.6 10.5 + - - +
146B LEU* 3.5 15.9 + - - +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 3.1 45.4 + - + +
136B GLN* 2.9 23.6 + - - +
138B LEU* 2.7 30.1 + - + -
139B GLU 3.6 7.4 - - - +
140B PRO* 3.0 36.6 + - - +
142B GLU* 1.3 76.2 - - - +
144B GLN* 1.3 67.4 + - - +
145B ALA 3.4 0.2 + - - -
146B LEU* 3.6 3.8 + - - +
147B LEU* 3.4 23.4 + - - +
164B GLU* 5.9 0.2 - - - -
206B MET* 4.9 0.6 - - - +
207B LEU* 3.0 27.7 + - - +
208B THR 4.7 0.2 - - - -
209B ASP* 2.9 35.3 + - - -
217B ARG* 3.9 19.1 - - - +
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PRO 4.4 1.8 + - - -
141B SER 4.8 4.8 + - - +
142B GLU 3.5 0.4 - - - -
143B ARG* 1.3 77.1 - - - +
145B ALA* 1.3 59.1 + - - +
147B LEU* 3.1 6.4 + - - +
148B ASP* 2.9 59.4 + - - +
217B ARG* 2.8 60.4 + - - +
220B ASN* 3.5 18.0 + - + +
221B ALA* 3.4 9.3 - - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B SER 5.3 1.5 + - - +
142B GLU* 3.6 11.7 + - - +
143B ARG 3.4 0.6 - - - -
144B GLN* 1.3 76.7 - - - +
146B LEU* 1.3 63.9 + - - +
148B ASP* 3.8 11.6 - - - +
149B LYS* 3.3 21.8 + - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.4 7.6 - - + -
118B ILE* 3.5 52.5 - - + +
119B ARG* 5.5 5.2 - - + +
123B ILE* 4.5 1.1 - - + -
131B LEU* 4.2 13.7 - - + -
135B LEU* 4.2 13.2 - - + -
138B LEU* 3.9 23.6 - - + -
142B GLU 3.5 5.0 + - - +
143B ARG 4.1 6.5 - - - +
144B GLN 3.4 0.8 - - - -
145B ALA* 1.3 77.9 - - - +
147B LEU* 1.3 56.8 + - - +
149B LYS* 3.4 16.5 + - - +
150B ILE* 3.1 43.7 + - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.1 21.1 - - + -
135B LEU* 4.3 22.2 - - + -
143B ARG 3.4 14.1 + - - +
144B GLN* 3.1 9.4 + - - +
146B LEU* 1.3 72.8 - - - +
148B ASP* 1.3 68.1 + - - +
150B ILE* 3.3 5.9 + - + +
151B TYR* 2.9 24.3 + - - +
160B LEU* 4.0 26.0 - - + -
162B LEU* 4.9 5.2 - - + -
214B HIS* 5.1 0.9 - - - +
217B ARG* 3.8 32.8 - - + +
218B LEU* 4.2 17.7 - - + -
221B ALA* 3.6 13.8 - - + +
223B PHE* 4.4 3.3 - - + -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLN* 2.9 47.1 + - - +
145B ALA* 3.8 10.4 - - - +
147B LEU* 1.3 75.5 - - - +
149B LYS* 1.3 60.7 + - - +
151B TYR* 3.4 4.0 + - - +
152B GLN* 3.1 28.4 + - + +
220B ASN 3.8 4.0 - - - +
221B ALA* 3.2 19.9 - - - +
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ILE 2.7 25.9 + - - -
119B ARG* 3.4 20.1 + - - +
120B ASP 4.0 1.0 - - - -
121B ILE 2.6 31.4 + - - +
122B ALA* 4.7 4.0 - - - -
123B ILE* 4.0 17.5 - - + +
145B ALA 3.3 10.4 + - - +
146B LEU* 3.5 23.6 - - - +
147B LEU 3.2 0.6 - - - -
148B ASP* 1.3 75.8 - - - +
150B ILE* 1.3 60.8 + - - +
152B GLN* 3.2 7.1 + - - +
153B GLY* 2.8 27.9 + - - -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 3.7 14.8 - - + -
123B ILE* 3.4 26.8 - - + +
129B VAL* 3.6 31.6 - - + -
131B LEU* 3.8 16.6 - - + -
146B LEU* 3.1 37.2 + - + +
147B LEU* 3.7 11.4 - - + +
149B LYS* 1.3 75.6 - - - +
151B TYR* 1.3 64.4 + - - +
153B GLY 3.1 1.6 + - - -
154B LEU* 2.9 28.7 + - + +
160B LEU* 4.2 20.4 - - + -
223B PHE* 4.6 0.9 - - + -
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Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU 2.9 12.0 + - - +
148B ASP 3.4 5.8 - - - +
150B ILE* 1.3 79.7 - - - +
152B GLN* 1.3 83.0 + - - +
154B LEU* 3.3 6.7 + - - +
221B ALA 3.2 25.4 - - - +
222B GLY* 3.3 23.7 + - - -
223B PHE* 3.6 41.9 - + + -
224B GLU* 2.6 26.8 + - - -
242B LYS* 2.8 63.5 + - + +
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 3.1 16.2 + - + +
149B LYS* 3.2 8.3 + - - +
151B TYR* 1.3 102.8 - - - +
153B GLY* 1.3 60.7 + - - +
154B LEU 3.5 7.3 + - - +
221B ALA 4.8 2.8 + - - -
242B LYS* 3.7 7.5 + - - +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ILE* 3.2 32.1 - - - -
124B GLU* 3.8 1.1 - - - -
125B ASN* 3.5 11.3 + - - -
126B ALA* 3.4 19.6 + - - +
149B LYS 2.8 14.7 + - - -
150B ILE 3.1 2.7 + - - -
152B GLN* 1.3 77.0 - - - +
154B LEU* 1.3 61.9 + - - +
155B ASN* 4.7 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