Contacts of the helix formed by residues 141 - 152 (chain D) in PDB entry 4OA5
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 SER 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASN* 2.7 35.6 + - - -
118D LEU* 4.8 0.7 - - - -
138D ASN* 3.1 19.7 + - - -
140D SER* 1.3 79.7 + - - +
142D TYR* 1.3 63.3 + - - +
143D LEU 3.2 2.7 - - - -
144D ALA* 3.0 14.6 + - - +
145D TYR* 3.0 45.7 + - - -
304D IOD 4.2 2.8 - - - +
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Residues in contact with TYR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ILE* 3.4 27.3 + - + -
136D ASP* 3.8 8.7 + - - -
137D ALA 3.2 23.8 + - - -
138D ASN 3.5 9.9 - - - -
139D LYS* 3.2 34.9 + - + +
141D SER* 1.3 76.4 - - - +
143D LEU* 1.3 56.1 + - - +
145D TYR* 3.2 7.7 + + - +
146D LEU 2.9 25.3 + - - -
161D ALA* 3.8 15.3 - - + -
162D ASP 2.6 30.3 + - - -
163D ASN* 4.5 1.7 - - - +
164D THR* 4.3 0.4 - - + -
186D SER* 3.4 4.6 + - - +
187D MET* 3.4 30.5 - - + -
190D PHE* 3.4 36.4 - + + -
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.6 0.2 - - + -
185A ALA* 3.6 31.4 - - + +
189A ALA* 4.0 12.6 - - + -
321A EDO 4.0 16.2 - - - +
141D SER 3.2 0.6 - - - -
142D TYR* 1.3 77.2 - - - +
144D ALA* 1.3 58.3 + - - +
146D LEU* 3.3 12.4 + - + +
147D ASN* 2.9 43.5 + - - +
186D SER* 3.3 18.6 + - - +
189D ALA* 3.9 32.5 - - + +
190D PHE* 4.0 14.3 - - - +
193D GLU* 5.1 2.2 - - + -
316D IOD 4.2 17.7 - - + -
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 4.1 18.6 - - - +
182A ASN* 3.6 20.9 - - - +
185A ALA* 4.0 12.3 - - + +
118D LEU* 3.8 21.8 - - + +
141D SER* 3.0 11.1 + - - +
143D LEU* 1.3 79.2 - - - +
145D TYR* 1.3 57.7 + - - +
147D ASN* 3.3 5.2 + - - +
148D TRP* 3.0 26.5 + - - +
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Residues in contact with TYR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL* 3.9 12.0 - - + +
117D ALA* 3.4 33.6 - - + +
118D LEU* 3.8 21.1 - - + -
121D LEU* 3.8 17.5 - - + -
133D ILE* 4.4 8.7 - - + +
135D ILE* 3.7 37.9 - - + -
137D ALA 3.5 21.8 - - - -
138D ASN* 2.5 23.0 + - - -
141D SER* 3.0 29.4 + - - -
142D TYR* 3.6 5.8 - - - +
144D ALA* 1.3 71.5 - - - +
146D LEU* 1.3 66.2 + - - +
148D TRP* 3.2 8.3 + - - +
149D ALA* 2.9 22.3 + - - +
301D SAH 4.1 0.2 - - - -
304D IOD 3.5 9.5 - - - +
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ILE* 4.4 2.8 - - - +
142D TYR 2.9 12.7 + - - +
143D LEU* 3.5 13.7 - - + +
145D TYR* 1.3 77.4 - - - +
147D ASN* 1.3 59.5 + - - +
149D ALA* 3.1 4.6 + - - +
150D LYS* 2.9 41.5 + - + +
159D ILE* 3.9 24.5 - - + -
190D PHE* 3.8 32.8 - - + +
193D GLU* 3.5 33.9 - - + -
194D LEU* 3.8 25.4 - - + -
200D TYR* 4.5 1.6 - - - +
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Residues in contact with ASN 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 5.2 12.5 + - + +
175A PRO* 5.6 10.3 - - + +
184A HIS* 5.1 5.5 + - - -
185A ALA* 3.4 34.2 + - - +
188A ARG* 5.4 5.5 - - - +
321A EDO 4.9 5.5 + - - -
143D LEU* 2.9 31.0 + - - +
144D ALA* 3.3 6.7 + - - +
146D LEU* 1.3 77.7 - - - +
148D TRP* 1.3 63.3 + - - +
150D LYS* 3.5 39.6 + - - +
151D MET* 3.7 6.9 + - - +
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Residues in contact with TRP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D VAL* 4.0 9.0 - - + -
118D LEU* 5.8 2.2 - - + -
121D LEU* 3.1 69.9 + - + +
122D ASN* 4.9 2.7 - - - -
124D LEU* 4.3 9.2 - - + -
125D LYS* 4.0 10.9 - - - +
130D PHE* 3.9 22.7 - + - -
133D ILE* 4.0 17.5 - - + -
144D ALA 3.0 13.3 + - - +
145D TYR* 3.5 10.8 - - - +
146D LEU 3.2 0.2 - - - -
147D ASN* 1.3 76.4 - - - +
149D ALA* 1.3 63.4 + - - +
151D MET* 3.1 4.0 + - - -
152D TYR* 3.0 79.8 + + + -
153D ILE* 4.3 15.3 - - + -
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.0 19.5 - - + -
135D ILE* 5.7 0.2 - - + -
145D TYR 2.9 13.4 + - - +
146D LEU* 3.1 12.1 + - - +
148D TRP* 1.3 77.9 - - - +
150D LYS* 1.3 63.3 + - - +
153D ILE* 2.9 48.2 + - + +
159D ILE* 4.2 14.6 - - + -
216D LYS* 3.4 5.7 - - - -
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 3.4 35.9 + - + +
321A EDO 5.1 8.7 + - - -
146D LEU* 2.9 28.6 + - + +
147D ASN* 3.5 34.0 + - - +
148D TRP 3.3 0.2 - - - -
149D ALA* 1.3 75.7 - - - +
151D MET* 1.3 58.7 + - - +
159D ILE* 5.8 0.4 - - + -
193D GLU* 3.4 28.1 + - - +
199D LYS* 4.4 7.9 - - - +
200D TYR* 3.3 22.0 - - + +
216D LYS* 3.3 26.3 + - - +
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Residues in contact with MET 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A HIS* 5.6 11.2 - - + -
129D PRO* 5.7 0.2 - - - +
147D ASN 3.7 6.0 + - - +
148D TRP* 3.1 9.1 + - - +
150D LYS* 1.3 80.9 - - + +
152D TYR* 1.3 86.4 + - + +
153D ILE 3.7 4.0 - - - +
302D IOD 4.3 10.2 - - - +
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Residues in contact with TYR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LYS* 6.2 0.4 - - - -
218C THR* 4.8 19.2 - - + +
125D LYS* 3.4 43.3 - - + +
128D ALA* 3.5 24.7 - - + -
129D PRO* 3.2 8.3 - - - +
130D PHE* 2.9 28.1 + - - -
148D TRP* 3.0 72.6 + + + +
151D MET* 1.3 94.8 - - + +
153D ILE* 1.3 63.4 + - - +
302D IOD 4.2 9.2 - - + -
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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