Contacts of the helix formed by residues 139 - 143 (chain D) in PDB entry 2IDK
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 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C GLU* 3.5 30.2 + - - +
64D ALA* 3.6 26.6 + - - +
117D TRP* 3.5 8.6 - - - -
135D CYS* 4.6 2.7 + - - -
136D LEU* 3.2 18.1 + - - +
137D GLY 4.0 4.0 + - - -
138D ASN* 1.3 74.4 - - - +
140D PHE* 1.3 66.7 + - - +
141D ALA 3.0 2.9 - - - -
142D HIS* 2.9 30.7 + - - +
173D ASP* 4.7 1.4 + - - -
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Residues in contact with PHE 140 (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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117D TRP* 3.5 20.8 - + - -
135D CYS* 4.3 6.1 + - - -
138D ASN 3.6 0.6 - - - -
139D SER* 1.3 79.3 - - - +
141D ALA* 1.3 60.1 + - - +
142D HIS 3.1 1.6 + - - -
143D LEU* 3.1 34.1 + - + +
153D HIS* 3.7 18.6 - + + -
156D ALA* 3.7 19.3 - - + -
157D LEU* 3.5 31.2 - - + -
160D ILE* 4.3 9.0 - - + -
172D ILE* 4.1 26.5 - - + -
173D ASP 4.7 8.3 + - - +
174D HIS* 6.2 0.4 - - + -
245D HIS* 3.8 20.3 + + + -
250D PHE* 3.6 29.6 - + + -
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Residues in contact with ALA 141 (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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138D ASN* 3.5 28.1 + - - +
139D SER 3.0 0.6 + - - -
140D PHE* 1.3 75.2 - - - +
142D HIS* 1.3 65.3 + - - +
143D LEU 3.1 3.2 + - - +
173D ASP 5.5 0.4 + - - -
174D HIS* 5.4 2.8 - - + +
177D TYR* 4.0 14.1 - - + +
242D TYR* 3.3 7.5 - - + -
243D TYR 2.8 46.5 + - - +
245D HIS* 4.2 13.6 - - + -
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Residues in contact with HIS 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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14C ALA* 3.5 20.0 - - + +
15C GLU* 2.8 56.5 + - - +
17C ILE* 4.0 19.3 - - + +
117D TRP* 5.5 0.7 - - + -
137D GLY 5.4 2.2 + - - -
138D ASN 4.0 6.7 + - - -
139D SER* 2.9 23.6 + - - +
141D ALA* 1.3 78.1 - - - +
143D LEU* 1.3 58.4 + - - +
144D PRO* 3.1 14.7 - - - +
240D LEU* 5.6 5.8 - - + +
241D SER 4.4 12.3 - - - +
242D TYR* 3.6 36.6 + + - -
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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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16C GLY 5.2 1.3 - - - +
17C ILE* 4.3 13.0 - - + +
116D ASN* 6.0 0.2 - - - +
117D TRP* 4.1 17.0 - - + -
118D LEU* 4.4 23.6 - - + -
139D SER 4.4 0.2 + - - -
140D PHE* 3.1 21.8 + - + +
141D ALA 3.1 1.8 - - - +
142D HIS* 1.3 78.0 - - - +
144D PRO* 1.3 72.6 - - + +
152D GLU* 3.8 15.9 - - + +
153D HIS* 2.9 42.8 + - + -
156D ALA* 3.7 29.4 - - + -
243D TYR* 3.6 11.4 - - - +
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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