Contacts of the helix formed by residues 140 - 146 (chain D) in PDB entry 1OIK
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 THR 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D THR* 5.2 0.2 - - - +
138D ALA 4.3 0.2 - - - +
139D ASN* 1.3 70.3 - - - +
141D ALA* 1.3 58.7 + - - +
143D ALA* 3.8 8.7 - - - +
144D TYR 3.3 14.4 + - - -
209D ALA* 3.3 3.7 - - - +
210D LEU* 3.0 46.3 + - - +
238D VAL* 3.8 26.2 - - + -
260D ARG 4.4 0.5 + - - -
261D ALA* 3.0 27.6 + - - -
262D THR 3.5 23.0 + - - +
263D GLN* 4.0 9.2 - - + +
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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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53D LYS* 4.3 7.6 - - - +
139D ASN* 3.0 9.4 + - - +
140D THR* 1.3 78.1 + - - +
142D ALA* 1.3 65.5 + - - +
143D ALA 3.2 0.2 - - - -
144D TYR* 3.3 3.6 + - - +
145D GLN* 3.0 24.6 + - - +
207D GLU* 3.8 28.7 - - + +
208D ARG 3.4 21.0 - - - +
209D ALA* 3.9 7.8 - - + +
261D ALA* 4.0 4.8 + - + -
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Residues in contact with ALA 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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23D ARG* 3.8 21.2 + - + +
139D ASN* 2.9 31.0 + - + +
141D ALA* 1.3 77.4 - - - +
143D ALA* 1.3 61.9 + - - +
145D GLN* 3.3 6.5 + - - +
146D GLU* 3.1 25.3 + - - +
243D ASN* 3.7 16.4 - - - +
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Residues in contact with ALA 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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139D ASN 3.0 16.7 + - - +
140D THR* 3.8 9.4 - - - +
142D ALA* 1.3 77.0 - - - +
144D TYR* 1.3 61.2 + - - +
146D GLU* 3.4 13.8 - - - +
147D LEU* 3.4 18.7 - - - +
210D LEU* 3.9 10.5 - - + -
237D HIS* 3.7 7.8 - - - +
238D VAL* 3.6 31.2 - - + +
243D ASN* 3.9 11.1 - - - +
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Residues in contact with TYR 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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140D THR 3.3 12.5 + - - +
141D ALA 3.6 7.0 - - - +
143D ALA* 1.3 75.5 - - - +
145D GLN* 1.3 86.2 + - - +
147D LEU* 3.2 23.8 + - + +
152D ARG* 3.3 48.0 + - + +
155D ALA* 4.6 0.2 - - + -
156D ASP* 2.5 32.7 + - - -
199D VAL* 3.6 27.6 - - + -
208D ARG* 3.1 53.9 + - + +
209D ALA* 4.3 1.3 - - - -
210D LEU* 3.9 15.1 - - + +
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Residues in contact with GLN 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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141D ALA 3.0 16.9 + - - +
142D ALA* 3.3 7.1 + - - +
144D TYR* 1.3 95.0 - - - +
146D GLU* 1.3 61.2 + - - +
147D LEU 3.3 0.5 + - - -
152D ARG* 3.8 38.6 + - - +
207D GLU* 6.2 0.2 - - - +
208D ARG* 5.0 6.9 + - - +
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Residues in contact with GLU 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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23D ARG* 3.0 14.5 + - - +
142D ALA 3.1 8.7 + - - +
143D ALA* 3.4 14.6 - - - +
144D TYR 3.2 0.8 - - - -
145D GLN* 1.3 76.4 - - - +
147D LEU* 1.3 64.5 + - - +
148D PRO* 3.6 4.9 - - - +
237D HIS* 2.6 34.0 + - + +
240D ARG* 2.8 43.2 + - - +
243D ASN* 2.9 23.2 + - - -
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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