Contacts of the helix formed by residues 142 - 151 (chain D) in PDB entry 1S89
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 ASP 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 4.1 0.5 - - - +
2D GLU* 2.6 34.0 + - + +
3D LEU 4.5 2.8 - - - +
4D THR* 3.6 29.1 - - - +
140D ILE 3.4 2.0 + - - -
141D PRO* 1.3 69.2 - - - +
143D TYR* 1.3 63.9 + - - +
144D GLN* 3.4 13.5 + - - +
145D ARG* 3.4 32.3 + - + +
146D TYR* 3.0 22.0 + - - +
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Residues in contact with TYR 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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46C GLY* 3.9 10.0 - - - -
63C MET 4.1 1.1 + - - -
64C LEU* 3.5 29.7 - - + -
65C SER* 2.8 39.1 + - - -
68C MET* 3.8 34.5 - - + -
112D TRP* 4.5 12.3 - + + -
141D PRO 2.9 10.7 + - - +
142D ASP* 1.3 71.8 + - - +
144D GLN* 1.3 67.0 + - - +
146D TYR* 3.1 14.2 + + - +
147D LEU* 2.8 51.1 + - + +
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Residues in contact with GLN 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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142D ASP* 3.3 11.2 + - - +
143D TYR* 1.3 83.3 - - - +
145D ARG* 1.3 66.6 + - + +
147D LEU* 3.3 5.1 + - - +
148D ALA* 2.9 23.5 + - + +
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Residues in contact with ARG 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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2D GLU* 3.6 45.0 + - + +
142D ASP* 3.4 27.4 + - + +
143D TYR 3.3 0.4 - - - -
144D GLN* 1.3 82.2 - - + +
146D TYR* 1.3 65.8 + - - +
148D ALA* 3.0 18.4 + - + +
149D ASP* 3.1 24.1 + - - +
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Residues in contact with TYR 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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65C SER* 3.4 35.1 + - - -
67C PRO* 4.0 17.9 - - + +
68C MET* 3.7 17.9 - - + -
1D MET* 3.9 30.7 - - + +
142D ASP 3.0 14.5 + - - +
143D TYR* 3.1 28.7 + + - +
145D ARG* 1.3 79.1 - - - +
147D LEU* 1.3 66.5 + - - +
149D ASP* 3.3 12.7 + - - +
150D ARG* 3.2 44.7 + - + +
93E LEU* 6.2 2.9 - - + -
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Residues in contact with LEU 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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46C GLY* 4.2 3.6 - - - +
47C THR* 4.1 32.8 - - - +
50C ASN* 3.9 20.4 - - - +
65C SER* 5.2 2.9 - - - -
143D TYR* 2.8 51.9 + - + +
144D GLN* 3.8 4.5 - - - +
146D TYR* 1.3 73.5 - - - +
148D ALA* 1.3 65.3 + - - +
150D ARG* 3.2 17.8 + - + +
151D LEU* 3.3 25.8 + - + +
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Residues in contact with ALA 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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144D GLN* 2.9 16.1 + - + +
145D ARG* 3.2 15.0 - - + +
147D LEU* 1.3 77.8 - - - +
149D ASP* 1.3 64.5 - - - +
151D LEU* 3.1 16.6 + - - +
152D LYS* 3.1 11.8 + - - +
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Residues in contact with ASP 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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2D GLU* 6.0 1.7 - - - +
145D ARG* 3.1 17.7 + - - +
146D TYR* 3.7 8.9 - - - +
148D ALA* 1.3 77.2 - - - +
150D ARG* 1.3 63.5 + - + +
152D LYS* 3.0 24.9 + - - +
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Residues in contact with ARG 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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20C ASP* 3.1 35.9 + - - -
47C THR* 3.1 35.8 + - + +
51C LEU* 5.5 2.6 - - - +
65C SER* 4.5 1.4 + - - -
67C PRO* 5.8 2.3 - - - +
203C PGA 2.8 29.9 + - - -
146D TYR* 3.2 48.7 + - + +
147D LEU* 3.2 15.9 + - + +
149D ASP* 1.3 76.5 - - + +
151D LEU* 1.3 64.0 + - + +
152D LYS 5.2 0.5 - - - +
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Residues in contact with LEU 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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47C THR* 4.0 23.8 - - + -
50C ASN* 4.0 37.0 - - + +
51C LEU* 4.2 20.6 - - + -
147D LEU* 3.3 24.0 - - + +
148D ALA* 3.1 9.2 + - - +
149D ASP 3.1 0.4 - - - -
150D ARG* 1.3 82.6 - - + +
152D LYS* 1.3 65.1 + - - +
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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