Contacts of the helix formed by residues 142 - 151 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F MET* 3.9 2.3 - - - +
2F GLU* 3.0 31.3 + - + +
3F LEU 4.2 1.1 - - - +
4F THR* 3.8 30.0 - - + +
140F ILE 3.4 0.8 + - - -
141F PRO* 1.3 68.1 - - - +
143F TYR* 1.3 65.0 + - - +
144F GLN* 3.9 14.8 + - - +
145F ARG* 2.8 31.6 + - - +
146F TYR* 2.9 20.7 + - - +
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Residues in contact with TYR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY* 3.5 15.1 - - - -
63A MET 3.7 2.6 + - - -
64A LEU* 3.4 29.1 - - + -
65A SER* 2.8 46.3 + - - -
68A MET* 3.9 18.8 - - + -
112F TRP* 4.8 13.5 - + + -
141F PRO 3.3 6.6 + - - -
142F ASP* 1.3 73.0 + - - +
144F GLN* 1.3 64.1 + - + +
146F TYR* 2.9 22.7 + + - +
147F LEU* 2.7 61.7 + - + +
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Residues in contact with GLN 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ASP* 3.2 13.5 + - - +
143F TYR* 1.3 87.9 - - + +
145F ARG* 1.3 59.2 + - - +
147F LEU* 3.2 7.7 + - - +
148F ALA* 2.8 33.0 + - - +
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Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F GLU* 3.6 31.3 - - + +
142F ASP* 2.8 24.1 + - - +
144F GLN* 1.3 78.5 - - - +
146F TYR* 1.3 60.7 + - - +
148F ALA* 4.0 7.0 - - - +
149F ASP* 3.1 24.1 + - - +
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Residues in contact with TYR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 3.5 31.6 + - - -
67A PRO* 4.0 16.6 - - + +
68A MET* 3.8 16.6 - - + -
93C LEU* 6.5 2.0 - - + -
1F MET* 4.0 29.8 - - + -
2F GLU* 5.3 1.1 - - - +
142F ASP 2.9 12.7 + - - +
143F TYR* 2.9 31.6 + + - +
145F ARG* 1.3 78.7 - - - +
147F LEU* 1.3 60.9 + - + +
149F ASP* 3.2 7.6 + - + +
150F ARG* 3.0 59.9 + - + +
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY* 3.9 2.5 - - - -
47A THR* 3.8 33.9 - - - +
50A ASN* 3.5 22.9 - - - +
65A SER* 5.2 1.3 - - - -
143F TYR* 2.7 55.8 + - + +
144F GLN* 3.8 8.5 - - - +
146F TYR* 1.3 72.5 - - - +
148F ALA* 1.3 66.0 + - - +
150F ARG* 2.9 17.0 + - + +
151F LEU* 3.0 32.1 + - + +
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLN 2.8 23.3 + - - +
145F ARG* 4.1 7.0 - - - +
147F LEU* 1.3 72.4 - - - +
149F ASP* 1.3 61.2 + - - +
151F LEU* 3.1 26.8 + - - +
152F LYS* 4.8 5.6 - - - +
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Residues in contact with ASP 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ARG 3.1 18.0 + - - +
146F TYR* 3.3 7.0 - - + +
147F LEU 3.1 0.2 - - - -
148F ALA* 1.3 75.7 - - - +
150F ARG* 1.3 66.6 + - + +
151F LEU 3.1 10.0 + - - +
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Residues in contact with ARG 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP* 2.8 44.0 + - - -
47A THR* 2.9 42.4 + - + +
51A LEU* 5.8 0.9 - - - +
65A SER* 4.5 1.7 + - - -
67A PRO* 6.0 2.1 - - - +
201A PGA 2.8 24.5 + - - -
146F TYR* 3.0 57.9 + - + +
147F LEU* 2.9 12.2 + - + +
149F ASP* 1.3 78.1 - - + +
151F LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 4.3 13.7 - - + +
50A ASN* 4.1 28.3 - - + -
51A LEU* 3.6 32.8 - - + -
54A ARG* 4.4 1.8 - - - +
147F LEU* 3.0 35.1 + - + +
148F ALA* 3.1 17.9 - - - +
149F ASP 3.1 10.1 - - - +
150F ARG* 1.3 81.6 - - - +
152F LYS* 1.3 101.2 + - + +
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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