Contacts of the helix formed by residues 142 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 4.9 0.8 - - - +
2B GLU* 2.9 32.0 + - + +
3B LEU 4.2 8.6 - - - +
4B THR* 3.9 20.3 - - + -
140B ILE 3.5 0.6 + - - -
141B PRO* 1.3 69.3 - - - +
143B TYR* 1.3 63.4 + - - +
144B GLN* 3.4 12.3 + - - +
145B ARG* 3.1 28.5 + - + +
146B TYR* 2.9 22.2 + - - +
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Residues in contact with TYR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TRP* 4.5 14.4 - + + -
141B PRO 3.2 7.4 + - - +
142B ASP* 1.3 70.8 + - - +
144B GLN* 1.3 75.4 + - + +
146B TYR* 2.8 27.9 + + - +
147B LEU* 2.6 67.5 + - + +
46E GLY* 4.0 4.5 - - - -
63E MET 4.1 1.3 + - - -
64E LEU* 3.5 30.4 - - + -
65E SER* 2.8 38.5 + - - -
68E MET* 4.0 20.6 - - + -
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 3.3 8.7 - - - +
143B TYR* 1.3 104.2 - - + +
145B ARG* 1.3 63.1 + - - +
147B LEU* 3.3 10.8 + - - +
148B ALA* 3.0 24.7 + - - +
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLU* 4.4 15.5 - - + +
142B ASP* 3.1 26.7 + - + +
144B GLN* 1.3 78.4 - - - +
146B TYR* 1.3 62.4 + - - +
148B ALA* 3.4 6.8 + - - +
149B ASP* 3.2 23.4 + - - +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 5.7 5.2 - - + -
1B MET* 4.4 27.1 - - + -
142B ASP 2.9 13.6 + - - +
143B TYR* 2.8 27.3 + + - +
145B ARG* 1.3 78.2 - - - +
147B LEU* 1.3 63.7 + - - +
149B ASP* 3.5 7.2 + - + +
150B ARG* 3.3 45.9 + - + +
65E SER* 2.9 40.5 + - - -
67E PRO* 3.9 20.1 - - + +
68E MET* 3.6 21.3 - - + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TYR* 2.6 55.0 + - + +
144B GLN* 3.6 11.7 - - - +
146B TYR* 1.3 75.3 - - - +
148B ALA* 1.3 66.2 + - - +
150B ARG* 2.9 23.5 + - + +
151B LEU* 3.0 31.9 + - + +
46E GLY* 4.4 19.1 - - - +
47E THR* 4.4 6.1 - - - +
50E ASN* 4.3 15.7 - - - +
65E SER* 5.1 2.9 - - - -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLN 3.0 17.2 + - - +
145B ARG* 3.7 8.1 - - - +
147B LEU* 1.3 75.2 - - - +
149B ASP* 1.3 65.3 + - - +
151B LEU* 3.0 19.4 + - - +
152B LYS* 3.2 15.1 + - - +
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ARG 3.2 10.6 + - - +
146B TYR* 3.5 13.5 - - - +
148B ALA* 1.3 78.0 - - - +
150B ARG* 1.3 70.1 + - - +
152B LYS* 3.3 45.8 + - - +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 3.3 43.9 + - + +
147B LEU* 2.9 16.8 + - + +
149B ASP* 1.3 80.1 - - - +
151B LEU* 1.3 57.4 + - - +
152B LYS 3.1 12.3 + - - -
20E ASP* 2.9 39.7 + - - -
47E THR* 3.1 36.9 + - + +
51E LEU* 5.8 1.2 - - - +
65E SER* 4.6 1.6 + - - -
67E PRO* 5.5 4.5 - - - +
205E PGA 2.8 29.9 + - - -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.0 29.8 + - + +
148B ALA* 3.0 10.5 + - - +
150B ARG* 1.3 77.3 - - - +
152B LYS* 1.3 60.2 + - - +
47E THR* 4.3 22.9 - - + +
50E ASN* 3.8 40.4 - - + +
51E LEU* 4.4 15.7 - - + +
54E ARG* 3.4 39.3 + - - +
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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