Contacts of the helix formed by residues 128 - 136 (chain F) in PDB entry 2W3S
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 128 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126F ILE* 4.2 0.9 - - - +
127F LEU* 1.3 85.6 - - + +
129F LEU* 1.3 60.2 + - - +
130F ASP* 3.5 14.2 + - - +
131F GLN* 3.0 37.9 + - - +
132F ALA* 2.9 27.4 + - - +
296F ARG* 4.6 4.7 - - - +
333F THR* 4.5 4.7 - - - -
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Residues in contact with LEU 129 (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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128F THR* 1.3 71.9 - - - +
130F ASP* 1.3 56.3 + - - +
132F ALA* 3.1 5.2 + - - +
133F LEU* 2.6 38.7 + - - +
167F GLU* 4.6 8.1 - - - +
271F ASP* 4.9 8.5 - - - +
272F PHE* 4.8 1.8 - - - -
273F ARG* 3.9 45.8 - - + +
294F LEU* 4.0 10.1 - - + +
295F ALA 3.9 1.8 - - - -
296F ARG* 3.6 44.8 - - + +
331F LEU* 3.7 29.1 - - + +
333F THR* 5.0 1.6 - - + -
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Residues in contact with ASP 130 (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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128F THR* 3.6 13.9 + - - +
129F LEU* 1.3 74.7 + - - +
131F GLN* 1.3 54.6 + - + +
133F LEU* 3.5 7.9 - - - +
134F ALA* 2.7 36.1 + - - +
273F ARG* 2.8 40.4 + - - +
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Residues in contact with GLN 131 (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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125F ALA 3.6 10.9 + - - +
126F ILE* 3.5 10.9 - - + -
127F LEU* 2.5 39.2 + - - +
128F THR* 3.0 32.6 + - - +
130F ASP* 1.3 77.6 - - + +
132F ALA* 1.3 66.2 + - - +
134F ALA* 3.2 7.6 + - - +
135F ALA* 2.8 25.9 + - - +
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Residues in contact with ALA 132 (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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126F ILE* 3.3 14.6 - - + +
128F THR 2.9 10.3 + - - +
129F LEU 3.4 7.9 - - - +
131F GLN* 1.3 74.9 - - - +
133F LEU* 1.3 58.8 + - - +
136F ASP* 2.9 9.9 + - - -
137F SER* 2.8 39.9 + - - +
331F LEU* 3.9 12.1 - - + +
332F ARG 3.5 22.7 - - - +
333F THR* 3.8 8.5 - - + -
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Residues in contact with LEU 133 (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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129F LEU 2.6 19.9 + - - +
130F ASP* 3.5 8.7 - - - +
132F ALA* 1.3 70.8 - - - +
134F ALA* 1.3 66.6 + - - +
136F ASP* 3.2 12.9 + - - +
138F ARG* 3.9 15.6 + - - +
273F ARG* 5.8 1.3 - - - +
275F ARG* 5.5 4.5 - - - +
294F LEU* 3.8 34.1 - - + -
329F HIS* 4.5 11.9 - - + +
331F LEU* 3.3 30.5 - - + -
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Residues in contact with ALA 134 (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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130F ASP 2.7 20.6 + - - +
131F GLN* 3.4 7.2 - - - +
133F LEU* 1.3 74.5 - - - +
135F ALA* 1.3 62.6 + - - +
136F ASP* 3.1 1.6 + - - +
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Residues in contact with ALA 135 (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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126F ILE* 4.2 25.4 - - + -
131F GLN 2.8 19.4 + - - +
132F ALA 3.7 3.6 - - - +
134F ALA* 1.3 72.3 - - - +
136F ASP* 1.3 67.0 + - - +
137F SER* 4.0 4.9 - - - +
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Residues in contact with ASP 136 (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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132F ALA 2.9 6.1 + - - -
133F LEU 3.2 6.9 + - - +
134F ALA 3.1 6.5 + - - +
135F ALA* 1.3 81.0 - - - +
137F SER* 1.3 61.1 + - - +
138F ARG* 2.9 43.4 + - - +
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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