Contacts of the helix formed by residues 155 - 161 (chain E) 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 ALA 155 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E HIS* 4.0 12.9 + - + -
90E PRO* 5.4 3.0 - - + +
118E HIS* 4.7 0.6 + - - -
119E ASP* 4.6 1.6 + - - +
153E PRO 3.8 1.0 + - - -
154E PRO* 1.3 70.2 - - - +
156E ASP* 1.3 64.4 + - - +
157E TRP* 3.5 47.6 - - + -
158E LEU* 3.4 29.0 + - + +
159E GLN* 3.4 15.2 + - - +
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Residues in contact with ASP 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ARG* 5.4 5.2 + - - -
154E PRO 3.3 6.3 + - - +
155E ALA* 1.3 72.5 - - - +
157E TRP* 1.3 90.1 + - - +
159E GLN* 3.0 15.0 + - - +
160E ALA* 2.9 28.1 + - - +
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Residues in contact with TRP 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ARG* 3.0 25.2 + - - +
80E GLY 4.7 2.2 - - - -
81E ILE 3.1 28.9 + - - -
82E ALA 3.7 7.2 + - - -
83E ALA* 3.4 38.4 - - + -
84E PRO* 4.2 17.3 - - + -
87E ARG* 4.1 22.0 - - - -
88E LEU 3.6 22.2 - - - -
89E HIS* 4.2 7.9 - + - -
90E PRO* 5.0 3.4 - - + -
155E ALA* 3.5 28.3 - - + -
156E ASP* 1.3 102.2 + - - +
158E LEU* 1.3 76.4 + - + +
160E ALA* 3.6 17.0 - - - +
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E MET* 5.4 7.6 - - - -
52E ARG* 2.9 24.5 + - - +
76E ARG* 3.7 37.0 - - + +
80E GLY 4.0 5.4 - - - +
81E ILE* 4.4 8.7 - - + -
89E HIS* 3.6 33.4 - - + +
115E ALA* 4.7 15.3 - - + +
119E ASP* 4.2 15.5 - - + +
155E ALA* 3.4 12.9 + - + +
156E ASP 3.3 0.4 - - - -
157E TRP* 1.3 98.0 - - + +
159E GLN* 1.3 64.1 + - - +
160E ALA 3.5 0.5 + - - -
161E ASP* 3.6 11.4 + - - +
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Residues in contact with GLN 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ARG* 3.7 12.7 + - - +
119E ASP* 3.5 33.7 + - - +
154E PRO* 4.2 20.2 - - - +
155E ALA 3.4 11.1 + - - +
156E ASP* 3.0 15.3 + - - +
158E LEU* 1.3 77.0 - - - +
160E ALA* 1.3 65.9 + - - +
162E ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ASP 2.9 11.5 + - - +
157E TRP* 3.6 16.6 - - - +
159E GLN* 1.3 74.0 - - - +
161E ASP* 1.3 56.1 - - - +
162E ALA* 2.5 17.0 + - - +
163E ALA* 3.1 17.7 + - - +
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Residues in contact with ASP 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 4.0 21.1 - - + +
9E GLY* 4.2 9.9 + - - -
52E ARG* 3.5 17.5 - - + +
74E ALA* 3.7 28.5 - - + +
75E LEU 5.1 1.9 - - - +
76E ARG* 2.8 46.0 + - - +
157E TRP 3.9 1.9 - - - +
158E LEU 3.7 11.1 - - - +
159E GLN 3.1 0.8 + - - -
160E ALA* 1.3 74.1 - - - +
162E ALA* 1.3 60.0 + - - +
163E ALA 3.3 1.5 + - - -
164E PHE* 3.7 10.8 + - - +
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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