Contacts of the helix formed by residues 154 - 166 (chain A) in PDB entry 2OUX
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLN* 1.3 80.6 - - - +
155A VAL* 1.3 58.3 + - - +
156A ARG* 3.4 23.9 + - - +
157A SER* 3.0 24.2 + - - -
158A ALA* 2.9 24.4 + - - +
198A ASP 3.5 11.7 - - - -
199A ASP* 3.7 21.8 - - - +
200A THR 3.2 6.5 - - - -
201A LEU* 3.8 13.0 - - + -
202A ILE* 4.0 2.2 - - - -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 1.3 69.6 - - - +
156A ARG* 1.3 62.5 + - - +
158A ALA* 3.6 1.3 - - - +
159A MSE 2.6 46.4 + - + +
193A LEU* 4.1 16.2 - - + +
196A ASN* 4.1 12.1 - - + +
197A ASP 2.9 28.5 - - - +
198A ASP* 3.3 13.9 - - - +
200A THR* 3.0 18.5 + - - +
202A ILE* 4.0 12.3 - - + +
205A ILE* 3.8 29.4 - - + -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 3.4 23.2 + - - +
155A VAL* 1.3 85.9 - - - +
157A SER* 1.3 72.9 + - - +
159A MSE 3.8 6.9 - - - +
160A TYR* 3.2 20.8 + - - +
198A ASP* 3.1 42.4 + - - +
199A ASP* 4.9 9.7 + - - -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 2.4 43.1 + - - +
154A THR* 3.0 13.1 + - - -
156A ARG* 1.3 88.5 - - - +
158A ALA* 1.3 63.6 + - - +
160A TYR* 3.1 21.1 + - - +
161A VAL* 3.4 8.8 + - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 4.0 20.6 - - + +
153A GLN* 3.7 8.4 - - - +
154A THR 2.9 12.5 + - - +
155A VAL* 3.0 7.4 + - - +
157A SER* 1.3 75.0 - - - +
159A MSE 1.3 62.3 + - - +
160A TYR 3.1 0.2 - - - -
161A VAL* 3.2 17.6 + - - +
162A LEU* 3.3 19.4 + - + +
175A VAL* 5.6 1.8 - - + -
193A LEU* 4.5 11.4 - - + -
202A ILE* 3.8 22.9 - - + -
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Residues in contact with MSE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 2.6 34.8 + - + +
156A ARG* 3.8 7.6 - - - +
158A ALA* 1.3 70.3 - - - +
160A TYR* 1.3 63.2 + - - +
162A LEU* 3.7 22.9 - - + +
163A LYS* 3.2 24.8 + - + +
190A LEU* 4.2 7.0 - - - -
193A LEU* 3.9 21.5 - - + +
194A ILE* 4.3 12.8 - - + -
198A ASP* 6.1 0.4 - - - +
194B ILE* 3.2 42.6 - - + +
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Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.2 12.6 + - - +
157A SER* 3.1 14.7 + - - +
158A ALA 3.1 1.0 - - - -
159A MSE 1.3 76.9 - - - +
161A VAL* 1.3 74.2 + - + +
163A LYS* 4.8 0.9 - - - -
164A ASN* 2.9 58.0 + - + +
165A GLN* 4.5 20.3 + - + -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.6 19.3 - - + -
148A SER 5.7 1.8 - - - +
149A ILE* 4.9 11.0 - - + -
153A GLN* 4.7 9.6 - - - +
157A SER 3.8 11.7 - - - +
158A ALA* 3.2 10.5 + - - +
160A TYR* 1.3 82.6 - - + +
162A LEU* 1.3 60.4 + - + +
165A GLN* 2.5 63.7 + - + +
166A ALA* 4.8 1.6 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.1 24.0 - - + -
158A ALA* 3.3 14.4 - - + +
159A MSE 3.7 20.6 - - + +
160A TYR 3.2 0.4 - - - -
161A VAL* 1.3 77.6 - - - +
163A LYS* 1.3 63.0 + - - +
166A ALA* 3.3 21.4 + - + +
172A ILE* 3.9 33.5 - - + +
175A VAL* 4.3 10.5 - - + -
190A LEU* 3.8 11.9 - - + -
193A LEU* 3.7 30.3 - - + -
194B ILE* 4.3 13.4 - - + +
195B VAL* 3.9 10.2 - - - +
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MSE 3.2 16.6 + - + +
160A TYR* 4.8 0.4 - - - -
162A LEU* 1.3 81.8 - - - +
164A ASN* 1.3 83.1 + - - +
166A ALA 5.1 0.4 + - - -
194B ILE* 3.3 31.4 - - + +
195B VAL* 3.6 27.1 - - - +
196B ASN 4.3 13.3 + - - -
197B ASP* 3.9 22.3 + - - +
198B ASP 5.4 1.2 - - - +
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Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 2.9 49.4 + - + +
163A LYS* 1.3 102.1 + - - +
165A GLN* 1.3 83.5 + - - +
166A ALA 3.9 1.1 - - - -
167A ASP* 6.4 0.7 - - - -
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 4.5 19.6 + - + -
161A VAL* 2.5 48.9 + - + +
164A ASN* 1.3 97.9 + - + +
166A ALA* 1.3 55.9 + - - +
167A ASP 3.7 2.7 - - - +
168A MSE 3.5 22.6 - - - +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.5 9.0 - - + -
161A VAL* 3.0 7.4 + - + +
162A LEU* 3.3 33.8 + - + +
163A LYS 5.1 0.2 - - - -
164A ASN 3.9 0.4 - - - -
165A GLN* 1.3 79.6 - - - +
167A ASP* 1.3 59.6 + - - +
168A MSE 3.3 7.6 + - - -
169A ALA* 3.6 7.2 + - - +
172A ILE* 3.9 18.2 - - + +
191B ARG* 2.9 24.1 + - - -
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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