Contacts of the helix formed by residues 152 - 161 (chain B) in PDB entry 1OPL
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 SER 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B VAL* 1.3 79.7 - - - +
153B ARG* 1.3 60.2 + - - +
154B ASN* 3.7 7.7 + - - +
155B ALA* 3.1 23.6 + - - +
156B ALA* 2.8 27.7 + - - +
171B ARG* 4.2 2.5 - - - +
174B GLU* 3.6 21.7 + - - -
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Residues in contact with ARG 153 (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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152B SER* 1.3 73.1 - - - +
154B ASN* 1.3 70.5 + - - +
156B ALA* 3.3 4.0 + - - +
157B GLU* 3.1 34.2 + - - +
171B ARG* 3.7 29.1 - - - +
192B HIS* 3.4 51.9 + - + +
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Residues in contact with ASN 154 (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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152B SER* 3.2 6.0 + - - +
153B ARG* 1.3 83.2 - - - +
155B ALA* 1.3 64.9 + - - +
157B GLU* 3.3 15.7 + - - +
158B TYR* 3.1 19.4 + - - +
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Residues in contact with ALA 155 (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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151B VAL* 3.6 21.3 - - + -
152B SER* 3.1 22.3 + - - +
154B ASN* 1.3 76.0 - - - +
156B ALA* 1.3 63.4 + - - +
158B TYR* 3.0 10.1 + - - +
159B LEU* 2.9 27.5 + - + +
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Residues in contact with ALA 156 (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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151B VAL* 3.5 6.7 - - + +
152B SER 2.8 17.0 + - - +
153B ARG 3.4 5.4 - - - +
155B ALA* 1.3 76.9 - - - +
157B GLU* 1.3 58.5 + - - +
159B LEU* 3.2 1.3 + - - +
160B LEU* 2.8 36.4 + - - +
169B LEU* 4.1 15.3 - - + -
171B ARG* 3.8 13.0 - - - +
183B SER* 3.7 29.4 - - - +
192B HIS* 4.4 0.9 - - + -
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Residues in contact with GLU 157 (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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153B ARG* 3.1 26.9 + - - +
154B ASN* 3.6 15.3 - - - +
155B ALA 3.2 0.4 - - - -
156B ALA* 1.3 74.8 - - - +
158B TYR* 1.3 53.7 + - - +
160B LEU* 3.5 5.3 - - - -
161B SER* 2.6 35.0 + - - -
185B ARG* 3.7 4.0 + - - +
189B ARG* 6.1 0.9 - - - -
190B VAL* 4.1 19.6 - - + +
192B HIS* 2.9 31.6 + - + +
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Residues in contact with TYR 158 (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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154B ASN 3.1 11.2 + - - +
155B ALA* 3.0 12.4 + - - +
157B GLU* 1.3 75.5 - - - +
159B LEU* 1.3 75.5 + - + +
161B SER* 2.7 31.3 + - - -
162B SER* 4.0 1.9 + - - -
259B THR* 2.6 43.9 + - + -
260B ASP* 4.4 7.3 + - - -
281B LYS* 4.8 17.7 - - + +
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Residues in contact with LEU 159 (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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148B HIS* 3.7 27.1 - - + +
151B VAL* 4.3 20.4 - - + -
155B ALA* 2.9 19.0 + - + +
156B ALA 3.7 5.4 - - - +
158B TYR* 1.3 83.2 - - + +
160B LEU* 1.4 59.5 + - - +
162B SER* 2.5 29.7 + - - -
169B LEU* 3.7 19.1 - - + -
236B ALA* 4.8 10.6 - - + +
237B PRO* 5.1 9.4 - - - +
258B ARG* 4.8 1.7 - - - -
259B THR* 4.9 19.1 - - + +
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Residues in contact with LEU 160 (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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156B ALA 2.8 17.6 + - - +
157B GLU 3.5 0.2 - - - -
159B LEU* 1.4 75.0 - - - +
161B SER* 1.3 50.9 + - - +
162B SER 2.6 6.7 + - - -
163B GLY* 2.6 26.3 + - - +
167B SER* 3.5 41.1 - - - +
168B PHE* 3.9 4.0 - - - +
169B LEU* 4.0 15.3 - - + -
183B SER* 3.3 48.2 - - - +
184B LEU* 4.0 2.9 - - - +
185B ARG* 3.3 19.4 - - + -
190B VAL* 3.8 20.6 - - + -
236B ALA* 4.6 6.7 - - + -
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Residues in contact with SER 161 (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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157B GLU 2.6 20.8 + - - -
158B TYR* 2.7 27.3 + - - -
160B LEU* 1.3 72.4 - - - +
162B SER* 1.4 54.9 + - - +
163B GLY 3.5 1.7 + - - +
185B ARG* 3.2 25.6 + - - +
259B THR 6.0 2.3 - - - -
261B ILE 3.3 15.3 + - - +
262B THR* 3.5 16.0 + - - -
263B MET* 3.4 18.5 + - - +
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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