Contacts of the helix formed by residues 179 - 184 (chain B) in PDB entry 2O39
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 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B MET* 4.2 2.1 - - - +
151B SER* 5.1 1.8 + - - -
153B SER* 5.3 3.6 - - - -
154B ASN 4.9 2.7 + - - -
155B ASP* 2.7 46.2 + - - +
178B VAL* 1.3 73.4 - - - +
180B ASN* 1.3 66.1 + - - +
181B ASN* 4.2 7.9 + - - +
182B PHE* 3.1 9.7 + - - +
183B ASN* 3.0 21.5 + - - -
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL 4.2 7.1 + - - -
179B SER* 1.3 73.9 - - - +
181B ASN* 1.3 66.1 + - - +
183B ASN* 3.7 9.8 - - - +
184B MET* 3.1 36.9 + - + +
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Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 3.8 17.7 - - + -
151B SER* 5.1 7.1 + - - +
179B SER* 3.1 7.6 + - - +
180B ASN* 1.3 79.8 - - - +
182B PHE* 1.3 65.6 + - - +
184B MET* 3.1 19.1 + - - +
185B LEU* 3.7 10.6 + - - +
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Residues in contact with PHE 182 (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 ILE* 4.1 20.9 - - + -
148B MET* 3.3 29.2 - - + +
155B ASP* 4.2 5.8 - - + +
156B CYS* 3.7 18.2 - - + -
175B VAL* 4.2 12.1 - - + -
177B GLY* 3.3 36.6 - - - -
179B SER* 3.1 15.0 + - - +
181B ASN* 1.3 78.1 - - - +
183B ASN* 1.3 62.6 + - - +
184B MET 3.1 1.0 + - - -
185B LEU* 3.1 38.7 + - + +
193B PHE* 4.0 23.1 - + - -
311B LEU* 3.4 36.2 - - + +
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Residues in contact with ASN 183 (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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177B GLY* 3.6 10.0 + - - +
178B VAL* 3.4 23.6 + - - +
179B SER 3.0 22.6 + - - +
180B ASN* 3.7 11.5 - - - +
182B PHE* 1.3 77.2 - - - +
184B MET* 1.3 67.4 + - + +
185B LEU 3.3 1.1 + - - -
186B THR* 3.5 22.3 + - - +
308B ALA* 5.0 0.7 - - - +
309B THR 3.2 24.9 + - - +
310B THR* 2.9 16.4 + - - +
311B LEU* 2.9 31.4 + - - +
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Residues in contact with MET 184 (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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180B ASN* 3.1 26.6 + - + +
181B ASN* 3.1 11.0 + - - +
183B ASN* 1.3 77.0 - - + +
185B LEU* 1.3 58.6 + - - +
186B THR* 3.1 3.4 - - - -
187B THR* 2.5 36.3 + - - +
188B HIS* 3.5 6.8 + - + -
305B GLN* 5.7 3.1 - - - +
308B ALA* 4.1 25.6 - - + +
309B THR* 4.3 19.5 - - - +
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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