Contacts of the helix formed by residues 235 - 241 (chain B) in PDB entry 2CXO
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 ASP 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR* 6.4 0.2 - - + -
230B LEU* 3.5 13.4 - - - +
233B ALA* 3.0 10.4 + - - +
234B LYS* 1.3 79.5 - - - +
236B PRO* 1.3 66.4 - - - +
237B SER* 3.0 30.8 + - - -
238B ALA* 3.0 33.5 + - + +
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Residues in contact with PRO 236 (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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230B LEU* 3.9 19.3 - - + -
234B LYS 4.4 3.1 - - - +
235B ASP* 1.3 90.9 - - - +
237B SER* 1.3 59.4 + - - +
238B ALA 3.2 0.7 + - - -
239B VAL* 3.3 22.1 + - + +
240B ALA 4.7 0.2 + - - -
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Residues in contact with SER 237 (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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235B ASP* 3.0 26.4 + - - -
236B PRO* 1.3 79.5 - - - +
238B ALA* 1.3 59.8 + - - +
239B VAL 3.2 1.0 + - - -
240B ALA* 3.8 16.4 + - - +
241B LYS* 4.9 5.0 + - - +
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Residues in contact with ALA 238 (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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144B TYR* 3.8 27.6 - - + -
229B PHE* 3.7 11.4 - - + -
233B ALA* 4.2 5.8 - - + -
235B ASP* 3.0 25.1 + - + +
237B SER* 1.3 75.7 + - - +
239B VAL* 1.3 65.2 + - - +
240B ALA 3.2 2.7 - - - -
241B LYS* 3.0 23.0 + - + +
242B HIS* 3.5 15.9 - - - -
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Residues in contact with VAL 239 (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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226B LYS* 4.2 20.4 - - + -
229B PHE* 3.8 13.0 - - + -
230B LEU* 3.8 34.3 - - + -
236B PRO* 3.4 17.9 - - + +
237B SER 3.2 0.4 - - - -
238B ALA* 1.3 77.7 - - - +
240B ALA* 1.3 56.7 + - - +
242B HIS 2.9 19.6 + - - -
243B PHE* 3.0 37.7 + - + +
256B PHE* 5.4 0.7 - - + -
257B GLY 4.1 19.5 - - - +
258B ILE* 5.0 3.6 - - + -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TRP* 3.7 9.0 - - - -
237B SER 3.8 12.9 + - - +
238B ALA 3.2 0.6 - - - -
239B VAL* 1.3 80.5 - - - +
241B LYS* 1.3 60.8 + - + +
242B HIS 3.4 0.4 + - - -
243B PHE 4.2 1.5 - - - +
257B GLY 5.5 1.5 + - - +
258B ILE* 6.0 0.7 - - - +
259B ASP* 4.3 24.2 - - + +
262B ASN* 2.9 33.2 + - - +
1703B GOL 4.2 8.1 - - - +
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Residues in contact with LYS 241 (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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141B TRP* 2.8 32.8 + - - +
142B LYS 3.9 11.5 - - - +
143B GLY 4.3 2.6 + - - -
144B TYR* 4.0 34.2 + - + +
149B ILE* 4.8 1.0 - - - +
205B LEU* 3.6 4.3 - - - +
237B SER 5.0 3.8 - - - +
238B ALA* 3.0 19.7 + - - +
239B VAL 3.0 0.2 + - - -
240B ALA* 1.3 80.2 - - + +
242B HIS* 1.3 71.1 + - + +
243B PHE 3.9 0.4 - - - -
1703B GOL 3.7 29.8 - - - +
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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