Contacts of the helix formed by residues 248 - 254 (chain B) in PDB entry 2F4N
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 ASN 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ARG 4.7 3.8 + - - -
181B PHE 3.1 23.6 + - - +
182B GLY* 3.4 7.4 - - - +
247B ASP* 1.3 84.4 + - - +
249B ALA* 1.3 62.8 + - - +
250B SER* 3.1 12.8 - - - -
251B LYS* 2.8 45.6 + - + +
252B LEU* 2.9 15.7 + - - +
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Residues in contact with ALA 249 (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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182B GLY 3.6 9.1 + - - +
183B ASN* 4.9 1.0 + - - -
184B ILE* 4.0 11.7 - - + -
230B PHE* 4.2 20.2 - - + -
242B ILE* 4.1 19.7 - - + +
243B SER* 4.3 2.5 - - - -
244B LYS* 4.3 16.0 - - - +
247B ASP 3.9 2.6 + - - -
248B ASN* 1.3 72.3 - - - +
250B SER* 1.3 63.7 + - - +
252B LEU* 4.2 9.2 - - - -
253B LEU* 2.8 29.3 + - - +
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Residues in contact with SER 250 (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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178B ILE* 3.4 22.8 - - - +
182B GLY* 2.8 27.3 + - - -
184B ILE* 4.1 11.6 - - - +
248B ASN* 3.0 7.8 + - - -
249B ALA* 1.3 74.2 - - - +
251B LYS* 1.3 52.6 + - - +
254B ASN* 2.7 31.9 + - - -
255B VAL 2.9 30.7 + - - +
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Residues in contact with LYS 251 (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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248B ASN* 2.8 29.4 + - + +
250B SER* 1.3 71.7 - - - +
252B LEU* 1.3 67.5 + - + +
253B LEU 3.4 0.2 + - - -
254B ASN* 3.5 10.9 + - - +
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Residues in contact with LEU 252 (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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213B LYS* 4.3 5.7 + - - -
230B PHE* 3.9 24.2 - - + -
244B LYS* 3.8 21.5 - - + -
247B ASP* 3.6 37.9 - - + +
248B ASN 2.9 15.6 + - - +
249B ALA* 3.7 6.1 - - - +
251B LYS* 1.3 81.0 - - + +
253B LEU* 1.3 62.8 + - - +
254B ASN* 5.3 0.2 - - - +
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Residues in contact with LEU 253 (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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184B ILE* 3.7 23.3 - - + -
205B ILE* 4.5 6.5 - - + -
207B HIS* 3.3 11.3 + - - -
213B LYS* 2.9 32.1 + - + +
215B ILE* 3.8 44.9 - - + -
230B PHE* 4.0 28.3 - - + -
242B ILE* 4.6 2.9 - - + -
249B ALA 2.8 12.8 + - - +
252B LEU* 1.3 79.6 - - - +
254B ASN* 1.3 68.3 + - - +
255B VAL* 3.4 16.8 - - + -
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Residues in contact with ASN 254 (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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207B HIS* 3.0 20.5 + - - +
213B LYS* 3.7 12.3 + - - +
250B SER 2.7 9.3 + - - -
251B LYS* 3.5 8.1 + - - +
252B LEU 3.5 2.4 - - - +
253B LEU* 1.3 81.1 - - - +
255B VAL* 1.3 62.6 + - - +
256B ASP* 3.9 2.3 + - - +
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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