Contacts of the helix formed by residues 245 - 252 (chain B) in PDB entry 2IVF
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 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B PHE 5.2 0.4 - - - -
238B GLY* 5.1 1.1 - - - -
239B TYR 3.5 3.4 + - - -
242B ASP* 2.7 37.7 + - - -
243B THR 3.3 0.2 - - - -
244B THR* 1.3 80.0 + - - +
246B HIS* 1.3 64.1 + - - +
247B VAL* 3.3 16.7 - - - +
248B HIS* 3.0 16.8 + - - +
249B LYS* 3.1 26.3 + - - +
339B ASP 5.9 0.2 - - - -
342B GLY* 4.4 16.8 - - - -
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ALA* 3.8 19.5 - - + -
237B PHE 5.8 0.2 + - - -
244B THR 4.9 2.2 + - - -
245B SER* 1.3 73.0 - - - +
247B VAL* 1.3 64.0 + - - +
249B LYS* 3.2 8.6 + - - +
250B LEU* 2.9 34.6 + - + +
330B ASP 5.1 0.2 + - - -
331B LEU* 3.5 39.1 + - + +
334B SER* 3.1 30.2 + - - -
339B ASP* 3.4 38.3 + - + +
340B ARG* 3.9 15.9 - - + +
342B GLY* 5.7 1.6 - - - +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.4 33.0 - - + +
22B VAL* 3.8 19.3 - - + +
236B ALA* 3.5 13.0 - - + +
237B PHE* 3.4 33.4 + - - +
238B GLY* 3.7 22.4 - - - +
239B TYR 3.9 4.7 - - - +
240B LEU* 4.6 0.9 - - - +
245B SER* 3.3 12.8 - - - +
246B HIS* 1.3 75.8 - - - +
248B HIS* 1.3 67.4 + - - +
251B VAL* 3.0 30.4 + - - +
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Residues in contact with HIS 248 (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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240B LEU* 2.6 29.8 + - - +
241B ASP* 4.3 4.5 - - - -
242B ASP 3.0 25.9 + - - +
243B THR* 3.7 35.3 - - + +
245B SER* 3.0 10.0 + - - +
247B VAL* 1.3 77.4 - - - +
249B LYS* 1.3 61.8 + - + +
252B LYS* 2.8 58.8 + - + +
253B LYS* 3.3 10.5 + - + +
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Residues in contact with LYS 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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243B THR 3.6 23.8 - - - +
244B THR* 3.4 21.7 + - - +
245B SER 3.1 14.5 + - - +
246B HIS* 3.2 5.5 + - - +
248B HIS* 1.3 78.6 - - + +
250B LEU* 1.3 57.3 + - - +
253B LYS* 3.9 24.5 - - + +
254B TRP* 2.8 36.5 + - - -
327B GLU* 3.8 21.7 + - - +
331B LEU* 3.6 33.8 - - + +
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Residues in contact with LEU 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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22B VAL* 3.9 25.4 - - + -
236B ALA* 5.0 3.8 - - + -
246B HIS* 2.9 32.3 + - + +
247B VAL 4.2 1.6 - - - +
249B LYS* 1.3 77.8 - - - +
251B VAL* 1.3 56.8 + - - +
255B LYS 3.1 4.3 + - - -
256B VAL* 2.7 37.2 + - + -
257B ALA* 3.3 15.3 + - + -
273B VAL* 5.0 0.2 - - + -
328B LEU* 3.4 31.6 - - + -
331B LEU* 4.0 24.9 - - + +
332B LEU* 3.6 25.4 - - + -
340B ARG* 5.4 4.0 - - - +
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Residues in contact with VAL 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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20B VAL* 5.0 0.4 - - + -
22B VAL* 3.6 25.1 - - + -
240B LEU* 3.8 23.6 - - + -
247B VAL* 3.0 20.5 + - + +
250B LEU* 1.3 76.2 - - - +
252B LYS* 1.3 68.6 + - + +
255B LYS* 3.3 21.4 - - - +
257B ALA* 3.9 10.0 - - + +
271B TYR* 3.6 49.1 - - + +
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Residues in contact with LYS 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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240B LEU* 3.8 33.4 - - + +
248B HIS* 2.8 47.2 + - + +
251B VAL* 1.3 88.7 - - + +
253B LYS* 1.3 57.3 + - - +
255B LYS* 3.2 28.8 + - - +
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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