Contacts of the helix formed by residues 326 - 334 (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 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B GLU* 2.7 48.7 + - - +
320B MET* 3.7 14.6 - - - -
325B GLY* 1.3 76.2 - - - -
327B GLU* 1.3 64.7 + - - +
328B LEU 3.1 5.0 + - - -
329B MET* 3.1 16.7 + - - +
330B ASP* 3.0 28.4 + - - +
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Residues in contact with GLU 327 (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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249B LYS* 3.8 18.4 + - - +
253B LYS* 2.6 38.3 + - - -
254B TRP* 2.9 30.3 + - + +
326B SER* 1.3 71.6 - - - +
328B LEU* 1.3 57.9 + - - +
330B ASP* 3.2 11.8 + - + +
331B LEU* 2.8 43.4 + - + +
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Residues in contact with LEU 328 (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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250B LEU* 3.4 31.4 - - + -
254B TRP* 3.8 30.0 - - + +
256B VAL* 3.7 22.0 - - + -
312B VAL* 3.8 20.0 - - + +
313B LEU* 4.1 15.9 - - + -
316B GLU* 3.8 25.4 - - + -
326B SER* 3.1 9.2 + - - +
327B GLU* 1.3 79.2 - - - +
329B MET* 1.3 59.7 + - + +
331B LEU* 3.2 4.9 + - - +
332B LEU* 2.9 39.0 + - + +
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Residues in contact with MET 329 (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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273A TYR* 3.3 52.0 - - + +
276B MET* 6.1 0.2 - - - -
313B LEU* 3.5 33.7 - - + +
316B GLU* 3.6 19.1 - - + +
317B ARG* 3.9 7.4 - - + +
320B MET* 3.4 39.5 - - + -
326B SER* 3.1 6.7 + - - +
328B LEU* 1.3 80.9 - - + +
330B ASP* 1.3 55.9 + - - +
332B LEU* 3.8 19.7 - - + +
333B ILE* 2.9 37.6 + - + +
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Residues in contact with ASP 330 (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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246B HIS* 5.1 0.2 + - - -
320B MET* 4.3 14.9 - - - +
326B SER 3.0 24.4 + - - +
327B GLU* 3.2 14.0 + - + +
329B MET* 1.3 76.5 - - - +
331B LEU* 1.3 54.5 + - + +
333B ILE* 4.0 4.7 - - - +
334B SER* 2.8 33.4 + - - -
335B LYS 4.5 1.4 + - - -
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Residues in contact with LEU 331 (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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246B HIS* 3.5 43.4 - - + +
249B LYS* 3.6 43.5 - - + +
250B LEU* 4.0 24.2 - - + +
254B TRP* 4.1 10.8 - - + -
327B GLU* 2.8 38.1 + - + +
328B LEU* 3.5 4.7 - - - +
330B ASP* 1.3 79.2 - - + +
332B LEU* 1.3 58.6 + - - +
334B SER* 2.6 23.6 + - - -
340B ARG* 3.4 4.9 + - - -
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Residues in contact with LEU 332 (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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273A TYR* 3.7 33.7 - - + +
24B ASP* 3.7 14.6 - - + +
27B LYS* 3.1 28.1 + - - +
250B LEU* 3.6 32.3 - - + -
256B VAL* 4.9 0.2 - - + -
273B VAL* 4.0 15.7 - - + -
313B LEU* 3.6 31.6 - - + -
328B LEU* 2.9 25.7 + - + +
329B MET* 3.9 13.9 - - + +
331B LEU* 1.3 74.9 - - - +
333B ILE* 1.3 61.2 + - - +
340B ARG* 3.1 9.7 + - - +
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Residues in contact with ILE 333 (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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120A VAL* 3.5 29.8 - - + -
245A LEU* 5.9 1.3 - - + -
270A GLU* 3.4 32.9 - - + +
273A TYR* 3.7 18.4 - - + -
274A LYS* 3.8 19.5 - - + +
27B LYS* 3.4 6.8 + - - -
233B ARG* 2.9 24.4 + - - -
320B MET* 4.0 19.5 - - + -
329B MET 2.9 21.1 + - - +
330B ASP* 4.0 4.0 - - - +
332B LEU* 1.3 77.3 - - - +
334B SER* 1.3 61.2 + - - +
335B LYS* 4.1 7.4 - - + +
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Residues in contact with SER 334 (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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233B ARG* 2.7 27.4 + - - -
246B HIS* 3.1 19.4 + - - -
330B ASP 2.8 19.5 + - - -
331B LEU 2.6 24.4 + - - -
333B ILE* 1.3 72.6 - - - +
335B LYS* 1.3 61.3 + - - +
336B LYS 3.1 8.7 + - - -
339B ASP* 5.4 0.7 - - - -
340B ARG* 3.0 32.3 + - - -
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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