Contacts of the helix formed by residues 321 - 327 (chain B) in PDB entry 1O94
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 ALA 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.8 6.7 - - + +
29B HIS* 3.9 21.5 - - + -
320B CYS* 1.3 74.1 - - - +
322B ARG* 1.3 66.4 + - - +
323B PRO 3.3 0.4 - - - -
324B SER* 2.7 24.5 + - - -
325B ILE* 3.3 11.9 + - - +
1730B FMN 2.7 56.0 + - + +
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Residues in contact with ARG 322 (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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267B ASP 4.3 0.6 + - - -
268B ALA* 3.6 13.4 - - - +
269B GLY* 2.9 40.0 + - - +
278B HIS* 4.9 1.8 + - - -
299B ARG* 3.7 25.0 - - + +
321B ALA* 1.3 73.5 - - - +
323B PRO* 1.3 65.6 - - + +
325B ILE* 2.9 14.3 + - - -
326B ALA* 2.9 12.8 + - - +
345B CYS* 3.5 16.4 - - - -
347B GLY* 4.0 5.1 - - - -
349B ASN* 2.8 36.4 + - - -
351B CYS* 3.9 2.7 - - - -
352B ILE* 4.3 2.9 - - - -
1730B FMN 2.7 76.1 + - + +
1732B SF4 3.3 28.8 - - - -
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Residues in contact with PRO 323 (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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53B TRP* 4.7 2.7 - - + -
299B ARG* 4.0 6.7 - - + -
300B TYR 3.3 40.4 - - - +
301B THR* 3.8 18.8 - - + -
320B CYS* 4.0 11.0 - - + -
321B ALA 3.4 7.0 - - - +
322B ARG* 1.3 95.4 - - + +
324B SER* 1.3 54.5 + - - +
326B ALA* 3.9 1.8 - - + +
327B ASP* 3.0 31.1 + - - +
330B LEU* 4.3 11.3 - - + +
343B ARG 4.9 0.3 - - - +
345B CYS* 4.2 9.2 - - + -
1730B FMN 3.4 14.1 - - - +
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Residues in contact with SER 324 (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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26B GLN* 3.4 16.7 - - - +
29B HIS* 3.7 0.2 + - - -
48B LYS* 3.0 38.8 + - - -
53B TRP* 3.6 36.8 - - - -
320B CYS* 4.4 2.2 - - - +
321B ALA 2.7 19.5 + - - -
323B PRO* 1.3 75.6 - - - +
325B ILE* 1.4 58.4 + - - +
327B ASP 3.9 2.5 - - - -
328B PRO* 3.2 22.2 - - - +
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Residues in contact with ILE 325 (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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29B HIS* 3.5 37.5 - - + +
44B HIS* 4.3 4.4 - - - +
48B LYS* 4.3 4.9 - - - +
321B ALA 3.6 10.5 - - - +
322B ARG* 2.9 14.6 + - - +
324B SER* 1.4 77.5 - - - +
326B ALA* 1.3 64.9 + - - +
327B ASP 3.4 0.3 + - - -
328B PRO* 3.7 0.5 - - - +
351B CYS* 4.4 7.4 - - + -
362B MET* 3.7 33.9 - - + -
364B CYS* 3.9 19.3 - - + -
367B ASN* 3.0 23.7 + - - +
370B ALA* 4.1 3.5 - - + +
1730B FMN 4.2 17.0 - - + -
1732B SF4 3.7 11.7 - - - -
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Residues in contact with ALA 326 (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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322B ARG 2.9 11.9 + - - +
323B PRO 3.9 2.7 - - - +
325B ILE* 1.3 76.9 - - - +
327B ASP* 1.3 59.1 + - - +
328B PRO* 3.9 0.2 - - - -
343B ARG* 3.0 45.5 + - - +
345B CYS* 3.7 28.5 - - + +
364B CYS* 4.0 11.9 - - - -
366B GLN* 4.2 11.2 - - + -
367B ASN* 3.6 5.1 - - - +
1732B SF4 3.9 4.6 - - - -
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Residues in contact with ASP 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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53B TRP* 4.0 1.0 + - - -
323B PRO 3.0 15.0 + - - +
324B SER* 3.5 6.4 - - - +
325B ILE 3.2 0.4 - - - -
326B ALA* 1.3 79.7 - - - +
328B PRO* 1.3 66.1 - - - +
329B PHE* 2.9 21.8 + - - +
330B LEU* 3.0 32.6 + - + +
333B LYS* 2.8 30.8 + - - +
342B ILE* 3.4 7.1 - - - +
343B ARG* 2.8 42.8 + - - +
381B GLU* 4.0 0.9 - - - +
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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