Contacts of the helix formed by residues 360 - 366 (chain B) in PDB entry 3OX4
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 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LYS* 5.6 2.9 - - - +
264B ALA* 3.8 15.5 - - + -
267B HIS* 3.2 22.2 + - - +
268B GLN* 3.4 20.8 + - - +
356B HIS 3.2 3.2 + - - -
357B ALA 3.2 14.7 + - - +
358B LEU 4.3 0.9 - - - +
359B LYS* 1.3 78.9 - - - +
361B ALA* 1.3 67.0 + - - +
362B CYS* 2.8 41.9 + - - +
363B ALA* 3.1 19.2 + - - +
364B LEU 4.2 1.2 + - - -
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Residues in contact with ALA 361 (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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162B ALA* 4.8 18.8 - - + -
164B VAL* 5.6 8.1 - - + -
258B SER* 4.9 4.4 + - - -
359B LYS 3.7 2.4 + - - -
360B ASP* 1.3 75.8 + - - +
362B CYS* 1.3 63.5 + - - +
363B ALA 3.3 0.7 + - - -
364B LEU* 3.5 18.2 + - - +
365B THR* 4.8 0.9 + - - -
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Residues in contact with CYS 362 (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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258B SER* 4.6 10.1 - - - -
259B LEU* 4.1 17.7 - - + -
260B GLY* 3.3 35.7 - - - +
263B HIS* 4.0 9.2 - - - -
264B ALA 4.0 4.0 - - - +
267B HIS* 3.8 23.6 - - - -
360B ASP* 2.8 18.5 + - - +
361B ALA* 1.3 78.7 - - - +
363B ALA* 1.3 61.3 + - - +
365B THR* 3.2 17.5 + - - -
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Residues in contact with ALA 363 (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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261B TYR* 3.6 26.6 - - + -
264B ALA* 4.0 6.9 - - + +
357B ALA 3.7 18.4 - - - +
358B LEU* 4.1 12.3 - - + +
360B ASP 3.1 16.0 + - - +
362B CYS* 1.3 77.0 - - - +
364B LEU* 1.3 63.2 + - - +
365B THR 3.2 0.9 + - - -
366B ASN* 3.3 7.7 + - - +
369B GLN* 3.2 20.8 + - - +
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Residues in contact with LEU 364 (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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206B THR* 4.3 4.5 + - - +
360B ASP 4.2 1.0 + - - +
361B ALA* 3.5 13.2 + - - +
362B CYS 3.2 0.8 - - - -
363B ALA* 1.3 79.2 - - - +
365B THR* 1.3 64.4 + - + +
366B ASN 4.3 0.2 - - - +
369B GLN* 3.6 16.2 + - - +
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Residues in contact with THR 365 (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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205B SER* 3.3 22.5 - - - +
206B THR* 3.1 32.4 + - - +
207B ALA* 4.0 11.9 - - + -
257B ALA 3.8 8.1 - - - +
258B SER* 3.6 16.5 + - - -
259B LEU 2.5 25.8 + - - -
361B ALA 4.9 0.5 + - - -
362B CYS* 3.2 6.6 + - - -
363B ALA 3.2 0.4 - - - -
364B LEU* 1.3 83.1 - - + +
366B ASN* 1.3 68.4 + - - +
367B PRO 3.2 1.2 - - - -
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Residues in contact with ASN 366 (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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201B GLU* 4.2 1.6 - - - +
206B THR* 4.2 3.8 - - - +
259B LEU 4.0 0.6 + - - -
260B GLY* 3.7 7.2 - - - -
261B TYR* 2.8 63.2 + - + +
292B ASN* 2.8 38.7 + - - -
362B CYS 4.0 1.6 + - - -
363B ALA 3.3 5.8 + - - +
364B LEU 4.3 0.2 - - - +
365B THR* 1.3 77.4 + - - +
367B PRO* 1.3 69.0 - - - +
368B ARG 2.7 27.7 + - - +
369B GLN* 2.8 22.6 + - - +
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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