Contacts of the helix formed by residues 360 - 366 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D LYS* 5.6 4.2 - - - +
264D ALA* 3.8 15.3 - - + -
267D HIS* 3.1 23.9 + - - +
268D GLN* 3.3 16.7 + - - +
356D HIS 3.0 8.8 + - - +
357D ALA 3.1 16.0 + - - +
358D LEU 4.2 1.0 - - - +
359D LYS* 1.3 80.5 - - - +
361D ALA* 1.3 67.9 + - - +
362D CYS* 2.8 38.6 + - - +
363D ALA* 3.1 18.0 + - - +
364D LEU* 4.2 1.4 + - - +
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Residues in contact with ALA 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ALA* 4.5 21.9 - - + +
164D VAL* 5.6 7.4 - - + -
258D SER* 4.9 3.8 + - - -
359D LYS 3.6 3.0 + - - -
360D ASP* 1.3 77.0 + - - +
362D CYS* 1.3 64.1 + - - +
363D ALA 3.4 0.3 + - - -
364D LEU* 3.5 17.4 + - - +
365D THR* 4.9 0.7 + - - +
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Residues in contact with CYS 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D SER* 4.5 11.7 - - - -
259D LEU* 4.2 10.5 - - + -
260D GLY* 3.6 29.5 - - - +
263D HIS* 4.0 11.4 - - + -
264D ALA 4.0 5.4 - - - +
267D HIS* 3.8 23.6 - - - -
360D ASP* 2.8 16.9 + - - +
361D ALA* 1.3 80.1 - - - +
363D ALA* 1.3 63.3 + - - +
364D LEU 3.1 1.2 + - - -
365D THR* 3.2 18.9 + - - -
1385D NAD 4.0 8.1 - - - -
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Residues in contact with ALA 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D GLY 4.7 0.4 - - - -
261D TYR* 3.6 19.8 - - + -
264D ALA* 3.9 11.3 - - + +
357D ALA 3.5 20.0 - - - +
358D LEU* 4.0 16.4 - - + +
360D ASP 3.1 13.8 + - - +
362D CYS* 1.3 79.2 - - - +
364D LEU* 1.3 62.2 + - - +
365D THR 3.2 1.0 + - - -
366D ASN* 3.3 9.5 + - - +
369D GLN* 3.2 18.3 + - - +
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Residues in contact with LEU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D THR* 4.3 5.0 + - - +
360D ASP 4.2 1.2 + - - +
361D ALA* 3.5 13.5 + - - +
362D CYS 3.1 1.6 + - - -
363D ALA* 1.3 79.0 - - - +
365D THR* 1.3 65.7 + - + +
366D ASN 4.2 0.5 - - - +
369D GLN* 3.5 21.3 + - - +
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Residues in contact with THR 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D SER* 3.3 27.0 - - - +
206D THR* 3.1 28.8 + - - +
207D ALA* 4.0 13.9 - - + -
257D ALA 3.8 8.1 - - - +
258D SER* 3.5 16.7 + - - +
259D LEU 2.5 23.6 + - - -
361D ALA 5.1 0.3 + - - -
362D CYS 3.2 7.0 + - - -
363D ALA 3.3 0.4 - - - -
364D LEU* 1.3 82.4 - - + +
366D ASN* 1.3 67.8 + - - +
367D PRO 3.3 0.9 - - - -
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Residues in contact with ASN 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLU* 4.3 1.2 - - - +
206D THR* 3.9 6.1 - - - +
259D LEU 3.9 2.4 + - - -
260D GLY* 3.6 7.0 - - - -
261D TYR* 2.7 64.3 + - + +
292D ASN* 2.8 39.0 + - - -
362D CYS 4.1 0.2 + - - -
363D ALA 3.3 5.6 + - - +
364D LEU 4.2 0.3 - - - +
365D THR* 1.3 78.6 + - - +
367D PRO* 1.3 69.0 - - - +
368D ARG* 2.7 30.9 + - - +
369D GLN* 3.2 14.1 + - - +
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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