Contacts of the helix formed by residues 385 - 394 (chain A) in PDB entry 2OKC
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 LEU 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PRO 3.9 14.6 - - - +
158A LEU* 4.1 19.1 - - + -
161A ALA* 3.6 31.2 - - + -
334A LEU* 4.5 19.1 - - + -
336A LEU* 5.2 4.5 - - + -
367A TYR* 4.0 29.4 - - + -
380A LEU* 4.5 18.6 - - + -
381A GLU 4.9 1.3 - - - +
382A ARG* 3.1 14.3 + - - +
384A HIS* 1.3 78.2 - - - +
386A ASP* 1.3 58.7 + - - +
387A ASP 3.4 1.3 - - - -
388A PHE* 3.3 15.8 + - + +
389A VAL* 3.0 30.1 + - - +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG* 2.8 25.6 + - - +
383A HIS* 3.4 32.3 - - - +
384A HIS 3.3 1.4 - - - -
385A LEU* 1.3 74.7 - - - +
387A ASP* 1.3 61.9 + - - +
389A VAL* 3.2 5.0 + - - +
390A SER* 3.0 29.5 + - - -
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Residues in contact with ASP 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 2.5 34.7 + - - +
383A HIS 4.9 0.2 + - - -
384A HIS 4.6 5.6 + - - +
385A LEU 3.4 0.4 - - - -
386A ASP* 1.3 75.2 - - - +
388A PHE* 1.3 65.5 + - - +
390A SER* 3.4 7.5 + - - -
391A CYS* 2.9 32.5 + - - -
398A ILE* 4.3 10.7 - - - +
408A ARG* 5.3 1.2 - - - +
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Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 5.1 6.1 - - + -
162A MSE 5.8 0.2 - - - -
165A CYS* 3.7 19.3 - - - -
332A THR* 4.1 14.8 - - + -
334A LEU* 4.1 26.9 - - + -
352A PHE* 3.7 31.4 - + - -
365A TYR* 3.6 53.4 + + + -
384A HIS 5.1 0.4 + - - +
385A LEU* 3.3 24.2 + - + +
386A ASP 3.3 0.6 - - - -
387A ASP* 1.3 78.8 - - - +
389A VAL* 1.3 66.8 - - + +
391A CYS* 3.3 2.1 + - - +
392A TYR* 2.8 39.8 + + - +
409A TRP* 4.4 4.3 - + - -
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 4.1 15.7 - - + +
164A ASP* 4.7 9.6 - - + -
165A CYS* 4.0 21.8 - - - +
382A ARG* 3.6 31.0 - - - +
385A LEU 3.0 21.0 + - - +
386A ASP* 3.2 5.1 + - - +
388A PHE* 1.3 76.2 - - + +
390A SER* 1.3 65.4 + - - +
392A TYR* 3.3 9.6 + - - +
393A ASN* 3.1 36.6 + - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP 3.0 16.8 + - - -
387A ASP* 3.7 9.0 - - - -
389A VAL* 1.3 74.9 - - - +
391A CYS* 1.3 60.4 + - - +
393A ASN* 3.2 7.1 + - - +
394A ASN* 2.8 50.4 + - - +
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Residues in contact with CYS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A TYR* 3.9 10.8 - - + -
387A ASP* 2.9 22.9 + - - +
388A PHE 3.5 8.7 - - - +
390A SER* 1.3 76.2 + - - +
392A TYR* 1.3 63.5 + - - +
394A ASN* 2.8 25.8 + - - +
396A VAL 5.5 0.2 - - - -
398A ILE* 3.6 32.3 - - - -
409A TRP* 3.3 46.5 - - + +
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A CYS* 3.4 53.8 + - + -
166A ILE* 4.7 5.9 - - - +
331A HIS* 3.2 21.9 - + - -
332A THR* 3.7 9.2 - - + -
352A PHE* 3.4 35.1 - + - +
388A PHE* 2.8 30.9 + + + +
389A VAL 3.3 11.0 - - - +
391A CYS* 1.3 72.2 - - - +
393A ASN* 1.3 66.8 + - - +
395A ARG* 2.9 48.0 + - - +
409A TRP* 4.0 4.0 - - - -
501A GOL 3.3 22.0 + - - -
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Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP 5.3 1.9 - - - +
165A CYS* 5.2 5.7 - - - +
389A VAL* 3.1 31.1 + - - +
390A SER* 3.8 7.3 - - - +
391A CYS 3.1 0.2 - - - -
392A TYR* 1.3 89.7 - - - +
394A ASN* 1.3 65.1 + - - +
395A ARG* 3.8 5.5 + - - +
501A GOL 4.6 6.9 + - - -
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Residues in contact with ASN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A SER* 2.8 44.0 + - - +
391A CYS* 2.8 16.2 - - - +
393A ASN* 1.3 77.2 - - - +
395A ARG* 1.3 58.2 + - - +
396A VAL* 2.8 25.2 + - + +
409A TRP* 3.7 4.2 + - - -
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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