Contacts of the helix formed by residues 395 - 399 (chain B) in PDB entry 2O2C
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 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B PRO 3.0 8.0 + - - +
394B TYR* 1.3 78.5 - - - +
396B GLN* 1.3 58.6 + - - +
397B TYR* 3.0 45.2 + - - +
398B LEU* 3.0 40.5 + - + +
399B TRP 3.9 0.3 + - - -
436B ALA* 4.0 2.9 - - - +
437B GLY 4.4 0.8 + - - -
460B ILE 5.3 0.7 - - - +
461B GLY* 5.8 2.0 - - - -
462B ALA* 4.5 11.7 - - - +
476B PHE* 3.6 2.0 - - - -
534B LEU* 3.6 27.2 - - - +
234C ASN* 4.9 0.2 - - - -
236C ASP* 3.5 11.3 - - - +
238C THR* 5.9 0.2 - - - -
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Residues in contact with GLN 396 (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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395B ASP* 1.3 71.1 - - - +
397B TYR* 1.3 62.2 + - - +
399B TRP* 3.2 39.3 + - - +
436B ALA* 4.1 8.1 - - - +
439B ASN* 4.0 5.9 - - - +
7006B GOL 2.9 33.9 + - - -
234C ASN* 2.8 37.5 + - + +
236C ASP* 2.8 22.5 + - + +
238C THR* 3.9 12.6 - - + -
239C HIS* 3.6 39.6 + - + +
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET 4.6 0.7 - - - +
217B GLU* 3.3 30.3 - - - +
218B ALA* 3.2 37.1 + - - +
220B LYS* 3.9 11.9 - - + -
221B PRO* 3.4 31.4 - - + +
225B ARG* 4.5 0.5 + - - -
395B ASP* 3.0 19.7 + - - +
396B GLN* 1.3 77.3 - - - +
398B LEU* 1.3 55.3 + - - +
399B TRP* 3.2 6.5 + - - -
400B ARG 4.7 0.5 + - - -
466B GLN* 4.6 8.5 - - + -
467B ASN* 2.9 21.1 + - - -
534B LEU* 4.6 3.4 - - + -
7006B GOL 3.5 21.1 - - - -
238C THR* 3.4 31.4 - - + -
242C GLU* 2.5 30.9 + - - -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET* 4.9 2.2 - - - -
218B ALA* 3.8 13.9 - - + -
393B PRO* 3.5 31.9 - - + +
395B ASP* 3.0 23.5 + - + +
397B TYR* 1.3 75.3 - - - +
399B TRP* 1.3 56.5 + - - +
400B ARG 3.1 2.9 - - - -
401B LEU* 3.0 48.2 + - + +
460B ILE* 4.5 15.7 - - + +
461B GLY* 6.5 0.2 - - - -
531B ILE* 6.1 1.1 - - + -
534B LEU* 3.7 26.7 - - + -
539B LEU* 3.8 28.9 - - + -
542B ILE* 5.0 3.4 - - + -
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Residues in contact with TRP 399 (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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213B VAL* 5.7 1.6 - - + -
217B GLU* 2.8 37.5 + - + +
395B ASP 3.9 0.2 + - - -
396B GLN* 3.2 35.5 + - - +
397B TYR* 3.2 11.8 - - - -
398B LEU* 1.3 77.0 - - - +
400B ARG* 1.3 100.7 + - + +
401B LEU 3.4 0.2 - - - -
402B PRO* 3.6 13.1 - - - +
403B ALA 5.4 0.3 + - - -
435B GLU* 4.6 14.3 - - - +
436B ALA* 4.1 19.3 + - + +
7006B GOL 3.4 22.7 + - - -
399C TRP* 3.7 38.1 - + - -
400C ARG* 4.5 11.7 - - - -
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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