Contacts of the helix formed by residues 362 - 373 (chain D) in PDB entry 3ER8
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 362 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341D ASN 4.2 5.7 - - - +
342D ARG* 2.7 59.3 + - - +
360D TYR* 4.1 5.8 - - + +
361D LEU* 1.3 78.1 - - - +
363D GLU* 1.3 59.5 + - - +
364D ASN* 3.2 16.4 - - - +
365D VAL* 2.9 37.6 + - + +
366D LEU* 3.3 5.9 + - - +
399D TYR* 4.0 0.9 - - - -
461D ASP* 4.1 10.6 - - + +
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Residues in contact with GLU 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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56A HIS 4.5 17.2 - - - +
57A GLY* 5.7 0.2 - - - -
238D ARG* 3.9 19.4 + - - -
362D ASP* 1.3 72.2 - - - +
364D ASN* 1.3 57.7 + - - +
366D LEU* 4.0 5.6 - - + +
367D SER* 2.6 42.5 + - - +
386D ASN 4.1 2.2 - - - +
387D SER* 3.7 25.3 + - - -
388D VAL* 4.6 6.4 + - + +
399D TYR* 3.2 51.1 + - + +
461D ASP* 3.6 7.8 + - - +
463D LYS* 5.6 4.3 - - - +
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Residues in contact with ASN 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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58A ILE* 6.5 0.4 - - - -
213A ILE* 3.8 16.7 - - + +
214A TYR 4.0 10.5 + - - +
215A THR* 3.0 40.7 + - - +
362D ASP* 3.5 10.3 - - - +
363D GLU* 1.3 78.6 - - - +
365D VAL* 1.3 89.7 + - - +
367D SER* 4.0 3.4 + - - -
368D SER* 3.6 11.3 + - - -
461D ASP* 4.8 5.4 + - - +
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Residues in contact with VAL 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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215A THR* 3.5 24.0 - - + +
341D ASN 6.2 0.2 - - - +
343D ILE* 6.0 0.7 - - + -
360D TYR* 3.7 12.1 - - + -
362D ASP* 2.9 26.5 + - + +
364D ASN* 1.3 90.7 + - - +
366D LEU* 1.3 57.7 + - - +
367D SER 3.1 1.6 - - - -
368D SER* 2.5 31.4 + - - -
369D ASP* 2.9 33.9 + - - +
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D TYR* 3.8 33.1 - - + -
362D ASP 3.3 3.1 + - - +
363D GLU* 4.0 9.2 - - + +
365D VAL* 1.3 78.5 - - - +
367D SER* 1.3 57.8 + - - +
369D ASP* 4.0 2.5 - - + -
370D ILE* 2.8 71.0 + - + +
387D SER* 4.7 1.8 - - - +
388D VAL* 4.8 9.2 - - + -
397D TYR* 3.7 21.8 - - + +
398D THR* 3.2 37.9 - - - +
399D TYR* 3.5 15.0 - - + +
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Residues in contact with SER 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.6 45.4 + - - +
58A ILE* 4.8 5.8 - - - +
213A ILE* 3.3 26.2 - - - +
363D GLU* 2.6 30.1 + - - +
364D ASN* 4.0 6.6 - - - -
365D VAL 3.0 0.6 + - - -
366D LEU* 1.3 79.0 - - - +
368D SER* 1.3 59.4 + - - +
370D ILE* 3.9 4.5 - - - +
371D LEU* 3.5 13.0 + - - +
388D VAL* 5.7 0.5 - - - +
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Residues in contact with SER 368 (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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192A HIS* 5.1 1.9 + - - -
213A ILE* 3.2 36.7 + - - +
215A THR* 5.1 2.9 - - - -
220A ARG* 3.6 17.8 + - - -
364D ASN 3.6 8.7 + - - -
365D VAL* 2.5 19.5 + - - -
367D SER* 1.3 72.4 - - - +
369D ASP* 1.3 66.8 + - - -
370D ILE 3.1 1.1 - - - -
371D LEU* 3.0 16.0 + - - +
372D ASP* 3.1 19.4 + - - +
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Residues in contact with ASP 369 (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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360D TYR* 3.2 27.8 + - - +
365D VAL* 2.9 39.8 + - - +
366D LEU* 3.9 4.7 - - + +
368D SER* 1.3 77.7 - - - +
370D ILE* 1.3 63.9 + - + +
372D ASP* 3.0 26.0 + - - +
373D LEU* 3.0 18.5 + - + +
397D TYR* 6.0 2.9 - - + -
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Residues in contact with ILE 370 (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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56A HIS* 3.9 27.8 - - + +
366D LEU* 2.8 54.8 + - + +
367D SER 3.9 4.7 - - - +
369D ASP* 1.3 77.3 - - + +
371D LEU* 1.3 61.8 + - - +
373D LEU* 3.1 18.8 + - + +
375D ALA* 3.1 33.0 + - + +
378D SER* 3.4 23.6 - - - +
388D VAL* 4.5 6.3 - - + -
390D LEU* 3.8 22.7 - - + -
397D TYR* 4.8 4.5 - - + +
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Residues in contact with LEU 371 (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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12A TYR* 4.1 11.2 - - + +
52A LYS* 3.5 39.3 - - + +
193A GLY* 5.1 1.1 - - - -
194A ASN* 3.0 32.2 - - + +
211A LEU* 3.5 34.5 - - + +
212A SER* 4.5 4.9 - - - -
213A ILE* 4.3 17.0 - - + +
367D SER 3.5 12.3 + - - +
368D SER* 3.0 12.9 + - - +
370D ILE* 1.3 80.1 - - - +
372D ASP* 1.3 58.3 + - - +
374D ASN* 2.7 23.8 + - - +
375D ALA 4.7 4.3 - - - +
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Residues in contact with ASP 372 (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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14A GLU* 4.1 7.4 - - - +
192A HIS* 3.4 34.5 + - - -
193A GLY* 5.4 0.9 - - - -
194A ASN* 4.3 10.0 + - - +
220A ARG* 5.3 1.0 + - - -
368D SER* 3.4 15.4 + - - +
369D ASP* 3.0 20.5 + - - +
371D LEU* 1.3 78.3 - - - +
373D LEU* 1.3 60.6 + - + +
374D ASN* 2.9 22.1 + - - +
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Residues in contact with LEU 373 (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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340C ASN* 5.3 11.0 - - - +
369D ASP* 3.0 17.8 + - + +
370D ILE* 3.1 13.0 + - - +
372D ASP* 1.3 77.2 - - + +
374D ASN* 1.3 75.1 + - - +
375D ALA* 3.4 2.6 + - + +
390D LEU* 4.0 13.5 - - + -
392D HIS* 3.4 57.3 + - + +
397D TYR* 4.3 23.8 - - + +
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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