Contacts of the strand formed by residues 395 - 399 (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 ILE 395 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D LYS* 5.1 7.2 - - + -
356D LYS* 3.6 43.7 - - + +
358D LEU* 3.7 25.4 - - + +
390D LEU 3.2 2.1 - - - +
391D ILE* 3.2 2.9 - - - -
392D HIS 2.9 29.5 + - - +
393D ASP* 2.8 15.9 + - + +
394D ASN* 1.3 90.5 - - + +
396D MET* 1.3 63.2 + - - +
397D TYR* 3.2 35.2 - - + +
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Residues in contact with MET 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D PHE* 3.3 39.5 - - + -
356D LYS 3.4 6.7 + - - -
357D CYS* 2.8 38.1 - - + -
358D LEU 2.8 26.9 + - - -
389D TYR* 3.9 17.9 - - + -
390D LEU 3.3 10.5 - - - +
391D ILE* 4.1 11.7 - - + +
394D ASN 4.1 0.6 + - - -
395D ILE* 1.3 73.9 - - - +
397D TYR* 1.3 68.2 + - - +
398D THR* 5.0 0.4 - - - -
424D ILE* 4.1 11.4 - - + -
427D TYR* 3.1 41.5 - - + -
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Residues in contact with TYR 397 (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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358D LEU* 3.4 26.1 - - + +
360D TYR* 4.1 23.3 - + - -
366D LEU* 3.7 20.8 - - + +
369D ASP* 6.0 2.9 - - + -
370D ILE* 4.8 3.7 - - + +
373D LEU* 4.3 21.1 - - + +
388D VAL 3.9 0.7 - - - +
389D TYR* 3.6 3.5 - - - -
390D LEU* 2.9 40.9 + - + +
392D HIS* 3.8 18.0 + - + +
395D ILE* 3.2 48.9 - - + +
396D MET* 1.3 75.0 - - - +
398D THR* 1.3 64.5 + - - +
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Residues in contact with THR 398 (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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357D CYS* 3.9 13.7 - - - -
358D LEU 3.0 7.3 + - - +
359D VAL* 3.3 31.1 - - + -
360D TYR* 2.4 37.3 + - - +
366D LEU* 3.2 12.7 - - - +
387D SER* 3.2 0.5 + - - -
388D VAL 3.1 15.8 + - - -
389D TYR* 3.6 12.4 - - + -
396D MET* 5.0 0.2 - - - -
397D TYR* 1.3 78.4 - - - +
399D TYR* 1.3 59.3 + - - +
423D HIS* 3.1 33.5 + - + -
424D ILE* 5.6 0.2 - - + -
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Residues in contact with TYR 399 (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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359D VAL* 4.5 1.3 - - - -
360D TYR* 3.4 3.6 - - + +
361D LEU 3.2 29.2 - - - -
362D ASP 3.9 0.7 - - - -
363D GLU* 3.2 55.0 - - + -
366D LEU* 3.6 14.6 - - + -
386D ASN* 3.2 27.3 - - + +
387D SER* 2.8 36.7 + - - +
398D THR* 1.3 75.0 + - - +
400D PHE* 1.3 72.0 + - - +
401D SER* 3.6 17.2 + - - -
423D HIS* 3.8 9.3 + - - -
461D ASP* 2.3 24.6 + - - -
463D LYS* 3.1 23.3 + - - -
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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