Contacts of the strand formed by residues 381 - 385 (chain A) in PDB entry 1EUR
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 TYR 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A ILE* 4.2 6.1 - - + -
317A ALA* 2.6 40.6 + - + +
318A PHE* 4.1 11.6 - - - -
332A LEU* 3.7 27.6 - - + -
373A LEU* 4.9 2.7 - - + -
374A THR 3.5 4.7 - - - +
375A ALA* 3.8 23.8 - - + -
376A LEU* 3.9 2.0 - - - -
379A GLY 3.6 20.8 + - - -
380A THR* 1.3 77.8 - - - +
382A GLY* 1.3 61.5 + - - +
395A ASN* 2.9 18.7 - - - +
396A PHE* 2.9 59.1 + + + +
397A ASN* 4.6 2.5 - - - -
398A LEU* 3.9 27.8 - - + +
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Residues in contact with GLY 382 (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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72A LEU* 3.7 10.8 - - - +
373A LEU* 3.3 8.6 - - - +
374A THR 2.9 34.8 + - - -
376A LEU* 3.6 7.8 - - - +
381A TYR* 1.3 73.8 - - - +
383A LEU* 1.3 60.3 + - - +
393A TYR* 3.7 19.5 - - - -
394A ALA 3.6 5.8 - - - -
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Residues in contact with LEU 383 (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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51A TYR* 4.6 0.9 - - + +
334A SER* 4.5 3.1 - - - +
347A ILE* 4.3 8.3 - - + -
363A PHE* 3.6 44.9 - - + -
371A SER* 3.7 27.1 - - - +
372A THR 3.3 15.3 - - - +
373A LEU* 3.8 18.2 - - + -
382A GLY* 1.3 74.4 - - - +
384A LEU* 1.3 63.7 + - - +
385A TYR* 4.0 9.9 + - + -
392A ARG 3.6 1.2 - - - +
393A TYR* 3.4 7.1 - - - -
394A ALA* 2.7 54.2 + - + +
396A PHE* 4.3 9.4 - - + -
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Residues in contact with LEU 384 (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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56A LEU* 3.8 15.7 - - + -
70A PRO* 3.4 29.3 - - + +
71A ALA 3.3 27.4 - - - +
72A LEU* 4.0 20.2 - - + +
82A ALA* 3.9 11.7 - - + -
83A SER 4.0 3.1 - - - +
371A SER* 3.2 2.1 - - - -
372A THR* 2.9 38.2 + - - +
383A LEU* 1.3 71.9 - - - +
385A TYR* 1.3 60.9 + - - +
391A ILE* 3.2 33.4 - - + -
392A ARG 3.4 11.0 - - - +
393A TYR* 3.9 11.4 - - + -
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Residues in contact with TYR 385 (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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51A TYR* 4.2 2.9 - - - -
53A GLU* 2.7 34.1 + - - -
70A PRO* 4.4 3.3 - - - +
363A PHE* 3.8 22.8 + + - -
364A GLN* 3.1 35.1 + - + +
368A MET* 3.3 32.1 - - + -
370A TYR 3.2 6.7 - - - +
371A SER* 3.7 11.0 - - - -
383A LEU* 4.1 13.2 - - + -
384A LEU* 1.3 76.6 - - - +
386A GLU* 1.3 65.4 + - - +
387A PRO* 3.2 21.7 - - + +
391A ILE* 3.5 4.2 - - - -
392A ARG* 2.8 59.8 + - + +
394A ALA* 4.3 5.6 - - + -
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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