Contacts of the strand formed by residues 390 - 396 (chain A) in PDB entry 1EUT
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 GLY 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ALA 3.2 9.2 - - - -
59A ASN* 3.5 16.7 + - - +
67A TYR* 4.1 11.1 - - - +
386A GLU* 3.6 12.1 - - - +
387A PRO* 3.4 14.4 - - - +
388A GLY 3.5 3.1 + - - -
389A THR* 1.3 82.7 + - - +
391A ILE* 1.3 68.3 + - - +
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Residues in contact with ILE 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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55A ASP* 3.7 3.7 + - - -
56A LEU* 2.9 30.9 + - + -
57A ALA* 2.9 35.9 + - + +
67A TYR* 4.4 3.6 - - + -
68A ARG* 4.3 21.8 - - - +
70A PRO* 4.9 3.8 - - + -
84A TYR* 3.3 46.0 - - + -
384A LEU* 3.2 40.8 - - + -
385A TYR 3.2 9.9 - - - +
386A GLU* 4.6 5.4 - - + -
387A PRO* 4.3 0.2 - - - -
390A GLY* 1.3 79.8 - - - +
392A ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 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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53A GLU* 3.2 33.9 + - + -
54A GLN* 3.3 18.8 - - - +
55A ASP* 3.1 27.7 + - - +
56A LEU* 4.8 0.2 - - - -
364A GLN* 3.7 10.1 + - - -
384A LEU* 3.1 8.3 - - - +
385A TYR* 2.8 59.1 + - + -
387A PRO* 3.4 38.8 - - + +
389A THR* 3.8 13.3 + - - +
391A ILE* 1.3 75.3 - - - +
393A TYR* 1.3 69.4 + - - +
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Residues in contact with TYR 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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52A THR* 5.9 2.5 - - + -
53A GLU* 3.0 6.7 - - - +
54A GLN* 2.7 51.8 + - + +
56A LEU* 3.7 20.6 - - + +
72A LEU* 4.4 6.7 - - + -
80A LEU* 3.2 28.5 - - + +
107A GLY 4.5 1.6 + - - -
108A GLY* 3.6 29.8 - - - -
111A TRP* 3.8 16.4 - + - -
376A LEU* 3.6 17.3 - - - +
382A GLY* 3.7 14.9 - - - -
383A LEU 3.5 10.5 - - - -
384A LEU* 3.9 9.2 - - + -
392A ARG* 1.3 74.9 - - - +
394A ALA* 1.3 83.9 + - - +
395A ASN* 4.0 12.1 - - + +
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.3 31.4 - - + +
52A THR 3.2 11.7 - - - +
53A GLU* 3.8 7.2 - - + +
382A GLY* 3.5 0.3 - - - -
383A LEU* 2.6 54.6 + - + +
385A TYR* 4.3 3.4 - - + -
393A TYR* 1.3 85.0 - - - +
395A ASN* 1.3 58.8 + - - +
396A PHE* 5.4 0.2 - - - -
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Residues in contact with ASN 395 (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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50A LEU* 3.7 19.3 - - - +
51A TYR* 3.1 25.1 + - - -
52A THR* 3.0 25.9 + - + +
107A GLY 5.2 3.4 + - - -
376A LEU* 3.6 7.2 - - - +
378A ASP* 4.9 4.0 + - - -
380A THR* 2.9 30.3 + - - +
381A TYR 2.7 25.9 - - - +
393A TYR* 4.0 17.2 + - + +
394A ALA* 1.3 74.3 - - - +
396A PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 396 (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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50A LEU* 3.1 18.2 - - - +
51A TYR* 3.5 27.4 - + + -
332A LEU* 4.2 11.0 - - + -
347A ILE* 3.8 43.1 - - + -
373A LEU* 4.1 13.9 - - + -
380A THR* 3.2 7.0 - - - -
381A TYR* 3.1 58.9 + + + -
383A LEU* 4.4 11.4 - - + -
395A ASN* 1.3 76.3 + - - +
397A ASN* 1.3 73.7 + - - +
398A LEU* 5.3 0.4 - - + -
400A TRP* 3.9 15.5 - + + -
401A LEU* 4.8 8.1 - - + -
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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