Contacts of the strand formed by residues 51 - 58 (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 TYR 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PRO 4.3 0.6 + - - -
50A LEU* 1.3 79.5 - - - +
52A THR* 1.3 63.2 + - - +
53A GLU* 2.7 42.1 + - + -
363A PHE* 3.6 47.0 + - + +
383A LEU* 5.0 0.7 - - + -
385A TYR* 4.1 0.5 - - - -
394A ALA* 3.3 20.7 - - + +
395A ASN 3.1 6.5 - - - -
396A PHE* 3.5 26.2 - + + -
400A TRP* 3.5 37.0 - + + +
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Residues in contact with THR 52 (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* 4.7 14.1 - - + -
51A TYR* 1.3 75.7 - - - +
53A GLU* 1.3 69.5 + - - +
54A GLN* 6.0 2.0 - - - +
393A TYR* 5.9 2.9 - - + -
394A ALA* 3.2 5.8 - - - +
395A ASN* 3.0 49.7 + - + +
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Residues in contact with GLU 53 (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* 2.7 36.6 + - + -
52A THR* 1.3 84.2 + - - +
54A GLN* 1.3 62.2 + - - +
363A PHE 4.8 2.2 - - - +
364A GLN* 4.7 2.3 - - - +
385A TYR* 2.8 23.6 + - - -
392A ARG* 3.2 28.1 + - - -
393A TYR* 3.0 17.0 - - - +
394A ALA* 3.8 2.9 - - + -
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Residues in contact with GLN 54 (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* 6.0 2.3 - - - +
53A GLU* 1.3 77.1 - - - +
55A ASP* 1.3 63.3 + - - +
56A LEU* 4.4 5.7 - - + +
102A ARG* 5.6 2.4 - - - +
108A GLY 3.1 23.4 - - - +
109A ARG* 3.4 21.9 + - - +
110A THR* 5.0 1.2 - - - +
111A TRP* 3.9 15.5 - - - +
392A ARG* 3.8 5.8 - - - +
393A TYR* 2.7 50.5 + - + +
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Residues in contact with ASP 55 (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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54A GLN* 1.3 77.6 + - - +
56A LEU* 1.3 65.8 + - - +
57A ALA 4.5 1.0 - - - +
58A VAL* 4.0 26.4 - - + +
102A ARG* 4.5 6.1 + - - -
387A PRO* 4.1 0.7 - - - +
389A THR* 3.5 18.3 + - - -
391A ILE 3.7 7.0 - - - +
392A ARG* 3.1 41.7 + - - +
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Residues in contact with LEU 56 (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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54A GLN* 4.2 5.6 - - + +
55A ASP* 1.3 79.5 - - - +
57A ALA* 1.3 60.4 + - - +
58A VAL* 5.4 0.8 - - - +
82A ALA* 3.5 32.1 - - + -
84A TYR* 4.1 10.2 + - + -
102A ARG* 3.9 29.9 + - + +
111A TRP* 3.7 47.8 - - + +
114A GLN* 5.3 0.5 - - - +
384A LEU* 3.7 17.9 - - + -
391A ILE* 2.9 17.2 + - + -
393A TYR* 3.7 21.3 - - + +
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Residues in contact with ALA 57 (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* 4.4 2.8 - - - +
56A LEU* 1.3 78.9 - - - +
58A VAL* 1.3 65.9 + - - +
67A TYR* 3.5 34.1 - - + -
84A TYR* 3.8 13.9 - - + -
114A GLN* 5.0 0.9 - - - +
389A THR 3.8 1.2 - - - +
390A GLY* 3.2 4.7 - - - -
391A ILE* 2.9 47.4 + - + +
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Residues in contact with VAL 58 (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* 4.0 24.2 - - + +
56A LEU 5.4 0.7 - - - +
57A ALA* 1.3 78.3 - - - +
59A ASN* 1.3 70.1 + - + +
60A GLY 3.1 0.3 + - - -
61A ARG* 3.0 46.4 + - + +
67A TYR* 3.4 10.6 - - - -
389A THR* 3.4 15.3 - - - +
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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