Contacts of the strand formed by residues 60 - 67 (chain E) in PDB entry 5EJK
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 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E PRO* 4.7 15.3 - - + +
53E ARG* 3.5 11.9 - - - +
54E GLY* 3.5 29.2 - - - +
56E GLY 4.7 0.6 + - - -
59E GLN* 1.3 82.8 - - + +
61E TRP* 1.3 75.3 + - - +
62E GLN* 5.0 0.4 - - + -
82E ASP* 3.5 2.4 + - - +
83E THR* 3.0 49.2 + - + +
117E ALA* 3.6 6.1 - - + +
119E LYS* 4.8 16.6 - - + -
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Residues in contact with TRP 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 4.0 9.8 - - + +
60E ILE* 1.3 77.8 - - - +
62E GLN* 1.3 59.8 - - - +
80E THR* 3.6 20.6 - - + -
81E VAL 3.5 4.9 - - - -
82E ASP* 3.4 39.4 + - + +
105E TRP* 4.7 2.5 - + - -
108E ALA* 3.5 39.9 - - + -
109E ILE* 3.8 9.6 - - + -
112E MSE 3.7 24.9 - - + +
113E GLY 3.4 26.7 - - - -
115E PRO* 3.5 31.6 - - + +
117E ALA 2.9 13.7 + - - +
118E ILE* 3.8 22.0 - - + -
119E LYS* 2.6 36.5 + - - +
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Residues in contact with GLN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ASN* 2.9 27.4 - - - +
52E PRO 4.3 3.6 + - - -
60E ILE* 5.0 0.6 - - + +
61E TRP* 1.3 79.7 - - - +
63E THR* 1.3 65.9 + - - +
80E THR* 3.2 3.3 - - - +
81E VAL* 3.1 33.5 + - + +
83E THR* 4.1 16.3 - - + +
119E LYS* 3.2 28.9 - - + +
152E GLY 3.8 2.8 + - - -
153E GLN* 3.2 18.6 - - + +
155E MSE 3.6 13.9 - - + +
156E VAL* 3.2 39.7 + - + +
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Residues in contact with THR 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLN* 1.3 80.0 + - - +
64E ASP* 1.3 71.2 + - - +
65E PHE* 5.8 1.6 - - + -
78E ALA* 5.3 1.6 - - + -
79E VAL 3.3 6.7 - - - +
80E THR* 3.2 23.5 + - - +
101E VAL* 5.4 0.7 - - + -
104E HIS* 3.9 10.3 - - + -
105E TRP* 3.0 33.7 + - - +
118E ILE* 3.5 11.4 - - - +
119E LYS 3.2 6.3 + - - +
120E THR* 3.8 23.2 - - - -
121E ASP* 4.4 3.1 + - - +
126E PHE* 4.1 16.8 - - + -
153E GLN* 5.6 0.7 + - - -
156E VAL* 4.0 3.9 - - - +
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Residues in contact with ASP 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E THR* 1.3 79.6 - - - +
65E PHE* 1.3 93.4 + - - +
77E LEU 3.9 0.5 - - - +
78E ALA* 4.8 0.2 - - - -
79E VAL* 3.1 34.2 + - - +
121E ASP* 2.8 27.4 - - - +
126E PHE* 4.3 7.6 - - - -
153E GLN* 6.0 1.3 - - + -
156E VAL* 4.2 18.9 - - + +
157E GLU* 2.9 32.9 - - - +
160E ASN* 4.9 4.4 + - - +
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Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E THR* 5.8 1.8 - - + -
64E ASP* 1.3 99.4 + - - +
66E THR* 1.3 62.7 + - - +
76E TRP* 4.0 28.6 - + + -
77E LEU 3.6 2.0 - - - -
78E ALA* 3.9 31.2 - - + -
93E HIS* 4.2 12.6 - + + -
96E VAL* 3.6 46.0 - - + -
100E ALA* 4.0 22.0 - - + -
101E VAL* 3.7 26.5 - - + -
125E CYS* 4.1 0.2 - - - -
126E PHE* 3.7 20.4 - + + -
157E GLU* 5.1 0.2 - - - +
160E ASN* 5.3 0.2 - - - -
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Residues in contact with THR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E PHE* 1.3 74.9 - - - +
67E LEU* 1.3 58.6 + - - +
76E TRP* 3.4 7.9 - - - -
77E LEU* 2.9 55.3 + - + +
79E VAL* 4.0 4.3 - - + -
160E ASN* 3.5 36.8 + - + +
163E MSE 5.9 0.9 - - + -
164E LYS* 2.8 39.9 + - + +
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E THR* 1.3 74.3 + - - +
68E GLU* 1.3 59.1 + - - +
69E PRO* 3.7 18.6 - - + +
75E SER* 3.4 39.5 - - - +
76E TRP* 3.7 35.3 - - + +
164E LYS* 2.6 24.7 + - - +
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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